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
HPS6	79803	broad.mit.edu	36	10	103817524	103817524	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:103817524C>T	uc001kuj.1	+	c.2303C>T	c.(2302-2304)CCC>CTC	p.P768L		NM_024747	NP_079023	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome-6	768						cytosol|early endosome membrane|endoplasmic reticulum|microsome					0		Colorectal(252;0.122)												0.238095	46.0602	51.326266	20	64	CC		KEEP	---	---	---	---	capture		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)	Missense_Mutation	SNP	103817524	103817524	7635	10	C	T	T	22	22	HPS6	T	2	2
CCNY	219771	broad.mit.edu	36	10	35859178	35859178	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:35859178G>A	uc001iyw.2	+	c.579_splice	c.e7+1	p.L193_splice	CCNY_uc001iyu.2_Splice_Site_SNP_p.L139_splice|CCNY_uc001iyv.2_Splice_Site_SNP_p.L139_splice|CCNY_uc001iyx.2_Splice_Site_SNP_p.L139_splice|CCNY_uc009xmb.1_Splice_Site_SNP_p.L168_splice	NM_145012	NP_859049			cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein binding				0														0.531915	71.274363	71.316741	25	22	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	35859178	35859178	3063	10	G	A	A	44	44	CCNY	A	5	2
PTEN	5728	broad.mit.edu	36	10	89710659	89710659	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710659C>T	uc001kfb.1	+	c.830C>T	c.(829-831)ACA>ATA	p.T277I		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	277	C2 tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.D268_F279>VGQNVSLLGKYI(2)|p.T277I(1)|p.G165_*404del(1)|p.W274_F341del(1)|p.G165_K342del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.521739	64.58922	64.60772	24	22	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89710659	89710659	13192	10	C	T	T	17	17	PTEN	T	2	2
HTR3A	3359	broad.mit.edu	36	11	113361974	113361974	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113361974G>A	uc001pon.1	+	c.572G>A	c.(571-573)CGC>CAC	p.R191H	HTR3A_uc001pom.1_Missense_Mutation_p.R191H|HTR3A_uc009yyx.1_Intron	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	191	Extracellular (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)									0.327791	359.506252	370.578046	138	283	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	113361974	113361974	7744	11	G	A	A	38	38	HTR3A	A	1	1
AMICA1	120425	broad.mit.edu	36	11	117579477	117579477	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117579477G>A	uc001psk.2	-	c.648C>T	c.(646-648)GAC>GAT	p.D216D	AMICA1_uc001psg.2_Silent_p.D26D|AMICA1_uc001psh.2_Silent_p.D177D|AMICA1_uc009yzw.1_Non-coding_Transcript|AMICA1_uc001psi.2_Silent_p.D206D|AMICA1_uc001psj.2_Silent_p.D205D|AMICA1_uc001psl.1_Silent_p.D172D	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen	216	Ig-like V-type 2.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)												0.292763	225.284406	236.957074	89	215	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)	Silent	SNP	117579477	117579477	577	11	G	A	A	40	40	AMICA1	A	1	1
NAP1L4	4676	broad.mit.edu	36	11	2932397	2932397	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:2932397C>T	uc001lxc.1	-	c.971G>A	c.(970-972)CGT>CAT	p.R324H	NAP1L4_uc001lxb.1_5'Flank|NAP1L4_uc009ydt.1_Non-coding_Transcript	NM_005969	NP_005960	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	324					nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)												0.375	105.808168	107.230863	39	65	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)	Missense_Mutation	SNP	2932397	2932397	10555	11	C	T	T	19	19	NAP1L4	T	1	1
OR52K1	390036	broad.mit.edu	36	11	4467002	4467002	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4467002G>C	uc001lza.1	+	c.296G>C	c.(295-297)TGT>TCT	p.C99S		NM_001005171	NP_001005171	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K,	99	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)												0.273973	57.270081	60.628561	20	53	GG		KEEP	---	---	---	---	capture		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)	Missense_Mutation	SNP	4467002	4467002	11533	11	G	C	C	48	48	OR52K1	C	3	3
KLRC3	3823	broad.mit.edu	36	12	10464386	10464386	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10464386C>A	uc001qyi.1	-	c.31G>T	c.(31-33)GTG>TTG	p.V11L	KLRC3_uc001qyf.1_Missense_Mutation_p.V11L|KLRC3_uc001qyg.1_Missense_Mutation_p.V11L|KLRC3_uc001qyh.1_Intron|KLRC3_uc001qyj.1_Missense_Mutation_p.V11L|KLRC3_uc009zhl.1_Missense_Mutation_p.V11L	NM_007333	NP_031359	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C,	11	Cytoplasmic (Potential).				cellular defense response	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)	2														0.164948	26.834046	37.175911	16	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10464386	10464386	8731	12	C	A	A	20	20	KLRC3	A	3	3
