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
SLIT1	6585	broad.mit.edu	36	10	98798838	98798838	+	Silent	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98798838G>A	uc001kmw.2	-	c.1329C>T	c.(1327-1329)TGC>TGT	p.C443C	SLIT1_uc009xvh.1_Silent_p.C453C	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1	443	LRRCT 2.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)												0.641509	106.054399	106.986477	34	19	GG		KEEP	---	---	---	---	capture		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)	Silent	SNP	98798838	98798838	15237	10	G	A	A	38	38	SLIT1	A	1	1
ABCC8	6833	broad.mit.edu	36	11	17375914	17375914	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:17375914T>C	uc001mnc.1	-	c.3760A>G	c.(3760-3762)ATC>GTC	p.I1254V		NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	1254	Helical; Name=16; (By similarity).|ABC transmembrane type-1 2.				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)									0.378788	68.353353	69.205955	25	41	TT		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Missense_Mutation	SNP	17375914	17375914	59	11	T	C	C	51	51	ABCC8	C	4	4
MS4A14	84689	broad.mit.edu	36	11	59940196	59940196	+	Silent	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59940196C>T	uc001npj.1	+	c.1179C>T	c.(1177-1179)CAC>CAT	p.H393H	MS4A14_uc001npi.1_Silent_p.H281H|MS4A14_uc001npn.1_Silent_p.H131H|MS4A14_uc001npk.1_Silent_p.H376H|MS4A14_uc001npl.1_Silent_p.H131H|MS4A14_uc001npm.1_Silent_p.H131H	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	393						integral to membrane	receptor activity			breast(1)	1														0.425532	56.590345	56.818011	20	27	CC		KEEP	---	---	---	---	capture			Silent	SNP	59940196	59940196	10251	11	C	T	T	19	19	MS4A14	T	1	1
LRP5	4041	broad.mit.edu	36	11	67934101	67934101	+	Silent	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67934101G>A	uc001ont.1	+	c.2235G>A	c.(2233-2235)GCG>GCA	p.A745A	LRP5_uc009ysg.1_Silent_p.A155A	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	745	LDL-receptor class B 12.|Beta-propeller 3.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(1)|pancreas(1)	2														0.387097	101.279524	102.317734	36	57	GG		KEEP	---	---	---	---	capture			Silent	SNP	67934101	67934101	9333	11	G	A	A	38	38	LRP5	A	1	1
RBMXL2	27288	broad.mit.edu	36	11	7067649	7067649	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7067649G>A	uc001mfc.2	+	c.722G>A	c.(721-723)CGC>CAC	p.R241H		NM_014469	NP_055284	O75526	HNRGT_HUMAN	testes-specific heterogenous nuclear	241	Arg/Gly/Pro-rich.					nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0														0.372549	55.516362	56.242261	19	32	GG		KEEP	---	---	---	---	capture		Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Missense_Mutation	SNP	7067649	7067649	13616	11	G	A	A	38	38	RBMXL2	A	1	1
TDG	6996	broad.mit.edu	36	12	102902683	102902683	+	Missense_Mutation	SNP	T	A	A			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:102902683T>A	uc001tkg.1	+	c.819T>A	c.(817-819)AGT>AGA	p.S273R	TDG_uc009zuk.1_Missense_Mutation_p.S269R	NM_003211	NP_003202	Q13569	TDG_HUMAN	thymine-DNA glycosylase	273					depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(2)	2														0.097744	9.975331	31.520075	13	120	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.00114)	Missense_Mutation	SNP	102902683	102902683	16251	12	T	A	A	59	59	TDG	A	4	4
TMEM132D	121256	broad.mit.edu	36	12	128124478	128124478	+	Silent	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:128124478G>A	uc009zyl.1	-	c.3195C>T	c.(3193-3195)ATC>ATT	p.I1065I	TMEM132D_uc001uia.2_Silent_p.I603I	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	1065	Cytoplasmic (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)												0.353125	329.38216	335.468082	113	207	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)	Silent	SNP	128124478	128124478	16579	12	G	A	A	37	37	TMEM132D	A	1	1
CAPS2	84698	broad.mit.edu	36	12	73965048	73965048	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:73965048A>G	uc001sxl.2	-	c.1475T>C	c.(1474-1476)ATT>ACT	p.I492T	CAPS2_uc001sxm.2_Missense_Mutation_p.I279T|CAPS2_uc009zsa.1_Missense_Mutation_p.I101T|CAPS2_uc001sxi.2_Missense_Mutation_p.I247T|CAPS2_uc001sxj.2_Missense_Mutation_p.I422T|CAPS2_uc001sxk.2_Missense_Mutation_p.I511T|CAPS2_uc009zrz.1_Missense_Mutation_p.I279T	NM_032606	NP_115995	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	511	EF-hand 2.						calcium ion binding			ovary(2)	2														0.409091	96.614968	97.091073	27	39	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73965048	73965048	2757	12	A	G	G	4	4	CAPS2	G	4	4
EFNB2	1948	broad.mit.edu	36	13	105985196	105985196	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:105985196A>C	uc001vqi.1	-	c.118T>G	c.(118-120)TCC>GCC	p.S40A		NM_004093	NP_004084	P52799	EFNB2_HUMAN	ephrin B2	40	Extracellular (Potential).				cell differentiation|cell-cell signaling|interspecies interaction between organisms|nervous system development	integral to plasma membrane	ephrin receptor binding			ovary(1)	1	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)													0.333333	35.316236	36.126939	11	22	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105985196	105985196	5144	13	A	C	C	11	11	EFNB2	C	4	4
KCNK10	54207	broad.mit.edu	36	14	87724075	87724075	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:87724075T>C	uc001xwm.1	-	c.1000A>G	c.(1000-1002)ACA>GCA	p.T334A	KCNK10_uc001xwn.1_Missense_Mutation_p.T334A|KCNK10_uc001xwo.1_Missense_Mutation_p.T329A	NM_138318	NP_612191	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	329	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|pancreas(1)	3														0.369099	272.849846	276.372578	86	147	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87724075	87724075	8364	14	T	C	C	58	58	KCNK10	C	4	4
