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
SLC18A2	6571	broad.mit.edu	36	10	118993535	118993535	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118993535C>T	uc001ldd.1	+	c.185C>T	c.(184-186)ACG>ATG	p.T62M	SLC18A2_uc009xyy.1_De_novo_Start_InFrame	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine),	62	Lumenal, vesicle (Potential).				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)			Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)									0.388889	39.840699	40.230441	14	22	CC		KEEP	---	---	---	---	capture		all cancers(201;0.029)	Missense_Mutation	SNP	118993535	118993535	14922	10	C	T	T	19	19	SLC18A2	T	1	1
CLRN3	119467	broad.mit.edu	36	10	129572086	129572086	+	Silent	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:129572086C>T	uc001lka.1	-	c.273G>A	c.(271-273)TCG>TCA	p.S91S	CLRN3_uc001ljz.1_Silent_p.S23S	NM_152311	NP_689524	Q8NCR9	CLRN3_HUMAN	clarin 3	91						integral to membrane					0		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)												0.341463	83.876577	85.697116	28	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	129572086	129572086	3697	10	C	T	T	23	23	CLRN3	T	1	1
HTR3A	3359	broad.mit.edu	36	11	113362894	113362894	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113362894G>A	uc001pon.1	+	c.1150G>A	c.(1150-1152)GCC>ACC	p.A384T	HTR3A_uc001pom.1_Missense_Mutation_p.A352T|HTR3A_uc009yyx.1_Non-coding_Transcript	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	352	Cytoplasmic (Potential).				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)			Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)									0.279412	47.696488	50.672347	19	49	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Missense_Mutation	SNP	113362894	113362894	7744	11	G	A	A	38	38	HTR3A	A	1	1
OR51G1	79324	broad.mit.edu	36	11	4902096	4902096	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4902096G>A	uc001lzs.1	-	c.50C>T	c.(49-51)ACG>ATG	p.T17M		NM_001005237	NP_001005237	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G,	17	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)												0.314607	79.069397	81.790204	28	61	GG		KEEP	---	---	---	---	capture		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4902096	4902096	11508	11	G	A	A	40	40	OR51G1	A	1	1
OR51A2	401667	broad.mit.edu	36	11	4933512	4933512	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0140-01	TCGA-06-0140-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4933512A>G	uc001lzu.1	-	c.8T>C	c.(7-9)ATT>ACT	p.I3T		NM_001004748	NP_001004748	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A,	3	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)												0.23	68.275418	74.955226	23	77	AA		KEEP	---	---	---	---	capture		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4933512	4933512	11496	11	A	G	G	4	4	OR51A2	G	4	4
MS4A7	58475	broad.mit.edu	36	11	59917897	59917897	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59917897G>A	uc001npe.1	+	c.710G>A	c.(709-711)CGG>CAG	p.R237Q	MS4A7_uc001npf.1_Missense_Mutation_p.R237Q|MS4A7_uc001npg.1_Missense_Mutation_p.R192Q|MS4A7_uc001nph.1_Missense_Mutation_p.R192Q|MS4A14_uc001npi.1_Intron|MS4A14_uc001npn.1_5'Flank|MS4A14_uc001npj.1_5'Flank|MS4A14_uc001npk.1_5'Flank|MS4A14_uc001npl.1_5'Flank|MS4A14_uc001npm.1_5'Flank	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member	237	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2														0.253846	93.613115	100.761861	33	97	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59917897	59917897	10259	11	G	A	A	39	39	MS4A7	A	1	1
C12orf51	283450	broad.mit.edu	36	12	111205423	111205423	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:111205423C>T	uc009zwc.1	-	c.220G>A	c.(220-222)GAA>AAA	p.E74K		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)	1														0.204082	22.82313	26.804848	10	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111205423	111205423	1740	12	C	T	T	31	31	C12orf51	T	1	1