KLRC3	3823	broad.mit.edu	36	12	10479822	10479822	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10479822C>A	uc001qyh.1	-	c.31G>T	c.(31-33)GTG>TTG	p.V11L	KLRC2_uc001qyk.1_Missense_Mutation_p.V11L	NM_002261	NP_002252	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C,	11	Cytoplasmic (Potential).				cellular defense response	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)	2														0.103753	34.471574	105.294637	47	406	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10479822	10479822	8731	12	C	A	A	20	20	KLRC3	A	3	3
PUS1	80324	broad.mit.edu	36	12	130992427	130992427	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130992427G>C	uc001ujf.1	+	c.1182G>C	c.(1180-1182)TTG>TTC	p.L394F	PUS1_uc001ujg.1_Missense_Mutation_p.L366F|PUS1_uc001ujh.1_Missense_Mutation_p.L366F|PUS1_uc001uji.1_Missense_Mutation_p.L341F	NM_025215	NP_001002020	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1 isoform 1	394						mitochondrion	pseudouridine synthase activity|pseudouridylate synthase activity|RNA binding			breast(1)|central_nervous_system(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)					Esophageal Squamous(102;671 2009 17384 45666)								0.227273	8.574231	10.07632	5	17	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)	Missense_Mutation	SNP	130992427	130992427	13288	12	G	C	C	46	46	PUS1	C	3	3
ADAMTS20	80070	broad.mit.edu	36	12	42231191	42231191	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:42231191G>A	uc001rnn.1	-	c.241C>T	c.(241-243)CGC>TGC	p.R81C		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	81						proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)								2149				0.24359	44.083583	48.762186	19	59	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0473)	Missense_Mutation	SNP	42231191	42231191	267	12	G	A	A	37	37	ADAMTS20	A	1	1
LPAR5	57121	broad.mit.edu	36	12	6599862	6599862	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6599862G>A	uc001qps.1	-	c.814C>T	c.(814-816)CGC>TGC	p.R272C	LPAR5_uc009zer.1_Missense_Mutation_p.R272C	NM_020400	NP_065133	Q9H1C0	LPAR5_HUMAN	lysophosphatidic acid receptor 5	272	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1						NSCLC(74;891 2312 37538)								0.333333	13.170039	13.539029	5	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6599862	6599862	9281	12	G	A	A	39	39	LPAR5	A	1	1
PTPN6	5777	broad.mit.edu	36	12	6939365	6939365	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6939365G>A	uc009zfl.1	+	c.1376G>A	c.(1375-1377)CGC>CAC	p.R459H	PTPN6_uc001qsa.1_Missense_Mutation_p.R461H|PTPN6_uc001qsb.2_Missense_Mutation_p.R459H	NM_080549	NP_536859	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type	459	Tyrosine-protein phosphatase.|Substrate binding (By similarity).				apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity			breast(1)	1														0.270142	135.027011	145.059123	57	154	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6939365	6939365	13249	12	G	A	A	38	38	PTPN6	A	1	1
DIO3	1735	broad.mit.edu	36	14	101098457	101098457	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:101098457C>T	uc001yki.2	+	c.793C>T	c.(793-795)CGC>TGC	p.R265C	DIO3-OS_uc001ykd.1_5'Flank	NM_001362	NP_001353	P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	265	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|oxidation-reduction process	endosome membrane|integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|thyroxine 5-deiodinase activity			ovary(1)|central_nervous_system(1)	2		all_neural(303;0.185)												0.313725	85.172751	88.31723	32	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101098457	101098457	4705	14	C	T	T	19	19	DIO3	T	1	1
TTC8	123016	broad.mit.edu	36	14	88406286	88406286	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:88406286G>T	uc010ath.1	+	c.1088G>T	c.(1087-1089)CGG>CTG	p.R363L	TTC8_uc001xxl.1_Missense_Mutation_p.R108L|TTC8_uc010ati.1_Missense_Mutation_p.R149L|TTC8_uc001xxm.1_Missense_Mutation_p.R307L|TTC8_uc010atj.1_Missense_Mutation_p.R82L|TTC8_uc001xxi.1_Missense_Mutation_p.R347L|TTC8_uc001xxj.1_Missense_Mutation_p.R337L|TTC8_uc001xxk.1_Missense_Mutation_p.R307L	NM_198309	NP_938051	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8 isoform B	373	TPR 5.				cilium assembly|establishment of anatomical structure orientation|response to stimulus|sensory processing|visual perception	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0														0.272727	184.179108	195.94805	69	184	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88406286	88406286	17269	14	G	T	T	39	39	TTC8	T	3	3
ZNF768	79724	broad.mit.edu	36	16	30443434	30443434	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30443434C>T	uc002dyk.2	-	c.1528G>A	c.(1528-1530)GAG>AAG	p.E510K		NM_024671	NP_078947	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	510					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	DNA binding|zinc ion binding				0														0.214286	33.996751	39.266265	15	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30443434	30443434	18739	16	C	T	T	31	31	ZNF768	T	1	1