KBTBD13	390594	broad.mit.edu	36	15	63157075	63157075	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63157075A>C	uc010bhd.1	+	c.869A>C	c.(868-870)GAC>GCC	p.D290A		NM_001101362	NP_001094832	C9JR72	KBTBD_HUMAN	hypothetical protein LOC390594	290	Kelch 3.					cytoplasm					0														0.307692	7.756789	8.209725	4	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63157075	63157075	8297	15	A	C	C	10	10	KBTBD13	C	4	4
COMMD4	54939	broad.mit.edu	36	15	73417770	73417770	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73417770C>G	uc002azy.1	+	c.97C>G	c.(97-99)CTC>GTC	p.L33V	COMMD4_uc002azz.1_Missense_Mutation_p.L33V|COMMD4_uc002baa.1_Missense_Mutation_p.L33V	NM_017828	NP_060298	Q9H0A8	COMD4_HUMAN	COMM domain containing 4	33						cytoplasm	protein binding				0														0.5	9.375478	9.375478	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73417770	73417770	3856	15	C	G	G	28	28	COMMD4	G	3	3
TPSD1	23430	broad.mit.edu	36	16	1246965	1246965	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1246965T>C	uc002clb.1	+	c.421T>C	c.(421-423)TCC>CCC	p.S141P	TPSD1_uc010brm.1_Missense_Mutation_p.S70P	NM_012217	NP_036349	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	141	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)												0.375	16.398124	16.75161	9	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1246965	1246965	16969	16	T	C	C	54	54	TPSD1	C	4	4
DNAH3	55567	broad.mit.edu	36	16	20988308	20988308	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20988308C>T	uc002did.1	-	c.3310G>A	c.(3310-3312)GCC>ACC	p.A1104T		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1104	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(10)|large_intestine(2)|central_nervous_system(2)	14														0.34507	285.663582	291.683724	98	186	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.207)	Missense_Mutation	SNP	20988308	20988308	4786	16	C	T	T	28	28	DNAH3	T	2	2
CASKIN1	57524	broad.mit.edu	36	16	2171463	2171463	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2171463G>A	uc010bsg.1	-	c.1907C>T	c.(1906-1908)CCG>CTG	p.P636L		NM_020764	NP_065815	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	636					signal transduction	cytoplasm					0														0.230769	14.23745	15.964358	6	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2171463	2171463	2785	16	G	A	A	39	39	CASKIN1	A	1	1
ITGAX	3687	broad.mit.edu	36	16	31290500	31290500	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31290500G>A	uc002ebt.2	+	c.2054G>A	c.(2053-2055)CGC>CAC	p.R685H	ITGAX_uc002ebu.1_Missense_Mutation_p.R685H	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	685	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.372093	132.710119	134.546296	48	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31290500	31290500	8193	16	G	A	A	38	38	ITGAX	A	1	1
PDP2	57546	broad.mit.edu	36	16	65476031	65476031	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65476031G>A	uc002eqk.1	+	c.343G>A	c.(343-345)GCT>ACT	p.A115T	PDP2_uc010cdx.1_Missense_Mutation_p.A115T	NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	115					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)												0.415584	184.743187	185.680582	64	90	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)	Missense_Mutation	SNP	65476031	65476031	12107	16	G	A	A	42	42	PDP2	A	2	2
MYO15A	51168	broad.mit.edu	36	17	17987837	17987837	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:17987837T>G	uc010cpt.1	+	c.6046_splice	c.e27+2	p.G2016_splice	MYO15A_uc010cpu.1_Splice_Site_SNP_p.G2016_splice	NM_016239	NP_057323			myosin XV						sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	6	all_neural(463;0.228)													0.363636	6.986981	7.170695	4	7	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	17987837	17987837	10458	17	T	G	G	59	59	MYO15A	G	5	4
RNF43	54894	broad.mit.edu	36	17	53790336	53790336	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53790336T>G	uc002iwf.1	-	c.1800A>C	c.(1798-1800)AGA>AGC	p.R600S	RNF43_uc002iwh.2_Missense_Mutation_p.R600S|RNF43_uc002iwg.2_Missense_Mutation_p.R600S|RNF43_uc010dcw.1_Missense_Mutation_p.R473S	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43	600	Pro-rich.|Cytoplasmic (Potential).			R -> G (in Ref. 1; BAD51435 and 2; BAA91085).		endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.331897	244.020355	249.816786	77	155	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53790336	53790336	13974	17	T	G	G	50	50	RNF43	G	4	4
RGS9	8787	broad.mit.edu	36	17	60604338	60604338	+	Silent	SNP	C	T	T	rs61739619	unknown	TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:60604338C>T	uc002jfe.1	+	c.609C>T	c.(607-609)TAC>TAT	p.Y203Y	RGS9_uc010dem.1_Silent_p.Y203Y|RGS9_uc002jfd.1_Silent_p.Y203Y|RGS9_uc002jff.1_Non-coding_Transcript	NM_003835	NP_003826	O75916	RGS9_HUMAN	regulator of G-protein signaling 9 isoform 1	203					intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)	2														0.270833	172.371461	183.737884	65	175	CC		KEEP	---	---	---	---	capture			Silent	SNP	60604338	60604338	13787	17	C	T	T	19	19	RGS9	T	1	1
CDH7	1005	broad.mit.edu	36	18	61640409	61640409	+	Silent	SNP	A	G	G			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:61640409A>G	uc002ljz.1	+	c.738A>G	c.(736-738)ACA>ACG	p.T246T	CDH7_uc002lka.2_Silent_p.T246T|CDH7_uc002lkb.1_Silent_p.T246T	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	246	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.129)												0.381579	83.258472	84.192384	29	47	AA		KEEP	---	---	---	---	capture			Silent	SNP	61640409	61640409	3244	18	A	G	G	8	8	CDH7	G	4	4