RB1	5925	broad.mit.edu	36	13	47849145	47849145	+	Nonsense_Mutation	SNP	C	T	T	rs4151534	by-hapmap	TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47849145C>T	uc001vcb.1	+	c.1306C>T	c.(1306-1308)CAG>TAG	p.Q436*	RB1_uc010act.1_Nonsense_Mutation_p.Q137*	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	436	Domain A.|Pocket; binds T and E1A.				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			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)			Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6	p.Q436*(COLO668-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.434109	163.573778	164.063375	56	73	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Nonsense_Mutation	SNP	47849145	47849145	13559	13	C	T	T	17	17	RB1	T	5	2
ATP10A	57194	broad.mit.edu	36	15	23476096	23476096	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:23476096G>A	uc010ayu.1	-	c.3985C>T	c.(3985-3987)CGC>TGC	p.R1329C		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1329	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)								877				0.203822	72.022908	84.798769	32	125	GG		KEEP	---	---	---	---	capture		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)	Missense_Mutation	SNP	23476096	23476096	1135	15	G	A	A	40	40	ATP10A	A	1	1
RASGRP1	10125	broad.mit.edu	36	15	36605877	36605877	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:36605877G>A	uc001zke.2	-	c.241C>T	c.(241-243)CGA>TGA	p.R81*	RASGRP1_uc001zkd.2_Nonsense_Mutation_p.R81*	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a	81	Ras exchanger motif region; required for transforming activity (By similarity).|N-terminal Ras-GEF.				cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)												0.185714	27.232696	33.714861	13	57	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)	Nonsense_Mutation	SNP	36605877	36605877	13535	15	G	A	A	37	37	RASGRP1	A	5	1
DNAH3	55567	broad.mit.edu	36	16	20883575	20883575	+	Silent	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20883575C>T	uc002did.1	-	c.9132G>A	c.(9130-9132)ACG>ACA	p.T3044T	DNAH3_uc002dic.1_Silent_p.T479T	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3044					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														0.253012	49.130648	53.734655	21	62	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.207)	Silent	SNP	20883575	20883575	4786	16	C	T	T	19	19	DNAH3	T	1	1
KIFC3	3801	broad.mit.edu	36	16	56352282	56352282	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0140-01	TCGA-06-0140-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56352282T>C	uc002emp.1	-	c.2089A>G	c.(2089-2091)ATC>GTC	p.I697V	KIFC3_uc002emm.1_Missense_Mutation_p.I558V|KIFC3_uc002emn.1_Non-coding_Transcript|KIFC3_uc002emo.2_Missense_Mutation_p.I558V|KIFC3_uc010cdf.1_Missense_Mutation_p.I558V|KIFC3_uc002emq.1_Missense_Mutation_p.I697V	NM_005550	NP_005541	Q9BVG8	KIFC3_HUMAN	kinesin family member C3 isoform 1	697	Kinesin-motor.				epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			ovary(1)|central_nervous_system(1)	2		all_neural(199;0.224)												0.244898	27.976072	30.880985	12	37	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56352282	56352282	8625	16	T	C	C	51	51	KIFC3	C	4	4
CHST6	4166	broad.mit.edu	36	16	74070887	74070887	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:74070887C>T	uc002fef.1	-	c.341G>A	c.(340-342)CGC>CAC	p.R114H	CHST6_uc002feg.1_Non-coding_Transcript|CHST6_uc002feh.1_Missense_Mutation_p.R114H|CHST6_uc010cgv.1_Missense_Mutation_p.R114H	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	114	Lumenal (Potential).				keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0														0.344444	87.099621	89.02206	31	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74070887	74070887	3542	16	C	T	T	27	27	CHST6	T	1	1
ADAMTS18	170692	broad.mit.edu	36	16	75912517	75912517	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:75912517C>G	uc002ffc.2	-	c.2247G>C	c.(2245-2247)AAG>AAC	p.K749N	ADAMTS18_uc010chc.1_Missense_Mutation_p.K337N|ADAMTS18_uc002ffe.1_Missense_Mutation_p.K445N	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	749	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|kidney(4)|skin(2)|pancreas(1)|ovary(1)	12										1451				0.230392	135.07219	148.62546	47	157	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75912517	75912517	264	16	C	G	G	20	20	ADAMTS18	G	3	3