SEPT12	124404	broad.mit.edu	36	16	4776008	4776008	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:4776008G>A	uc002cxq.1	-	c.266C>T	c.(265-267)ACG>ATG	p.T89M	SEPT12_uc010bty.1_Non-coding_Transcript|SEPT12_uc002cxr.1_Missense_Mutation_p.T89M	NM_144605	NP_653206	Q8IYM1	SEP12_HUMAN	septin 12	89		GTP (By similarity).			cell cycle|cell division	cleavage furrow|midbody|perinuclear region of cytoplasm|septin complex|spindle|stress fiber	GDP binding|GTP binding|phosphatidylinositol binding|protein homodimerization activity				0														0.272727	29.583892	31.630585	12	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4776008	4776008	14548	16	G	A	A	40	40	SEPT12	A	1	1
HYDIN	54768	broad.mit.edu	36	16	69459979	69459979	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69459979G>A	uc002ezr.1	-	c.11302C>T	c.(11302-11304)CGA>TGA	p.R3768*	HYDIN_uc010cfy.1_5'Flank	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	3769										ovary(1)	1		Ovarian(137;0.0654)												0.12931	19.260009	34.767729	15	101	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	69459979	69459979	7767	16	G	A	A	40	40	HYDIN	A	5	1
FLII	2314	broad.mit.edu	36	17	18094998	18094998	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0124-01	TCGA-06-0124-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:18094998T>C	uc002gsr.1	-	c.1655A>G	c.(1654-1656)GAG>GGG	p.E552G	FLII_uc002gsq.1_Missense_Mutation_p.E423G|FLII_uc010cpy.1_Missense_Mutation_p.E541G|FLII_uc002gss.1_Missense_Mutation_p.E551G	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	552	Interaction with ACTL6A.|Gelsolin-like 1.				multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)	1	all_neural(463;0.228)													0.194444	8.283429	11.459039	7	29	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18094998	18094998	6163	17	T	C	C	54	54	FLII	C	4	4
NF1	4763	broad.mit.edu	36	17	26686128	26686128	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26686128C>T	uc002hgg.1	+	c.5959C>T	c.(5959-5961)CAG>TAG	p.Q1987*	NF1_uc002hgh.1_Nonsense_Mutation_p.Q1966*|NF1_uc010cso.1_Nonsense_Mutation_p.Q175*	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1987					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.Q1987*(1)|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)								847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.289474	78.432013	82.960294	33	81	CC		KEEP	---	---	---	---	capture		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)	Nonsense_Mutation	SNP	26686128	26686128	10756	17	C	T	T	17	17	NF1	T	5	2
NF1	4763	broad.mit.edu	36	17	26691722	26691722	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26691722C>A	uc002hgg.1	+	c.6995C>A	c.(6994-6996)TCA>TAA	p.S2332*	NF1_uc002hgh.1_Nonsense_Mutation_p.S2311*|NF1_uc010cso.1_Nonsense_Mutation_p.S520*	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2332					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.S2332*(1)|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)								847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.336735	86.230587	88.548227	33	65	CC		KEEP	---	---	---	---	capture		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)	Nonsense_Mutation	SNP	26691722	26691722	10756	17	C	A	A	29	29	NF1	A	5	3
KRT37	8688	broad.mit.edu	36	17	36832167	36832167	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36832167C>T	uc002hwp.1	-	c.778G>A	c.(778-780)GAG>AAG	p.E260K		NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	260	Linker 12.|Rod.					intermediate filament	structural molecule activity				0		Breast(137;0.000496)												0.272727	172.155272	183.878899	69	184	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36832167	36832167	8789	17	C	T	T	31	31	KRT37	T	1	1
CAMKK1	84254	broad.mit.edu	36	17	3726350	3726350	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3726350G>A	uc002fwv.1	-	c.1026C>T	c.(1024-1026)GAC>GAT	p.D342D	CAMKK1_uc002fwt.1_Silent_p.D304D|CAMKK1_uc002fwu.1_Silent_p.D304D	NM_172207	NP_757344	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase 1	304	Protein kinase.				protein phosphorylation|synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1										485				0.275229	75.007575	79.96431	30	79	GG		KEEP	---	---	---	---	capture		LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)	Silent	SNP	3726350	3726350	2723	17	G	A	A	40	40	CAMKK1	A	1	1
CRLF1	9244	broad.mit.edu	36	19	18571609	18571609	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0124-01	TCGA-06-0124-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18571609A>G	uc010ebt.1	-	c.163T>C	c.(163-165)TCC>CCC	p.S55P		NM_004750	NP_004741	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	55	Ig-like C2-type.				negative regulation of neuron apoptosis|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	cytokine binding|protein heterodimerization activity|receptor activity			central_nervous_system(1)	1														0.208333	6.383195	8.270549	5	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18571609	18571609	4025	19	A	G	G	11	11	CRLF1	G	4	4