ZNF407	55628	broad.mit.edu	36	18	70904592	70904592	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70904592C>T	uc002llw.2	+	c.5927C>T	c.(5926-5928)TCG>TTG	p.S1976L		NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1976					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)												0.333333	14.534248	14.98196	6	12	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(31;0.184)	Missense_Mutation	SNP	70904592	70904592	18480	18	C	T	T	31	31	ZNF407	T	1	1
MAG	4099	broad.mit.edu	36	19	40496158	40496158	+	Silent	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40496158G>A	uc002nyy.1	+	c.1842G>A	c.(1840-1842)ACG>ACA	p.T614T	MAG_uc002nyz.1_Silent_p.T614T|MAG_uc002nyx.1_3'UTR|MAG_uc010eds.1_Silent_p.T589T	NM_002361	NP_002352	P20916	MAG_HUMAN	myelin associated glycoprotein isoform a	614	Cytoplasmic (Potential).			T -> S (in Ref. 2).	blood coagulation|cell adhesion|leukocyte migration|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane	sugar binding			central_nervous_system(1)	1	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)												0.325301	81.257144	83.473963	27	56	GG		KEEP	---	---	---	---	capture	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Silent	SNP	40496158	40496158	9539	19	G	A	A	39	39	MAG	A	1	1
IL4I1	259307	broad.mit.edu	36	19	55084793	55084793	+	Silent	SNP	T	G	G			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55084793T>G	uc002pqu.1	-	c.1716A>C	c.(1714-1716)CCA>CCC	p.P572P	IL4I1_uc002pqw.1_Silent_p.P572P|IL4I1_uc002pqv.1_Silent_p.P559P|IL4I1_uc010eno.1_Silent_p.P558P|IL4I1_uc002pqt.1_Silent_p.P550P	NM_172374	NP_758962	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 2	550					oxidation-reduction process	lysosome	L-amino-acid oxidase activity			ovary(1)	1		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)												0.301587	102.793059	107.296458	38	88	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Silent	SNP	55084793	55084793	7998	19	T	G	G	55	55	IL4I1	G	4	4
C1orf103	55791	broad.mit.edu	36	1	111295993	111295993	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:111295993G>A	uc001eaa.1	-	c.1036C>T	c.(1036-1038)CGA>TGA	p.R346*	C1orf103_uc001dzz.1_Intron|C1orf103_uc001eab.1_Intron|C1orf103_uc001eac.1_Intron	NM_018372	NP_060842	Q5T3J3	CA103_HUMAN	receptor-interacting factor 1 isoform 1	346							protein binding				0		all_cancers(81;1.02e-05)|all_epithelial(167;1.87e-05)|all_lung(203;0.000234)|Lung NSC(277;0.000451)												0.34589	278.673579	284.802717	101	191	GG		KEEP	---	---	---	---	capture		Lung(183;0.0155)|Colorectal(144;0.0314)|all cancers(265;0.082)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0891)|COAD - Colon adenocarcinoma(174;0.134)	Nonsense_Mutation	SNP	111295993	111295993	2044	1	G	A	A	38	38	C1orf103	A	5	1
PVRL4	81607	broad.mit.edu	36	1	159316352	159316352	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159316352C>T	uc001fxo.1	-	c.91G>A	c.(91-93)GCG>ACG	p.A31T		NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	31					adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)					NSCLC(76;1160 1387 14476 16172 29359)								0.384615	85.433225	86.342863	30	48	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00165)		Missense_Mutation	SNP	159316352	159316352	13300	1	C	T	T	27	27	PVRL4	T	1	1
XCL1	6375	broad.mit.edu	36	1	166817051	166817051	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:166817051C>T	uc001gfo.1	+	c.314C>T	c.(313-315)TCG>TTG	p.S105L		NM_002995	NP_002986	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	105					CD4-positive, alpha-beta T cell proliferation|CD8-positive, alpha-beta T cell proliferation|cell-cell signaling|cellular response to interleukin-4|cellular response to transforming growth factor beta stimulus|immunoglobulin production in mucosal tissue|lymphocyte chemotaxis|negative regulation of interferon-gamma production|negative regulation of interleukin-2 production|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T cell cytokine production|negative regulation of T-helper 1 cell activation|negative regulation of T-helper 1 type immune response|negative regulation of transcription, DNA-dependent|neutrophil chemotaxis|positive regulation of activated T cell proliferation|positive regulation of B cell chemotaxis|positive regulation of granzyme A production|positive regulation of granzyme B production|positive regulation of interleukin-10 production|positive regulation of natural killer cell chemotaxis|positive regulation of neutrophil chemotaxis|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of T cell chemotaxis|positive regulation of T cell cytokine production|positive regulation of T cell mediated cytotoxicity|positive regulation of thymocyte migration|positive regulation of transforming growth factor-beta production|regulation of inflammatory response|release of sequestered calcium ion into cytosol|response to virus|signal transduction|T-helper 1 cell cytokine production|T-helper 2 cell cytokine production	extracellular space	chemokine activity|protein homodimerization activity				0	all_hematologic(923;0.208)													0.272727	62.366622	66.460435	24	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166817051	166817051	18004	1	C	T	T	31	31	XCL1	T	1	1