KRT16	3868	broad.mit.edu	36	17	37020871	37020871	+	Silent	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37020871G>A	uc002hxg.2	-	c.909C>T	c.(907-909)GAC>GAT	p.D303D		NM_005557	NP_005548	P08779	K1C16_HUMAN	keratin 16	303	Rod.|Coil 2.				cell proliferation|epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000307)												0.212245	115.892662	134.62741	52	193	GG		KEEP	---	---	---	---	capture			Silent	SNP	37020871	37020871	8768	17	G	A	A	40	40	KRT16	A	1	1
UNC13A	23025	broad.mit.edu	36	19	17592515	17592515	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17592515G>T	uc002nhd.1	-	c.4523C>A	c.(4522-4524)CCA>CAA	p.P1508Q		NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A	1420	MHD2.				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3														0.4	8.387173	8.477376	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17592515	17592515	17542	19	G	T	T	47	47	UNC13A	T	3	3
CILP2	148113	broad.mit.edu	36	19	19517153	19517153	+	Silent	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19517153G>A	uc002nmw.2	+	c.2817G>A	c.(2815-2817)CCG>CCA	p.P939P	CILP2_uc002nmv.2_Silent_p.P933P	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	933						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1														0.206897	12.75758	15.049437	6	23	GG		KEEP	---	---	---	---	capture			Silent	SNP	19517153	19517153	3564	19	G	A	A	38	38	CILP2	A	1	1
NKPD1	284353	broad.mit.edu	36	19	50347987	50347987	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50347987G>T	uc002pau.1	-	c.882C>A	c.(880-882)TAC>TAA	p.Y294*		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)												0.333333	8.322702	8.543757	3	6	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)	Nonsense_Mutation	SNP	50347987	50347987	10847	19	G	T	T	44	44	NKPD1	T	5	3
LMTK3	114783	broad.mit.edu	36	19	53705189	53705189	+	Silent	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53705189C>T	uc002pjk.1	-	c.351G>A	c.(349-351)GCG>GCA	p.A117A		NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)								193				0.289474	31.410312	32.919328	11	27	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)	Silent	SNP	53705189	53705189	9189	19	C	T	T	23	23	LMTK3	T	1	1
ZNF71	58491	broad.mit.edu	36	19	61825098	61825098	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61825098G>A	uc002qnm.2	+	c.631G>A	c.(631-633)GAG>AAG	p.E211K	ZNF71_uc010eto.1_Missense_Mutation_p.E211K	NM_021216	NP_067039	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	211					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.19697	27.552128	33.18707	13	53	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)	Missense_Mutation	SNP	61825098	61825098	18710	19	G	A	A	37	37	ZNF71	A	1	1
OPTC	26254	broad.mit.edu	36	1	201739364	201739364	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:201739364C>T	uc001gzu.1	+	c.892C>T	c.(892-894)CGC>TGC	p.R298C		NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	opticin precursor	298						proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0														0.256198	82.872274	89.391566	31	90	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(75;0.109)		Missense_Mutation	SNP	201739364	201739364	11294	1	C	T	T	23	23	OPTC	T	1	1
ABCA4	24	broad.mit.edu	36	1	94236046	94236046	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:94236046G>A	uc001dqh.1	-	c.6688C>T	c.(6688-6690)CTC>TTC	p.L2230F		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	2230	Cytoplasmic.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|central_nervous_system(2)|breast(1)	7		all_lung(203;0.000757)|Lung NSC(277;0.00335)												0.389831	72.711543	73.339002	23	36	GG		KEEP	---	---	---	---	capture		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)	Missense_Mutation	SNP	94236046	94236046	35	1	G	A	A	34	34	ABCA4	A	2	2
THBD	7056	broad.mit.edu	36	20	22977200	22977200	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:22977200G>T	uc002wss.1	-	c.942C>A	c.(940-942)TAC>TAA	p.Y314*	THBD_uc002wst.1_5'Flank|THBD_uc002wsu.1_Nonsense_Mutation_p.Y255*	NM_000361	NP_000352	P07204	TRBM_HUMAN	thrombomodulin precursor	314	EGF-like 2.|Extracellular (Potential).				blood coagulation|leukocyte migration|negative regulation of fibrinolysis|negative regulation of platelet activation	cell surface|integral to plasma membrane	calcium ion binding|protein binding|transmembrane receptor activity				0	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)									0.210526	6.691599	8.165653	4	15	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	22977200	22977200	16380	20	G	T	T	44	44	THBD	T	5	3