NCAN	1463	broad.mit.edu	36	19	19198603	19198603	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19198603G>C	uc002nlz.1	+	c.1381G>C	c.(1381-1383)GGC>CGC	p.G461R	NCAN_uc010ecc.1_Missense_Mutation_p.G25R	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3	461					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4														0.255814	50.705797	55.359999	22	64	GG		KEEP	---	---	---	---	capture	Epithelial(12;0.00544)		Missense_Mutation	SNP	19198603	19198603	10603	19	G	C	C	35	35	NCAN	C	3	3
PAPL	390928	broad.mit.edu	36	19	44283809	44283809	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44283809C>T	uc002oki.1	+	c.1015C>T	c.(1015-1017)CGA>TGA	p.R339*	PAPL_uc010egl.1_Silent_p.N297N	NM_001004318	NP_001004318	Q6ZNF0	PAPL_HUMAN	FLJ16165 protein	339						extracellular region	acid phosphatase activity|metal ion binding				0														0.161017	31.753567	44.656035	19	99	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	44283809	44283809	11844	19	C	T	T	19	19	PAPL	T	5	1
XAB2	56949	broad.mit.edu	36	19	7598308	7598308	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7598308C>T	uc002mgx.1	-	c.343G>A	c.(343-345)GAT>AAT	p.D115N		NM_020196	NP_064581	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	115	HAT 3.				nuclear mRNA splicing, via spliceosome|transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4														0.3	8.698426	9.443311	6	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7598308	7598308	17992	19	C	T	T	32	32	XAB2	T	2	2
CLEC4M	10332	broad.mit.edu	36	19	7737634	7737634	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7737634G>A	uc002mib.1	+	c.877G>A	c.(877-879)GTC>ATC	p.V293I	CLEC4M_uc002mhy.1_3'UTR|CLEC4M_uc002mhz.1_Missense_Mutation_p.V201I|CLEC4M_uc002mia.1_Missense_Mutation_p.V157I|CLEC4M_uc010dvs.1_Missense_Mutation_p.V269I|CLEC4M_uc002mic.1_Missense_Mutation_p.V265I|CLEC4M_uc010dvt.1_Missense_Mutation_p.V270I|CLEC4M_uc002mie.1_3'UTR|CLEC4M_uc002mif.1_3'UTR|CLEC4M_uc002mig.1_3'UTR|CLEC4M_uc002mih.1_Missense_Mutation_p.V270I|CLEC4M_uc002mii.1_Missense_Mutation_p.V12I	NM_214675	NP_999840	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M isoform	293	Extracellular (Probable).|C-type lectin.				cell-cell recognition|endocytosis|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to plasma membrane	ICAM-3 receptor activity|mannose binding|metal ion binding|peptide antigen binding|virion binding			pancreas(1)	1														0.271676	107.752531	115.885	47	126	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7737634	7737634	3656	19	G	A	A	40	40	CLEC4M	A	1	1
PRMT6	55170	broad.mit.edu	36	1	107401838	107401838	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:107401838C>G	uc001dvb.1	+	c.801C>G	c.(799-801)AAC>AAG	p.N267K		NM_018137	NP_060607	Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	326					base-excision repair|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|histone methyltransferase activity (H2A-R3 specific)|histone methyltransferase activity (H3-R2 specific)|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity				0		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)												0.192308	7.254816	9.563635	5	21	CC		KEEP	---	---	---	---	capture		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)	Missense_Mutation	SNP	107401838	107401838	12983	1	C	G	G	19	19	PRMT6	G	3	3
IGSF3	3321	broad.mit.edu	36	1	116960586	116960586	+	Silent	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:116960586C>T	uc001egq.1	-	c.60G>A	c.(58-60)CAG>CAA	p.Q20Q	IGSF3_uc001egr.1_Silent_p.Q20Q	NM_001542	NP_001533	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 1	20	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)												0.265306	30.849016	33.291186	13	36	CC		KEEP	---	---	---	---	capture		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)	Silent	SNP	116960586	116960586	7902	1	C	T	T	28	28	IGSF3	T	2	2
FLG	2312	broad.mit.edu	36	1	150542281	150542281	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150542281G>T	uc001ezu.1	-	c.11705C>A	c.(11704-11706)CCC>CAC	p.P3902H		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3902	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.328358	109.443747	112.949632	44	90	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150542281	150542281	6160	1	G	T	T	43	43	FLG	T	3	3
SELE	6401	broad.mit.edu	36	1	167965398	167965398	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167965398G>A	uc001ggm.2	-	c.756C>T	c.(754-756)TTC>TTT	p.F252F	C1orf112_uc001ggj.1_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor	252	Sushi 2.|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)													0.263441	120.594254	130.005182	49	137	GG		KEEP	---	---	---	---	capture			Silent	SNP	167965398	167965398	14499	1	G	A	A	37	37	SELE	A	1	1