SELE	6401	broad.mit.edu	36	1	167963936	167963936	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167963936C>T	uc001ggm.2	-	c.1166G>A	c.(1165-1167)CGT>CAT	p.R389H	C1orf112_uc001ggj.1_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor	389	Sushi 4.|Extracellular (Potential).				actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)	3	all_hematologic(923;0.208)													0.358209	204.545664	208.103167	72	129	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167963936	167963936	14499	1	C	T	T	19	19	SELE	T	1	1
PIGR	5284	broad.mit.edu	36	1	205174421	205174421	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205174421C>T	uc001hez.1	-	c.1672G>A	c.(1672-1674)GTC>ATC	p.V558I	PIGR_uc009xbz.1_Missense_Mutation_p.V558I	NM_002644	NP_002635	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	558	Ig-like V-type 5.|Extracellular (Potential).					extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2														0.386792	115.549793	116.7404	41	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205174421	205174421	12321	1	C	T	T	19	19	PIGR	T	1	1
KIF26B	55083	broad.mit.edu	36	1	243916439	243916439	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:243916439G>C	uc001ibf.1	+	c.3531G>C	c.(3529-3531)CAG>CAC	p.Q1177H	KIF26B_uc001ibg.1_Missense_Mutation_p.Q795H|KIF26B_uc001ibh.1_Missense_Mutation_p.Q419H	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1177					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)													0.428571	24.369502	24.463311	9	12	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.022)		Missense_Mutation	SNP	243916439	243916439	8606	1	G	C	C	34	34	KIF26B	C	3	3
OR2M3	127062	broad.mit.edu	36	1	246433773	246433773	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246433773C>T	uc001ieb.1	+	c.781C>T	c.(781-783)CGG>TGG	p.R261W		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.377934	473.794086	479.354881	161	265	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0245)		Missense_Mutation	SNP	246433773	246433773	11417	1	C	T	T	19	19	OR2M3	T	1	1
SSTR4	6754	broad.mit.edu	36	20	22964341	22964341	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:22964341G>A	uc002wsr.2	+	c.221G>A	c.(220-222)CGC>CAC	p.R74H		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	74	Cytoplasmic (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity				0	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					Esophageal Squamous(15;850 1104 16640)								0.227273	160.423302	181.430849	70	238	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22964341	22964341	15716	20	G	A	A	38	38	SSTR4	A	1	1
SLC12A5	57468	broad.mit.edu	36	20	44107151	44107151	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44107151G>A	uc002xrb.1	+	c.1534G>A	c.(1534-1536)GCC>ACC	p.A512T		NM_020708	NP_065759	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	535					potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)									0.313167	220.017076	228.738932	88	193	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44107151	44107151	14881	20	G	A	A	42	42	SLC12A5	A	2	2
TUBB1	81027	broad.mit.edu	36	20	57032939	57032939	+	Silent	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:57032939C>T	uc002yak.1	+	c.1062C>T	c.(1060-1062)TGC>TGT	p.C354C		NM_030773	NP_110400	Q9H4B7	TBB1_HUMAN	beta tubulin 1, class VI	354					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity			ovary(1)	1	all_lung(29;0.00711)				Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)									0.288462	76.348288	80.498178	30	74	CC		KEEP	---	---	---	---	capture	Colorectal(105;0.109)		Silent	SNP	57032939	57032939	17308	20	C	T	T	27	27	TUBB1	T	1	1
LZTR1	8216	broad.mit.edu	36	22	19670179	19670179	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:19670179T>C	uc002zto.1	+	c.313T>C	c.(313-315)TGG>CGG	p.W105R	LZTR1_uc002ztn.1_Missense_Mutation_p.W64R|LZTR1_uc010gsr.1_5'Flank	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	105	Kelch 1.				anatomical structure morphogenesis		sequence-specific DNA binding transcription factor activity			ovary(2)|lung(2)	4	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)								1299				0.509091	87.590347	87.594131	28	27	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		Missense_Mutation	SNP	19670179	19670179	9514	22	T	C	C	55	55	LZTR1	C	4	4
MPST	4357	broad.mit.edu	36	22	35750752	35750752	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35750752C>G	uc003aqj.1	+	c.550C>G	c.(550-552)CGA>GGA	p.R184G	MPST_uc003aqi.1_Missense_Mutation_p.R184G|MPST_uc003aqk.1_Missense_Mutation_p.R184G|MPST_uc003aql.1_Missense_Mutation_p.R184G|MPST_uc003aqm.1_Missense_Mutation_p.R184G|MPST_uc003aqn.1_Missense_Mutation_p.R184G|MPST_uc003aqo.1_Missense_Mutation_p.R184G	NM_001013440	NP_066949	P25325	THTM_HUMAN	3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) (MST).	184	Rhodanese 2.				cyanate catabolic process|response to toxin|sulfate transport		3-mercaptopyruvate sulfurtransferase activity|thiosulfate sulfurtransferase activity				0														0.235294	6.720597	7.798664	4	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35750752	35750752	10136	22	C	G	G	23	23	MPST	G	3	3
TTN	7273	broad.mit.edu	36	2	179155152	179155152	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179155152T>C	uc002umr.1	-	c.58486A>G	c.(58486-58488)ATT>GTT	p.I19496V	TTN_uc002ums.1_Missense_Mutation_p.I13191V|TTN_uc010frc.1_Missense_Mutation_p.I13124V|TTN_uc010frd.1_Missense_Mutation_p.I12999V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20423										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153									p.I19496F(BXPC3-Tumor)	8722				0.382022	235.678022	237.843522	68	110	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179155152	179155152	17290	2	T	C	C	49	49	TTN	C	4	4