SLC4A11	83959	broad.mit.edu	36	20	3157652	3157652	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0140-01	TCGA-06-0140-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:3157652A>C	uc002wig.1	-	c.2072T>G	c.(2071-2073)GTG>GGG	p.V691G	SLC4A11_uc002wih.1_Non-coding_Transcript	NM_032034	NP_114423	Q8NBS3	S4A11_HUMAN	solute carrier family 4 member 11	691	Membrane (bicarbonate transporter).				cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity			ovary(1)	1						NSCLC(190;922 2139 10266 10292 38692)								0.3	7.746072	9.035753	9	21	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3157652	3157652	15149	20	A	C	C	6	6	SLC4A11	C	4	4
PTPRT	11122	broad.mit.edu	36	20	40534500	40534500	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:40534500C>T	uc010ggj.1	-	c.1270G>A	c.(1270-1272)GTG>ATG	p.V424M	PTPRT_uc002xkg.1_Missense_Mutation_p.V424M	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	424	Extracellular (Potential).|Fibronectin type-III 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.238095	47.678296	52.928656	20	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40534500	40534500	13270	20	C	T	T	19	19	PTPRT	T	1	1
IL17RA	23765	broad.mit.edu	36	22	15970582	15970582	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:15970582G>C	uc002zly.1	+	c.2473G>C	c.(2473-2475)GCC>CCC	p.A825P	IL17RA_uc010gqt.1_Missense_Mutation_p.A773P	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor	825	Cytoplasmic (Potential).				fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)												0.375	8.622595	8.732498	3	5	GG		KEEP	---	---	---	---	capture		Colorectal(9;0.241)	Missense_Mutation	SNP	15970582	15970582	7940	22	G	C	C	42	42	IL17RA	C	3	3
PLXNB2	23654	broad.mit.edu	36	22	49063290	49063290	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49063290G>C	uc003bkv.2	-	c.2964C>G	c.(2962-2964)TTC>TTG	p.F988L	PLXNB2_uc003bkt.1_5'Flank|PLXNB2_uc003bku.1_5'Flank	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2	988	IPT/TIG 3.|Extracellular (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.3	6.920083	7.278265	3	7	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49063290	49063290	12550	22	G	C	C	37	37	PLXNB2	C	3	3
ADM2	79924	broad.mit.edu	36	22	49268088	49268088	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49268088G>A	uc003blj.1	+	c.337G>A	c.(337-339)GGC>AGC	p.G113S		NM_024866	NP_079142	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2 precursor	113						extracellular region	hormone activity				0		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.307692	10.595366	11.023835	4	9	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49268088	49268088	323	22	G	A	A	43	43	ADM2	A	2	2
ST6GAL2	84620	broad.mit.edu	36	2	106826520	106826520	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:106826520C>T	uc002tdr.1	-	c.346G>A	c.(346-348)GTG>ATG	p.V116M	ST6GAL2_uc002tds.2_Missense_Mutation_p.V116M	NM_032528	NP_115917	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	116	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(3)	9														0.17757	75.816066	96.774713	38	176	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106826520	106826520	15740	2	C	T	T	18	18	ST6GAL2	T	2	2
PRPF40A	55660	broad.mit.edu	36	2	153223931	153223931	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:153223931C>T	uc002tyh.2	-	c.2428G>A	c.(2428-2430)GAT>AAT	p.D810N	PRPF40A_uc002tyg.2_Missense_Mutation_p.D266N	NM_017892	NP_060362	O75400	PR40A_HUMAN	formin binding protein 3	837					mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding				0														0.169492	17.206629	23.315392	10	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153223931	153223931	13014	2	C	T	T	29	29	PRPF40A	T	2	2
NBAS	51594	broad.mit.edu	36	2	15411216	15411216	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:15411216C>T	uc002rcc.1	-	c.4001G>A	c.(4000-4002)CGT>CAT	p.R1334H	NBAS_uc010exl.1_Missense_Mutation_p.R406H|NBAS_uc002rcd.1_Non-coding_Transcript	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1334										ovary(2)|liver(1)	3														0.253012	162.725875	176.504064	63	186	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15411216	15411216	10582	2	C	T	T	19	19	NBAS	T	1	1