KIF17	57576	broad.mit.edu	36	1	20886957	20886957	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:20886957G>A	uc001bdr.2	-	c.1449C>T	c.(1447-1449)AGC>AGT	p.S483S	KIF17_uc001bdp.2_5'Flank|KIF17_uc001bdq.2_5'Flank|KIF17_uc009vpx.1_Intron|KIF17_uc001bds.2_Silent_p.S483S	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a	483					microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)	3		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)												0.272	81.698514	87.555548	34	91	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)	Silent	SNP	20886957	20886957	8590	1	G	A	A	38	38	KIF17	A	1	1
COL8A2	1296	broad.mit.edu	36	1	36336189	36336189	+	Silent	SNP	G	T	T			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36336189G>T	uc001bzv.1	-	c.1680C>A	c.(1678-1680)GGC>GGA	p.G560G	COL8A2_uc001bzw.1_Silent_p.G495G	NM_005202	NP_005193	P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	560	Nonhelical region (NC1).				angiogenesis|cell-cell adhesion|extracellular matrix organization	basement membrane|collagen	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)												0.5	8.30403	8.30403	6	6	GG		KEEP	---	---	---	---	capture			Silent	SNP	36336189	36336189	3844	1	G	T	T	46	46	COL8A2	T	3	3
FOXJ3	22887	broad.mit.edu	36	1	42516810	42516810	+	Silent	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:42516810C>T	uc001che.1	-	c.165G>A	c.(163-165)AAG>AAA	p.K55K	FOXJ3_uc001chf.1_Silent_p.K55K|FOXJ3_uc001chg.1_Silent_p.K55K|FOXJ3_uc001chh.1_Silent_p.K55K	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	55					embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific 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			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.271186	206.361891	220.29552	80	215	CC		KEEP	---	---	---	---	capture			Silent	SNP	42516810	42516810	6259	1	C	T	T	32	32	FOXJ3	T	2	2
GNAS	2778	broad.mit.edu	36	20	56862963	56862963	+	Silent	SNP	A	C	C			TCGA-06-0124-01	TCGA-06-0124-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:56862963A>C	uc002xzw.1	+	c.1248A>C	c.(1246-1248)GCA>GCC	p.A416A	GNAS_uc002xzt.1_Intron|GNAS_uc002xzu.2_Intron|GNAS_uc010gjq.1_Intron|GNAS_uc002xzv.1_Non-coding_Transcript	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	Error:Variant_position_missing_in_P63092_after_alignment					activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|large_intestine(5)|parathyroid(5)|kidney(5)|lung(2)|testis(1)|autonomic_ganglia(1)	279	all_lung(29;0.0104)					Colon(117;935 1597 6045 8307 46442)				461	TSP Lung(22;0.16)			0.444444	8.99334	9.018179	4	5	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)		Silent	SNP	56862963	56862963	6779	20	A	C	C	6	6	GNAS	C	4	4
RSPO4	343637	broad.mit.edu	36	20	895858	895858	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:895858G>A	uc002wej.1	-	c.368C>T	c.(367-369)CCG>CTG	p.P123L	RSPO4_uc002wek.1_Missense_Mutation_p.P123L	NM_001029871	NP_001025042	Q2I0M5	RSPO4_HUMAN	R-spondin family, member 4 isoform 1 precursor	123	FU.				Wnt receptor signaling pathway	extracellular region	heparin binding				0														0.35	77.085052	78.668908	28	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	895858	895858	14192	20	G	A	A	39	39	RSPO4	A	1	1
POTED	317754	broad.mit.edu	36	21	13904799	13904799	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:13904799G>A	uc002yjb.1	+	c.379G>A	c.(379-381)GCC>ACC	p.A127T		NM_174981	NP_778146	Q86YR6	POTED_HUMAN	pote protein	127						plasma membrane				ovary(3)	3														0.432	144.317555	144.823026	54	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13904799	13904799	12693	21	G	A	A	38	38	POTED	A	1	1
PRDM15	63977	broad.mit.edu	36	21	42164746	42164746	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42164746C>T	uc002yzq.1	-	c.467G>A	c.(466-468)GGG>GAG	p.G156E	PRDM15_uc002yzo.1_Intron|PRDM15_uc002yzp.1_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	156					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.295455	68.918677	72.210612	26	62	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42164746	42164746	12898	21	C	T	T	22	22	PRDM15	T	2	2
MICAL3	57553	broad.mit.edu	36	22	16654039	16654039	+	Silent	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:16654039C>A	uc002zng.2	-	c.2598G>T	c.(2596-2598)CTG>CTT	p.L866L	MICAL3_uc010grd.1_Silent_p.L9L|MICAL3_uc010gre.1_Non-coding_Transcript			Q7RTP6	MICA3_HUMAN	Uncharacterized protein KIAA0819.	1893	Potential.				oxidation-reduction process	cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)												0.210526	15.876163	18.8251	8	30	CC		KEEP	---	---	---	---	capture		Lung(27;0.0427)	Silent	SNP	16654039	16654039	9961	22	C	A	A	29	29	MICAL3	A	3	3
CLDN5	7122	broad.mit.edu	36	22	17891273	17891273	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:17891273G>C	uc002zpu.1	-	c.506C>G	c.(505-507)GCG>GGG	p.A169G	CLDN5_uc010grr.1_Missense_Mutation_p.A169G	NM_003277	NP_003268	O00501	CLD5_HUMAN	claudin 5	169	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity				0	Colorectal(54;0.0993)													0.375	8.72234	8.983974	6	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17891273	17891273	3625	22	G	C	C	38	38	CLDN5	C	3	3