ADD2	119	broad.mit.edu	36	2	70755402	70755402	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:70755402C>T	uc002sgz.1	-	c.1657G>A	c.(1657-1659)GTG>ATG	p.V553M	ADD2_uc010fds.1_Non-coding_Transcript|ADD2_uc002sgy.1_Missense_Mutation_p.V553M|ADD2_uc002sha.1_Missense_Mutation_p.V247M|ADD2_uc002sgx.2_Missense_Mutation_p.V553M|ADD2_uc010fdt.1_Missense_Mutation_p.V553M	NM_001617	NP_001608	P35612	ADDB_HUMAN	adducin 2 isoform a	553					actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3														0.327189	193.102504	198.824335	71	146	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70755402	70755402	306	2	C	T	T	18	18	ADD2	T	2	2
HCLS1	3059	broad.mit.edu	36	3	122833445	122833445	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122833445G>A	uc003eeh.2	-	c.1399C>T	c.(1399-1401)CGG>TGG	p.R467W		NM_005335	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	467	SH3.				erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|regulation of transcription, DNA-dependent|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.394118	191.799264	193.46261	67	103	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0912)	Missense_Mutation	SNP	122833445	122833445	7277	3	G	A	A	38	38	HCLS1	A	1	1
ABTB1	80325	broad.mit.edu	36	3	128879293	128879293	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:128879293G>T	uc003ejt.1	+	c.946G>T	c.(946-948)GGC>TGC	p.G316C	ABTB1_uc003ejr.1_Missense_Mutation_p.G174C|ABTB1_uc003ejs.1_Missense_Mutation_p.G291C|ABTB1_uc003eju.1_Missense_Mutation_p.G174C|ABTB1_uc010hsm.1_Missense_Mutation_p.G43C	NM_172027	NP_742024	Q969K4	ABTB1_HUMAN	ankyrin repeat and BTB (POZ) domain containing 1	316	BTB 2.					cytoplasm|nucleolus|plasma membrane	translation elongation factor activity				0														0.333333	27.715822	28.526734	11	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128879293	128879293	103	3	G	T	T	43	43	ABTB1	T	3	3
EPHB1	2047	broad.mit.edu	36	3	136449967	136449967	+	Silent	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:136449967G>A	uc003eqt.1	+	c.2616G>A	c.(2614-2616)GCG>GCA	p.A872A	EPHB1_uc003equ.1_Silent_p.A433A	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	872	Cytoplasmic (Potential).|Protein kinase.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(7)|ovary(4)|stomach(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	18										376				0.321429	81.047461	83.399462	27	57	GG		KEEP	---	---	---	---	capture			Silent	SNP	136449967	136449967	5367	3	G	A	A	39	39	EPHB1	A	1	1
ZIC4	84107	broad.mit.edu	36	3	148591441	148591441	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:148591441G>A	uc003ewd.1	-	c.971C>T	c.(970-972)GCG>GTG	p.A324V	ZIC4_uc003ewc.1_Missense_Mutation_p.A254V	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4	324						nucleus	DNA binding|zinc ion binding				0														0.558824	55.825229	55.928705	19	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148591441	148591441	18272	3	G	A	A	38	38	ZIC4	A	1	1
BTD	686	broad.mit.edu	36	3	15661979	15661979	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:15661979C>T	uc003cah.1	+	c.1612C>T	c.(1612-1614)CGC>TGC	p.R538C		NM_000060	NP_000051	P43251	BTD_HUMAN	biotinidase precursor	538			R -> C (in BTD deficiency).		central nervous system development|epidermis development|nitrogen compound metabolic process	extracellular space	biotin carboxylase activity|biotinidase activity				0														0.35461	142.511852	145.13681	50	91	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15661979	15661979	1584	3	C	T	T	27	27	BTD	T	1	1
MST1	4485	broad.mit.edu	36	3	49698920	49698920	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49698920T>G	uc003cxg.1	-	c.806_splice	c.e8-1	p.G269_splice	MST1_uc010hkx.1_Intron	NM_020998	NP_066278			macrophage stimulating 1 (hepatocyte growth						proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1						GBM(110;181 1524 8005 22865 46297)								0.176471	13.128336	16.482827	6	28	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Splice_Site_SNP	SNP	49698920	49698920	10283	3	T	G	G	56	56	MST1	G	5	4
OR5H2	79310	broad.mit.edu	36	3	99485276	99485276	+	Silent	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99485276C>T	uc003dsj.1	+	c.855C>T	c.(853-855)ATC>ATT	p.I285I		NM_001005482	NP_001005482	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H,	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3														0.35443	81.977679	83.453	28	51	CC		KEEP	---	---	---	---	capture			Silent	SNP	99485276	99485276	11572	3	C	T	T	29	29	OR5H2	T	2	2
ATP8A1	10396	broad.mit.edu	36	4	42200284	42200284	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:42200284G>C	uc003gwr.2	-	c.2091C>G	c.(2089-2091)CAC>CAG	p.H697Q	ATP8A1_uc003gws.2_Missense_Mutation_p.H682Q|ATP8A1_uc003gwq.2_5'UTR	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	697	Cytoplasmic (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			central_nervous_system(1)	1					Phosphatidylserine(DB00144)									0.369048	102.702613	103.968935	31	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42200284	42200284	1211	4	G	C	C	36	36	ATP8A1	C	3	3
SLC4A4	8671	broad.mit.edu	36	4	72535788	72535788	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:72535788G>A	uc003hfy.1	+	c.1228G>A	c.(1228-1230)GGA>AGA	p.G410R	SLC4A4_uc010iib.1_Missense_Mutation_p.G410R|SLC4A4_uc003hfz.1_Missense_Mutation_p.G410R|SLC4A4_uc010iic.1_Missense_Mutation_p.G410R|SLC4A4_uc003hga.1_Missense_Mutation_p.G288R|SLC4A4_uc003hgb.2_Missense_Mutation_p.G366R|SLC4A4_uc003hgc.2_Missense_Mutation_p.G366R|SLC4A4_uc010iid.1_5'UTR	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate	410	Cytoplasmic (Potential).					basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)	4														0.318519	114.970889	118.926262	43	92	GG		KEEP	---	---	---	---	capture	Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Missense_Mutation	SNP	72535788	72535788	15153	4	G	A	A	47	47	SLC4A4	A	2	2