SCG2	7857	broad.mit.edu	36	2	224170624	224170624	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:224170624C>T	uc002vnm.1	-	c.1621G>A	c.(1621-1623)GAA>AAA	p.E541K	SCG2_uc010fwv.1_Missense_Mutation_p.E541K	NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	541					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)												0.140496	26.314854	41.395778	17	104	CC		KEEP	---	---	---	---	capture		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)	Missense_Mutation	SNP	224170624	224170624	14372	2	C	T	T	30	30	SCG2	T	2	2
CYP26B1	56603	broad.mit.edu	36	2	72213838	72213838	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:72213838C>T	uc002sih.1	-	c.968G>A	c.(967-969)CGG>CAG	p.R323Q		NM_019885	NP_063938	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily b,	323					cell fate determination|embryonic limb morphogenesis|male meiosis|negative regulation of retinoic acid receptor signaling pathway|oxidation-reduction process|proximal/distal pattern formation|retinoic acid catabolic process|spermatogenesis|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding				0														0.352941	18.246723	18.570119	6	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72213838	72213838	4321	2	C	T	T	23	23	CYP26B1	T	1	1
PLA1A	51365	broad.mit.edu	36	3	120799505	120799505	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:120799505C>G	uc003ecu.1	+	c.55C>G	c.(55-57)CTC>GTC	p.L19V	PLA1A_uc003ecv.1_Missense_Mutation_p.L19V|PLA1A_uc003ecw.1_Non-coding_Transcript	NM_015900	NP_056984	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	19					lipid catabolic process|phosphatidylserine metabolic process	extracellular region	phospholipase A1 activity			ovary(1)|central_nervous_system(1)	2														0.294118	15.367988	16.013	5	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120799505	120799505	12414	3	C	G	G	28	28	PLA1A	G	3	3
MRPL3	11222	broad.mit.edu	36	3	132672804	132672804	+	Silent	SNP	T	C	C			TCGA-06-0140-01	TCGA-06-0140-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:132672804T>C	uc003eoh.1	-	c.639A>G	c.(637-639)AAA>AAG	p.K213K		NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	213					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0														0.289474	105.729128	110.25713	33	81	TT		KEEP	---	---	---	---	capture			Silent	SNP	132672804	132672804	10186	3	T	C	C	56	56	MRPL3	C	4	4
TRIM2	23321	broad.mit.edu	36	4	154435031	154435031	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:154435031G>A	uc003ing.1	+	c.649G>A	c.(649-651)GTG>ATG	p.V217M	TRIM2_uc003inh.1_Missense_Mutation_p.V217M	NM_015271	NP_056086	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 1	217						cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)												0.176471	34.982155	45.048991	18	84	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)	Missense_Mutation	SNP	154435031	154435031	17038	4	G	A	A	48	48	TRIM2	A	2	2
STOX2	56977	broad.mit.edu	36	4	185169239	185169239	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:185169239C>A	uc003ivz.1	+	c.2254C>A	c.(2254-2256)CAA>AAA	p.Q752K	STOX2_uc003iwa.1_Missense_Mutation_p.Q441K	NM_020225	NP_064610	Q9P2F5	STOX2_HUMAN	storkhead box 2	752					embryo development|maternal placenta development						0		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)												0.3	6.436847	6.785398	3	7	CC		KEEP	---	---	---	---	capture		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)	Missense_Mutation	SNP	185169239	185169239	15840	4	C	A	A	17	17	STOX2	A	3	3
RASSF6	166824	broad.mit.edu	36	4	74661281	74661281	+	Silent	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74661281C>T	uc003hhd.1	-	c.849G>A	c.(847-849)CCG>CCA	p.P283P	RASSF6_uc003hhc.1_Silent_p.P251P|RASSF6_uc010iik.1_Silent_p.P217P|RASSF6_uc010iil.1_Silent_p.P239P	NM_201431	NP_803876	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family 6	283	Ras-associating.				apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)													0.247911	223.200093	243.956874	89	270	CC		KEEP	---	---	---	---	capture	all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)		Silent	SNP	74661281	74661281	13551	4	C	T	T	27	27	RASSF6	T	1	1