NAGA	4668	broad.mit.edu	36	22	40788876	40788876	+	Silent	SNP	C	G	G			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40788876C>G	uc003bbw.2	-	c.858G>C	c.(856-858)CTG>CTC	p.L286L	NAGA_uc003bbx.1_Silent_p.L286L|NAGA_uc003bby.1_Silent_p.L286L	NM_000262	NP_000253	P17050	NAGAB_HUMAN	alpha-N-acetylgalactosaminidase precursor	286					glycoside catabolic process|glycosylceramide catabolic process|oligosaccharide metabolic process	lysosome	alpha-galactosidase activity|alpha-N-acetylgalactosaminidase activity|cation binding|protein homodimerization activity			central_nervous_system(1)	1														0.278195	98.737663	104.613039	37	96	CC		KEEP	---	---	---	---	capture			Silent	SNP	40788876	40788876	10537	22	C	G	G	25	25	NAGA	G	3	3
PKDREJ	10343	broad.mit.edu	36	22	45033872	45033872	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0124-01	TCGA-06-0124-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45033872T>G	uc003bhh.1	-	c.4012A>C	c.(4012-4014)ACT>CCT	p.T1338P		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1338	Cytoplasmic (Potential).|PLAT.				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)												0.262821	114.71623	122.645895	41	115	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)	Missense_Mutation	SNP	45033872	45033872	12395	22	T	G	G	59	59	PKDREJ	G	4	4
APOB	338	broad.mit.edu	36	2	21092836	21092836	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21092836G>A	uc002red.1	-	c.3312C>T	c.(3310-3312)GTC>GTT	p.V1104V		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1104					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.357143	98.100687	99.860922	35	63	GG		KEEP	---	---	---	---	capture			Silent	SNP	21092836	21092836	796	2	G	A	A	37	37	APOB	A	1	1
CD207	50489	broad.mit.edu	36	2	70912450	70912450	+	Silent	SNP	C	G	G			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:70912450C>G	uc002shg.1	-	c.726G>C	c.(724-726)CTG>CTC	p.L242L		NM_015717	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 antigen, langerin	242	C-type lectin.|Extracellular (Potential).				defense response to virus	endocytic vesicle|integral to membrane	mannose binding			ovary(1)|lung(1)	2														0.318681	86.042714	88.701662	29	62	CC		KEEP	---	---	---	---	capture			Silent	SNP	70912450	70912450	3110	2	C	G	G	17	17	CD207	G	3	3
GPAT2	150763	broad.mit.edu	36	2	96052616	96052616	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:96052616G>C	uc002svf.1	-	c.2114C>G	c.(2113-2115)GCC>GGC	p.A705G	GPAT2_uc002svd.1_Missense_Mutation_p.A524G|GPAT2_uc002sve.1_Missense_Mutation_p.A507G|GPAT2_uc002svg.1_Missense_Mutation_p.A584G|GPAT2_uc002svh.1_Intron	NM_207328	NP_997211	Q6NUI2	GPAT2_HUMAN	hypothetical protein LOC150763	705					glycerol-3-phosphate metabolic process|phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity				0														0.222222	7.886885	9.169537	4	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96052616	96052616	6863	2	G	C	C	42	42	GPAT2	C	3	3
ZAP70	7535	broad.mit.edu	36	2	97717604	97717604	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:97717604G>A	uc002syd.1	+	c.1079G>A	c.(1078-1080)CGC>CAC	p.R360H	ZAP70_uc002sye.1_Missense_Mutation_p.R250H|ZAP70_uc002syf.1_Missense_Mutation_p.R53H	NM_001079	NP_997402	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	360	Protein kinase.				immune response|intracellular protein kinase cascade|positive thymic T cell selection|T cell receptor signaling pathway	cytosol|T cell receptor complex	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5										138				0.224719	39.76297	45.956634	20	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97717604	97717604	18097	2	G	A	A	38	38	ZAP70	A	1	1
MORC1	27136	broad.mit.edu	36	3	110236999	110236999	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110236999C>T	uc003dxl.1	-	c.1337G>A	c.(1336-1338)AGA>AAA	p.R446K		NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1	446					cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|breast(2)	5														0.243902	24.829653	27.280132	10	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110236999	110236999	10092	3	C	T	T	32	32	MORC1	T	2	2
ADAM29	11086	broad.mit.edu	36	4	176133506	176133506	+	Silent	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:176133506C>T	uc003iuc.1	+	c.255C>T	c.(253-255)GAC>GAT	p.D85D	ADAM29_uc003iud.1_Silent_p.D85D|ADAM29_uc003iue.1_Silent_p.D85D|ADAM29_uc010irr.1_Silent_p.D85D	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	85					proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(1)	10		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)				Ovarian(140;1727 1835 21805 25838 41440)				106				0.297297	55.321694	58.040132	22	52	CC		KEEP	---	---	---	---	capture		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)	Silent	SNP	176133506	176133506	248	4	C	T	T	18	18	ADAM29	T	2	2