PPEF2	5470	broad.mit.edu	36	4	77016586	77016586	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77016586G>A	uc003hix.1	-	c.1198C>T	c.(1198-1200)CGG>TGG	p.R400W	PPEF2_uc003hiy.1_Non-coding_Transcript|PPEF2_uc003hiz.1_Missense_Mutation_p.R400W	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	400	Catalytic.				detection of stimulus involved in sensory perception|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4						NSCLC(105;1359 1603 15961 44567 47947)								0.344828	104.957029	107.427096	40	76	GG		KEEP	---	---	---	---	capture	Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)		Missense_Mutation	SNP	77016586	77016586	12738	4	G	A	A	38	38	PPEF2	A	1	1
GAK	2580	broad.mit.edu	36	4	854620	854620	+	Silent	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:854620C>T	uc003gbm.2	-	c.2127G>A	c.(2125-2127)GTG>GTA	p.V709V	GAK_uc010ibj.1_Non-coding_Transcript|GAK_uc003gbl.2_Silent_p.V573V|GAK_uc003gbn.2_Silent_p.V630V|GAK_uc010ibk.1_Silent_p.V603V	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	709	C2 tensin-type.				cell cycle|protein phosphorylation	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)	3										679				0.36036	110.268977	112.174306	40	71	CC		KEEP	---	---	---	---	capture		Colorectal(103;0.219)	Silent	SNP	854620	854620	6459	4	C	T	T	21	21	GAK	T	2	2
FAM190A	401145	broad.mit.edu	36	4	91540244	91540244	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:91540244A>G	uc003hsv.2	+	c.1544A>G	c.(1543-1545)GAT>GGT	p.D515G	FAM190A_uc010ikv.1_Non-coding_Transcript|FAM190A_uc003hsw.1_Missense_Mutation_p.D515G	NM_207491	NP_997374	Q9C0I3	F190A_HUMAN	similar to KIAA1680 protein isoform 2	515										large_intestine(1)|ovary(1)	2														0.208333	12.159047	14.053302	5	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91540244	91540244	5732	4	A	G	G	12	12	FAM190A	G	4	4
CTNND2	1501	broad.mit.edu	36	5	11618132	11618132	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:11618132C>T	uc003jfa.1	-	c.211G>A	c.(211-213)GCT>ACT	p.A71T	CTNND2_uc010itt.1_5'UTR|CTNND2_uc010itu.1_Non-coding_Transcript	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	71	Potential.				multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|pancreas(1)|lung(1)|skin(1)	7														0.295918	76.551076	80.195154	29	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11618132	11618132	4179	5	C	T	T	26	26	CTNND2	T	2	2
PRR16	51334	broad.mit.edu	36	5	120049867	120049867	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:120049867C>A	uc003ksq.1	+	c.479C>A	c.(478-480)CCA>CAA	p.P160Q	PRR16_uc003ksp.1_Missense_Mutation_p.P137Q|PRR16_uc003ksr.1_Missense_Mutation_p.P90Q	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16	160	Pro-rich.									pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)												0.386076	180.835384	182.633533	61	97	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)	Missense_Mutation	SNP	120049867	120049867	13032	5	C	A	A	21	21	PRR16	A	3	3
SGCD	6444	broad.mit.edu	36	5	156118889	156118889	+	Silent	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156118889C>T	uc003lwc.2	+	c.783C>T	c.(781-783)TTC>TTT	p.F261F	SGCD_uc003lwd.2_Silent_p.F260F	NM_000337	NP_000328	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 1	260	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)												0.350467	211.097078	215.301903	75	139	CC		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Silent	SNP	156118889	156118889	14692	5	C	T	T	31	31	SGCD	T	1	1
ADAMTS2	9509	broad.mit.edu	36	5	178484717	178484717	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178484717G>A	uc003mjw.1	-	c.2821C>T	c.(2821-2823)CGC>TGC	p.R941C		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	941	TSP type-1 3.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)								1974				0.344828	203.786388	208.646832	80	152	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)	Missense_Mutation	SNP	178484717	178484717	266	5	G	A	A	38	38	ADAMTS2	A	1	1
PIK3R1	5295	broad.mit.edu	36	5	67626881	67626881	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:67626881T>C	uc003jva.1	+	c.1718T>C	c.(1717-1719)CTG>CCG	p.L573P	PIK3R1_uc003jvb.1_Missense_Mutation_p.L573P|PIK3R1_uc003jvc.1_Missense_Mutation_p.L273P|PIK3R1_uc003jvd.1_Missense_Mutation_p.L303P|PIK3R1_uc003jve.1_Missense_Mutation_p.L252P	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	573					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.L570_D578del(1)|p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	99		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)			Isoproterenol(DB01064)					370	TCGA GBM(4;<1E-8)			0.316327	182.319564	188.235979	62	134	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Missense_Mutation	SNP	67626881	67626881	12342	5	T	C	C	55	55	PIK3R1	C	4	4
ATG5	9474	broad.mit.edu	36	6	106870752	106870752	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:106870752G>A	uc003prf.1	-	c.25C>T	c.(25-27)CGA>TGA	p.R9*	ATG5_uc010kdb.1_Nonsense_Mutation_p.R9*|ATG5_uc003prg.1_5'UTR|ATG5_uc010kdc.1_Nonsense_Mutation_p.R9*	NM_004849	NP_004840	Q9H1Y0	ATG5_HUMAN	APG5 autophagy 5-like	9					apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)												0.306931	174.073853	180.787636	62	140	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)	Nonsense_Mutation	SNP	106870752	106870752	1119	6	G	A	A	37	37	ATG5	A	5	1