DSPP	1834	broad.mit.edu	36	4	88753425	88753425	+	Missense_Mutation	SNP	G	A	A	rs61738515	unknown	TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:88753425G>A	uc003hqu.1	+	c.1063G>A	c.(1063-1065)GTA>ATA	p.V355I		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	355					biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)												0.191176	27.739261	33.796908	13	55	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000508)	Missense_Mutation	SNP	88753425	88753425	4966	4	G	A	A	40	40	DSPP	A	1	1
FCHSD1	89848	broad.mit.edu	36	5	141006401	141006401	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0140-01	TCGA-06-0140-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:141006401T>G	uc003llk.1	-	c.997A>C	c.(997-999)ACC>CCC	p.T333P	FCHSD1_uc010jgg.1_5'UTR|FCHSD1_uc003llj.1_Non-coding_Transcript	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	333									FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4														0.357143	7.820992	8.093024	5	9	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	141006401	141006401	6026	5	T	G	G	58	58	FCHSD1	G	4	4
SLC6A7	6534	broad.mit.edu	36	5	149564308	149564308	+	Silent	SNP	C	G	G			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149564308C>G	uc003lrr.1	+	c.1353C>G	c.(1351-1353)GTC>GTG	p.V451V		NM_014228	NP_055043	Q99884	SC6A7_HUMAN	solute carrier family 6, member 7	451						integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity				0		all_hematologic(541;0.224)			L-Proline(DB00172)									0.125	7.548941	16.360558	8	56	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Silent	SNP	149564308	149564308	15186	5	C	G	G	30	30	SLC6A7	G	3	3
GRIA1	2890	broad.mit.edu	36	5	153170960	153170960	+	Silent	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:153170960G>A	uc003luy.2	+	c.2703G>A	c.(2701-2703)TTG>TTA	p.L901L	GRIA1_uc003lva.2_Silent_p.L901L|GRIA1_uc003luz.2_Silent_p.L806L	NM_000827	NP_000818	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	901	Cytoplasmic (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(1)	5		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)			Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.309859	57.716175	60.007549	22	49	GG		KEEP	---	---	---	---	capture	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Silent	SNP	153170960	153170960	7045	5	G	A	A	47	47	GRIA1	A	2	2
IL7R	3575	broad.mit.edu	36	5	35912146	35912146	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:35912146G>A	uc003jjs.1	+	c.1181G>A	c.(1180-1182)GGC>GAC	p.G394D		NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	394	Cytoplasmic (Potential).				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)	4	all_lung(31;0.00015)													0.208955	31.615635	36.868072	14	53	GG		KEEP	---	---	---	---	capture	Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)		Missense_Mutation	SNP	35912146	35912146	8006	5	G	A	A	42	42	IL7R	A	2	2
UTP15	84135	broad.mit.edu	36	5	72900103	72900103	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:72900103G>A	uc003kcw.1	+	c.286G>A	c.(286-288)GTG>ATG	p.V96M	ANKRA2_uc003kcu.1_5'Flank|ANKRA2_uc003kcv.1_5'Flank|UTP15_uc010ize.1_Missense_Mutation_p.V96M	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,	96	WD 2.				rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)												0.241611	85.622537	94.699547	36	113	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)	Missense_Mutation	SNP	72900103	72900103	17662	5	G	A	A	48	48	UTP15	A	2	2
ECT2L	345930	broad.mit.edu	36	6	139249748	139249748	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:139249748G>A	uc003qif.1	+	c.2321G>A	c.(2320-2322)TGC>TAC	p.C774Y		NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	hypothetical protein LOC345930	774					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0														0.3	32.182767	33.613226	12	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139249748	139249748	5089	6	G	A	A	46	46	ECT2L	A	2	2