SEPSECS	51091	broad.mit.edu	36	4	24734739	24734739	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0124-01	TCGA-06-0124-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:24734739T>C	uc003gri.1	-	c.1415A>G	c.(1414-1416)TAT>TGT	p.Y472C	SEPSECS_uc003grg.1_Missense_Mutation_p.Y413C|SEPSECS_uc003grh.1_Missense_Mutation_p.Y394C	NM_153825	NP_722547	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine)	473					selenocysteine incorporation	cytoplasm|nucleus	pyridoxal phosphate binding|transferase activity, transferring selenium-containing groups|tRNA binding				0		Breast(46;0.173)			Pyridoxal Phosphate(DB00114)									0.278947	148.814666	157.151672	53	137	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24734739	24734739	14544	4	T	C	C	49	49	SEPSECS	C	4	4
RBM47	54502	broad.mit.edu	36	4	40135575	40135575	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:40135575G>A	uc003gvc.2	-	c.93C>T	c.(91-93)AAC>AAT	p.N31N	RBM47_uc003gve.2_Non-coding_Transcript|RBM47_uc003gvd.2_Silent_p.N31N|RBM47_uc003gvg.1_Silent_p.N31N	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	31						nucleus	nucleotide binding|RNA binding			breast(3)	3														0.230769	6.635904	7.487311	3	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	40135575	40135575	13603	4	G	A	A	40	40	RBM47	A	1	1
SLC6A19	340024	broad.mit.edu	36	5	1261942	1261942	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1261942G>A	uc003jbw.2	+	c.284G>A	c.(283-285)CGG>CAG	p.R95Q		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	95	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)													0.288136	87.964483	92.678586	34	84	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Missense_Mutation	SNP	1261942	1261942	15179	5	G	A	A	39	39	SLC6A19	A	1	1
FNIP1	96459	broad.mit.edu	36	5	131070045	131070045	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:131070045C>T	uc003kvs.1	-	c.872G>A	c.(871-873)CGC>CAC	p.R291H	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.R263H|FNIP1_uc010jdm.1_Missense_Mutation_p.R246H|FNIP1_uc003kvu.2_Missense_Mutation_p.R291H	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	291					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)	1		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)												0.312057	116.851801	121.284442	44	97	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)	Missense_Mutation	SNP	131070045	131070045	6217	5	C	T	T	27	27	FNIP1	T	1	1
PCDHA12	56137	broad.mit.edu	36	5	140236603	140236603	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140236603G>A	uc003lic.1	+	c.1362G>A	c.(1360-1362)GCG>GCA	p.A454A	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhs.1_Intron|PCDHA9_uc003lhu.1_Intron|PCDHA10_uc003lhx.1_Intron|PCDHA10_uc003lhw.1_Intron|PCDHA11_uc003lia.1_Intron|PCDHA12_uc003lib.1_Silent_p.A454A	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	454	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0						Pancreas(113;759 1672 13322 24104 50104)								0.244792	103.182596	114.547622	47	145	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140236603	140236603	11942	5	G	A	A	40	40	PCDHA12	A	1	1
BASP1	10409	broad.mit.edu	36	5	17328409	17328409	+	Silent	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:17328409C>T	uc003jfx.1	+	c.84C>T	c.(82-84)GGC>GGT	p.G28G	BASP1_uc010ity.1_Silent_p.G28G	NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein	28					glomerular visceral epithelial cell differentiation|negative regulation of gene-specific transcription	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	promoter binding|protein domain specific binding|specific transcriptional repressor activity|transcription corepressor activity				0														0.244444	27.015291	29.684449	11	34	CC		KEEP	---	---	---	---	capture			Silent	SNP	17328409	17328409	1338	5	C	T	T	27	27	BASP1	T	1	1
HMP19	51617	broad.mit.edu	36	5	173467064	173467064	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:173467064G>C	uc003mcx.1	+	c.466G>C	c.(466-468)GCA>CCA	p.A156P		NM_015980	NP_057064	Q9Y328	NSG2_HUMAN	HMP19 protein	156	Lumenal (Potential).				dopamine receptor signaling pathway	cytoplasmic vesicle membrane|Golgi cisterna membrane|integral to membrane|multivesicular body membrane	dopamine receptor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00925)|all_lung(126;0.0148)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)												0.296296	12.805083	13.866982	8	19	GG		KEEP	---	---	---	---	capture	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Missense_Mutation	SNP	173467064	173467064	7537	5	G	C	C	34	34	HMP19	C	3	3