PPP1R10	5514	broad.mit.edu	36	6	30678069	30678069	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30678069C>T	uc003nqn.1	-	c.2336G>A	c.(2335-2337)AGT>AAT	p.S779N	PPP1R10_uc010jsc.1_Missense_Mutation_p.S433N	NM_002714	NP_002705	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	779	Gly-rich.				protein import into nucleus	PTW/PP1 phosphatase complex	DNA binding|protein phosphatase inhibitor activity|RNA binding|transcription regulator activity|zinc ion binding			ovary(2)|lung(1)|kidney(1)	4														0.386228	373.278243	377.073125	129	205	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30678069	30678069	12787	6	C	T	T	20	20	PPP1R10	T	2	2
SFRS18	25957	broad.mit.edu	36	6	99962866	99962866	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:99962866C>T	uc003ppo.2	-	c.676G>A	c.(676-678)GCA>ACA	p.A226T	SFRS18_uc003ppp.2_Missense_Mutation_p.A226T|SFRS18_uc003ppq.2_Missense_Mutation_p.A226T|SFRS18_uc003ppr.2_Missense_Mutation_p.A226T	NM_032870	NP_116259	Q8TF01	SFR18_HUMAN	splicing factor, arginine/serine-rich 130	226						nuclear speck					0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)												0.307692	192.123671	199.405779	68	153	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0631)	Missense_Mutation	SNP	99962866	99962866	14664	6	C	T	T	27	27	SFRS18	T	1	1
ZAN	7455	broad.mit.edu	36	7	100174166	100174166	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100174166C>T	uc003uwj.1	+	c.760C>T	c.(760-762)CCT>TCT	p.P254S	ZAN_uc003uwk.1_Missense_Mutation_p.P254S|ZAN_uc003uwl.1_Non-coding_Transcript|ZAN_uc010lhh.1_Non-coding_Transcript|ZAN_uc010lhi.1_Non-coding_Transcript	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	254	MAM 2.|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)													0.217949	38.622428	44.356272	17	61	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.19)		Missense_Mutation	SNP	100174166	100174166	18096	7	C	T	T	22	22	ZAN	T	2	2
OPN1SW	611	broad.mit.edu	36	7	128202733	128202733	+	Silent	SNP	T	A	A			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:128202733T>A	uc003vnt.2	-	c.348A>T	c.(346-348)GTA>GTT	p.V116V		NM_001708	NP_001699	P03999	OPSB_HUMAN	opsin 1 (cone pigments), short-wave-sensitive	116	Helical; Name=3; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity				0														0.131737	62.5572	106.597386	44	290	TT		KEEP	---	---	---	---	capture			Silent	SNP	128202733	128202733	11286	7	T	A	A	53	53	OPN1SW	A	4	4
KLF14	136259	broad.mit.edu	36	7	130068674	130068674	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:130068674C>G	uc003vqk.1	-	c.727G>C	c.(727-729)GCC>CCC	p.A243P		NM_138693	NP_619638	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	243	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(18;0.0435)													0.222222	7.390103	8.669277	4	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130068674	130068674	8654	7	C	G	G	26	26	KLF14	G	3	3
TTC26	79989	broad.mit.edu	36	7	138504619	138504619	+	Silent	SNP	A	G	G			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138504619A>G	uc003vus.1	+	c.1050A>G	c.(1048-1050)GGA>GGG	p.G350G	TTC26_uc003vut.1_Silent_p.G210G	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1	350							binding			ovary(1)	1														0.258883	142.307503	152.706154	51	146	AA		KEEP	---	---	---	---	capture			Silent	SNP	138504619	138504619	17248	7	A	G	G	11	11	TTC26	G	4	4
GIMAP5	55340	broad.mit.edu	36	7	150070497	150070497	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150070497G>A	uc003whr.1	+	c.337G>A	c.(337-339)GTC>ATC	p.V113I	GIMAP5_uc010lpu.1_5'UTR	NM_018384	NP_060854	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	113	Cytoplasmic (Potential).					integral to membrane|mitochondrial outer membrane	GTP binding			ovary(1)|central_nervous_system(1)	2														0.280156	183.598187	194.763644	72	185	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150070497	150070497	6650	7	G	A	A	40	40	GIMAP5	A	1	1
PRPS1L1	221823	broad.mit.edu	36	7	18033090	18033090	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2562-01	TCGA-06-2562-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:18033090T>C	uc003stz.1	-	c.841A>G	c.(841-843)ATG>GTG	p.M281V		NM_175886	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like	281					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			ovary(1)	1	Lung NSC(10;0.0385)|all_lung(11;0.0736)													0.313725	502.309631	518.061776	160	350	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18033090	18033090	13022	7	T	C	C	50	50	PRPS1L1	C	4	4
PKD1L1	168507	broad.mit.edu	36	7	47833561	47833561	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47833561G>C	uc003tny.1	-	c.6766C>G	c.(6766-6768)CTG>GTG	p.L2256V	C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'UTR	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2256	Cytoplasmic (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.134615	11.114353	17.824524	7	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47833561	47833561	12388	7	G	C	C	35	35	PKD1L1	C	3	3
CALN1	83698	broad.mit.edu	36	7	70890791	70890791	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70890791C>T	uc003twb.2	-	c.691G>A	c.(691-693)GTC>ATC	p.V231I	CALN1_uc003twa.2_Missense_Mutation_p.V189I|CALN1_uc003twc.2_Missense_Mutation_p.V189I	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	189	Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)												0.261905	109.148753	117.752689	44	124	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70890791	70890791	2708	7	C	T	T	19	19	CALN1	T	1	1