IRF4	3662	broad.mit.edu	36	6	343928	343928	+	Silent	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:343928G>A	uc003msz.2	+	c.738G>A	c.(736-738)GCG>GCA	p.A246A	IRF4_uc010jne.1_Silent_p.A246A|IRF4_uc003mta.2_Non-coding_Transcript|IRF4_uc003mtb.2_Silent_p.A245A|IRF4_uc003mtc.1_Silent_p.A76A	NM_002460	NP_002451	Q15306	IRF4_HUMAN	interferon regulatory factor 4	246					interferon-gamma-mediated signaling pathway|positive regulation of interleukin-10 biosynthetic process|positive regulation of interleukin-13 biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|regulation of T-helper cell differentiation|T cell activation|type I interferon-mediated signaling pathway	cytoplasm	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding			ovary(1)	1		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)								223				0.205882	15.408659	18.134009	7	27	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)	Silent	SNP	343928	343928	8135	6	G	A	A	40	40	IRF4	A	1	1
REPIN1	29803	broad.mit.edu	36	7	149699283	149699283	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149699283G>A	uc010lpr.1	+	c.191G>A	c.(190-192)AGG>AAG	p.R64K	REPIN1_uc003whd.2_5'UTR|REPIN1_uc010lpq.1_Missense_Mutation_p.R7K|REPIN1_uc003whc.2_Missense_Mutation_p.R7K|REPIN1_uc003whe.2_Missense_Mutation_p.R7K	NM_001099695	NP_001093165	Q9BWE0	REPI1_HUMAN	replication initiator 1 isoform 3	7					DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding			pancreas(1)	1	Ovarian(565;0.183)|Melanoma(164;0.226)													0.2	11.260493	13.353869	5	20	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.011)		Missense_Mutation	SNP	149699283	149699283	13696	7	G	A	A	35	35	REPIN1	A	2	2
MAD1L1	8379	broad.mit.edu	36	7	1822376	1822376	+	Silent	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:1822376C>T	uc003slh.1	-	c.2013G>A	c.(2011-2013)TCG>TCA	p.S671S	MAD1L1_uc003sle.1_Silent_p.S400S|MAD1L1_uc003slf.1_Silent_p.S671S|MAD1L1_uc003slg.1_Silent_p.S671S|MAD1L1_uc010ksh.1_Silent_p.S671S|MAD1L1_uc003sli.1_Silent_p.S579S|MAD1L1_uc003sld.1_Silent_p.S127S	NM_001013836	NP_003541	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein	671					cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			central_nervous_system(1)	1		Ovarian(82;0.0272)												0.244898	89.504586	98.24674	36	111	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)	Silent	SNP	1822376	1822376	9524	7	C	T	T	23	23	MAD1L1	T	1	1
ELN	2006	broad.mit.edu	36	7	73095289	73095289	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:73095289G>A	uc003tzw.1	+	c.365G>A	c.(364-366)GGA>GAA	p.G122E	ELN_uc003tzm.1_Intron|ELN_uc003tzn.1_Missense_Mutation_p.G122E|ELN_uc003tzz.1_Missense_Mutation_p.G110E|ELN_uc003tzo.1_Missense_Mutation_p.G122E|ELN_uc003tzp.1_Missense_Mutation_p.G112E|ELN_uc003tzq.1_Intron|ELN_uc003tzr.1_Non-coding_Transcript|ELN_uc003tzs.1_Missense_Mutation_p.G122E|ELN_uc003tzt.1_Missense_Mutation_p.G122E|ELN_uc003tzu.1_Missense_Mutation_p.G122E|ELN_uc003tzv.1_Missense_Mutation_p.G112E|ELN_uc010lbk.1_Non-coding_Transcript|ELN_uc003tzx.1_Missense_Mutation_p.G112E|ELN_uc003tzy.1_Missense_Mutation_p.G112E	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	122					blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)					434				0.148936	31.54612	48.297231	21	120	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73095289	73095289	5263	7	G	A	A	41	41	ELN	A	2	2
GTF2IRD1	9569	broad.mit.edu	36	7	73560401	73560401	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:73560401C>T	uc010lbq.1	+	c.55C>T	c.(55-57)CGC>TGC	p.R19C	GTF2IRD1_uc003uaq.1_Missense_Mutation_p.R19C|GTF2IRD1_uc003uap.1_Missense_Mutation_p.R19C|GTF2IRD1_uc003uar.1_Missense_Mutation_p.R19C	NM_005685	NP_005676	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 2	19					regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4														0.164706	28.697916	37.767436	14	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73560401	73560401	7148	7	C	T	T	23	23	GTF2IRD1	T	1	1
NPTX2	4885	broad.mit.edu	36	7	98095861	98095861	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98095861G>A	uc003upl.1	+	c.1280G>A	c.(1279-1281)CGT>CAT	p.R427H		NM_002523	NP_002514	P47972	NPTX2_HUMAN	neuronal pentraxin II	427	Pentaxin.			R -> A (in Ref. 1; AAA68980/AAA92296).	synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)	2	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)													0.285714	14.745144	15.608269	6	15	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	98095861	98095861	11008	7	G	A	A	40	40	NPTX2	A	1	1
TCEA1	6917	broad.mit.edu	36	8	55085600	55085600	+	Silent	SNP	T	C	C			TCGA-06-0140-01	TCGA-06-0140-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:55085600T>C	uc003xru.1	-	c.69A>G	c.(67-69)GGA>GGG	p.G23G	TCEA1_uc003xrv.1_Intron|TCEA1_uc003xrw.1_Non-coding_Transcript	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1	23	TFIIS N-terminal.				positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|general RNA polymerase II transcription factor activity|transcription elongation regulator activity|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)							p.G23G(CMK115-Tumor)|p.G23G(SNU503-Tumor)|p.G23G(HCC70-Tumor)|p.G23G(HS688A.T-Tumor)|p.G23G(SNU8-Tumor)|p.G23G(MUTZ3-Tumor)|p.G23G(RS5-Tumor)|p.G23G(PECAPJ41CLONED2-Tumor)|p.G23G(SNU478-Tumor)|p.G23G(MDAMB134VI-Tumor)|p.G23G(SKM1-Tumor)	405				0.272727	6.408111	7.549806	6	16	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)		Silent	SNP	55085600	55085600	16193	8	T	C	C	54	54	TCEA1	C	4	4
C9orf96	169436	broad.mit.edu	36	9	135250644	135250644	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135250644G>T	uc004cdk.1	+	c.799G>T	c.(799-801)GTG>TTG	p.V267L	C9orf96_uc004cdl.1_Non-coding_Transcript	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	267	Protein kinase.				protein phosphorylation		ATP binding|protein kinase activity			central_nervous_system(2)|stomach(1)	3										527				0.321168	127.952483	131.843788	44	93	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)	Missense_Mutation	SNP	135250644	135250644	2624	9	G	T	T	48	48	C9orf96	T	3	3
WNK2	65268	broad.mit.edu	36	9	95091424	95091424	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:95091424G>A	uc004ati.1	+	c.4678G>A	c.(4678-4680)GTC>ATC	p.V1560I	WNK2_uc004atj.1_Missense_Mutation_p.V1523I|WNK2_uc004atk.2_Missense_Mutation_p.V1160I|WNK2_uc004atl.1_Missense_Mutation_p.V118I	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1560					intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|large_intestine(1)|central_nervous_system(1)	7										1420				0.235294	8.29625	9.382724	4	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95091424	95091424	17952	9	G	A	A	40	40	WNK2	A	1	1
GPC4	2239	broad.mit.edu	36	X	132376642	132376642	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0140-01	TCGA-06-0140-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:132376642C>A	uc004exc.1	-	c.18G>T	c.(16-18)TTG>TTT	p.L6F		NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4	6					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)													0.238095	7.624201	8.905066	5	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	132376642	132376642	6874	23	C	A	A	25	25	GPC4	A	3	3
AKAP4	8852	broad.mit.edu	36	X	49843985	49843985	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0140-01	TCGA-06-0140-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:49843985G>A	uc004dow.1	-	c.2119C>T	c.(2119-2121)CTC>TTC	p.L707F	AKAP4_uc004dov.1_Missense_Mutation_p.L324F|AKAP4_uc010njp.1_Missense_Mutation_p.L529F|AKAP4_uc004dou.1_Missense_Mutation_p.L698F	NM_003886	NP_647450	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	707					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)	7	Ovarian(276;0.236)									119				0.44	69.94514	70.101535	22	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49843985	49843985	456	23	G	A	A	34	34	AKAP4	A	2	2
ANKRD9	122416	broad.mit.edu	36	14	102043164	102043165	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-0140-01	TCGA-06-0140-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:102043164_102043165insC	uc001ylx.1	-	c.815_816insG	c.(814-816)GGCfs	p.G272fs	ANKRD9_uc001yly.1_Frame_Shift_Ins_p.G272fs|ANKRD9_uc001ylz.1_Frame_Shift_Ins_p.G272fs|ANKRD9_uc001yma.1_Frame_Shift_Ins_p.G272fs|ANKRD9_uc010awm.1_Frame_Shift_Ins_p.G272fs|ANKRD9_uc010awn.1_Frame_Shift_Ins_p.G272fs	NM_152326	NP_689539	Q96BM1	ANKR9_HUMAN	ankyrin repeat domain 9	272										pancreas(1)	1														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	102043164	102043165	695	14	-	C	C	42	42	ANKRD9	C	5	5