SAMD12	401474	broad.mit.edu	36	8	119662142	119662142	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:119662142G>A	uc003yom.2	-	c.185C>T	c.(184-186)ACG>ATG	p.T62M	SAMD12_uc010mda.1_Missense_Mutation_p.T62M|SAMD12_uc010mdb.1_Non-coding_Transcript	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform	62										ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)													0.352459	250.682984	255.36424	86	158	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00391)		Missense_Mutation	SNP	119662142	119662142	14297	8	G	A	A	40	40	SAMD12	A	1	1
DUSP4	1846	broad.mit.edu	36	8	29263424	29263424	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:29263424C>A	uc003xhm.1	-	c.291G>T	c.(289-291)TTG>TTT	p.L97F	DUSP4_uc003xhl.1_5'Flank	NM_001394	NP_001385	Q13115	DUS4_HUMAN	dual specificity phosphatase 4 isoform 1	97	Rhodanese.				endoderm formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity				0														0.5	8.128399	8.128399	3	3	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)	Missense_Mutation	SNP	29263424	29263424	5012	8	C	A	A	25	25	DUSP4	A	3	3
SLC46A2	57864	broad.mit.edu	36	9	114692478	114692478	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:114692478C>T	uc004bgk.1	-	c.305G>A	c.(304-306)CGC>CAC	p.R102H		NM_033051	NP_149040	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	102	Cytoplasmic (Potential).				response to antibiotic	integral to membrane|plasma membrane	symporter activity|tetracycline:hydrogen antiporter activity			central_nervous_system(1)	1														0.232759	112.735045	127.910541	54	178	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114692478	114692478	15142	9	C	T	T	27	27	SLC46A2	T	1	1
PIP5K1B	8395	broad.mit.edu	36	9	70795945	70795945	+	Silent	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:70795945C>T	uc004agu.1	+	c.1572C>T	c.(1570-1572)AAC>AAT	p.N524N	PIP5K1B_uc004agv.1_Non-coding_Transcript|PIP5K1B_uc010mok.1_Intron	NM_003558	NP_003549	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	524						endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding				0										223				0.309013	185.697203	193.280123	72	161	CC		KEEP	---	---	---	---	capture		Lung(182;0.133)	Silent	SNP	70795945	70795945	12364	9	C	T	T	17	17	PIP5K1B	T	2	2
FOXE1	2304	broad.mit.edu	36	9	99656448	99656448	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2562-01	TCGA-06-2562-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:99656448G>C	uc004axu.1	+	c.431G>C	c.(430-432)CGC>CCC	p.R144P		NM_004473	NP_004464	O00358	FOXE1_HUMAN	forkhead box E1	144	Fork-head.				cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thyroid gland development|thyroid hormone generation	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0		Acute lymphoblastic leukemia(62;0.158)								22				0.357143	7.906129	8.141579	5	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99656448	99656448	6248	9	G	C	C	38	38	FOXE1	C	3	3
MCF2	4168	broad.mit.edu	36	X	138507313	138507313	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2562-01	TCGA-06-2562-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:138507313A>G	uc004faw.2	-	c.2207T>C	c.(2206-2208)ATG>ACG	p.M736T	MCF2_uc004fau.2_Missense_Mutation_p.M676T|MCF2_uc004fav.2_Missense_Mutation_p.M692T|MCF2_uc010nsh.1_Missense_Mutation_p.M676T|MCF2_uc010nsg.1_Missense_Mutation_p.M152T	NM_001099855	NP_001093325	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	676					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)									693				0.745902	313.772298	320.464528	91	31	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	138507313	138507313	9767	23	A	G	G	8	8	MCF2	G	4	4
KCND1	3750	broad.mit.edu	36	X	48710866	48710866	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48710866C>G	uc004dlx.1	-	c.757G>C	c.(757-759)GCC>CCC	p.A253P	KCND1_uc004dlw.1_5'Flank	NM_004979	NP_004970	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related	253	Cytoplasmic (Potential).					voltage-gated potassium channel complex	metal ion binding|voltage-gated potassium channel activity			ovary(2)|lung(1)	3														0.235294	6.928055	7.997914	4	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48710866	48710866	8323	23	C	G	G	27	27	KCND1	G	3	3
EDA	1896	broad.mit.edu	36	X	69170044	69170044	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2562-01	TCGA-06-2562-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:69170044C>T	uc004dxs.1	+	c.865C>T	c.(865-867)CGC>TGC	p.R289C	EDA_uc004dxr.1_Missense_Mutation_p.R289C	NM_001399	NP_001390	Q92838	EDA_HUMAN	ectodysplasin A isoform EDA-A1	289	Extracellular (Potential).				cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3												OREG0019847	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.801418	383.852016	395.776032	113	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69170044	69170044	5090	23	C	T	T	23	23	EDA	T	1	1
NF1	4763	broad.mit.edu	36	17	26677102	26677105	+	Frame_Shift_Del	DEL	TCTC	-	-			TCGA-06-2562-01	TCGA-06-2562-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26677102_26677105delTCTC	uc002hgg.1	+	c.4974_4977delTCTC	c.(4972-4977)TTTCTCfs	p.F1658fs	NF1_uc002hgh.1_Frame_Shift_Del_p.F1637fs|NF1_uc002hgi.1_Frame_Shift_Del_p.F670fs|NF1_uc010cso.1_5'UTR	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1658_1659	CRAL-TRIO.				actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.S1660fs*37(2)|p.?(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.30			100	230				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	26677102	26677105	10756	17	TCTC	-	-	62	62	NF1	-	5	5