COL23A1	91522	broad.mit.edu	36	5	177622856	177622856	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:177622856C>T	uc003mje.1	-	c.598G>A	c.(598-600)GAC>AAC	p.D200N	COL23A1_uc010jkt.1_Silent_p.A47A	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	200	Extracellular (Potential).|Collagen-like 1.|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)												0.194805	30.486942	37.171985	15	62	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)	Missense_Mutation	SNP	177622856	177622856	3820	5	C	T	T	31	31	COL23A1	T	1	1
HCN1	348980	broad.mit.edu	36	5	45297962	45297962	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45297962C>A	uc003jok.1	-	c.2491G>T	c.(2491-2493)GGC>TGC	p.G831C		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	831	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.240506	34.900289	39.754606	19	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45297962	45297962	7278	5	C	A	A	22	22	HCN1	A	3	3
VCAN	1462	broad.mit.edu	36	5	82843802	82843802	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0124-01	TCGA-06-0124-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:82843802T>A	uc003kii.2	+	c.873T>A	c.(871-873)TTT>TTA	p.F291L	VCAN_uc003kih.2_Missense_Mutation_p.F291L|VCAN_uc003kik.2_Missense_Mutation_p.F291L|VCAN_uc010jau.1_Missense_Mutation_p.F291L|VCAN_uc003kij.2_Missense_Mutation_p.F291L	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1	291	Link 2.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)												0.342857	65.378393	66.905627	24	46	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Missense_Mutation	SNP	82843802	82843802	17703	5	T	A	A	63	63	VCAN	A	4	4
RFX6	222546	broad.mit.edu	36	6	117349961	117349961	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117349961C>A	uc003pxm.1	+	c.1391C>A	c.(1390-1392)GCT>GAT	p.A464D		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	464					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	promoter binding|protein binding|transcription activator activity			ovary(1)|pancreas(1)	2														0.292683	90.907773	95.671699	36	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117349961	117349961	13739	6	C	A	A	28	28	RFX6	A	3	3
PTPRK	5796	broad.mit.edu	36	6	128430587	128430587	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0124-01	TCGA-06-0124-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:128430587T>C	uc010kfc.1	-	c.1927A>G	c.(1927-1929)AAG>GAG	p.K643E	PTPRK_uc003qbj.1_Missense_Mutation_p.K643E|PTPRK_uc003qbk.1_Missense_Mutation_p.K643E|PTPRK_uc003qbl.1_Missense_Mutation_p.K513E	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	643	Extracellular (Potential).|Fibronectin type-III 4.	Cleavage (Probable).			cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8														0.27907	90.244104	95.908089	36	93	TT		KEEP	---	---	---	---	capture		all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)	Missense_Mutation	SNP	128430587	128430587	13262	6	T	C	C	63	63	PTPRK	C	4	4
RNF8	9025	broad.mit.edu	36	6	37444583	37444583	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:37444583G>A	uc003onq.2	+	c.586G>A	c.(586-588)GCC>ACC	p.A196T	RNF8_uc003onr.2_Missense_Mutation_p.A196T	NM_003958	NP_003949	O76064	RNF8_HUMAN	ring finger protein 8 isoform 1	196					cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1														0.294737	71.76017	75.343272	28	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37444583	37444583	13979	6	G	A	A	42	42	RNF8	A	2	2
PEX6	5190	broad.mit.edu	36	6	43045397	43045397	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43045397G>A	uc003otf.1	-	c.1354C>T	c.(1354-1356)CGC>TGC	p.R452C	PEX6_uc010jya.1_Non-coding_Transcript	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	452					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1														0.27027	77.329369	82.596267	30	81	GG		KEEP	---	---	---	---	capture	all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)		Missense_Mutation	SNP	43045397	43045397	12172	6	G	A	A	37	37	PEX6	A	1	1
MUC17	140453	broad.mit.edu	36	7	100468327	100468327	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100468327G>C	uc003uxp.1	+	c.6910G>C	c.(6910-6912)GTT>CTT	p.V2304L	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17	2304	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|36.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.196281	223.067757	264.655933	95	389	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100468327	100468327	10368	7	G	C	C	48	48	MUC17	C	3	3
RELN	5649	broad.mit.edu	36	7	102917441	102917441	+	Silent	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102917441G>A	uc003vca.1	-	c.9747C>T	c.(9745-9747)TGC>TGT	p.C3249C	RELN_uc010liz.1_Silent_p.C3249C	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	3249	EGF-like 8.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.183333	20.492075	26.139867	11	49	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Silent	SNP	102917441	102917441	13689	7	G	A	A	38	38	RELN	A	1	1
RIMS2	9699	broad.mit.edu	36	8	105333212	105333212	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105333212C>A	uc003yls.2	+	c.4092C>A	c.(4090-4092)TAC>TAA	p.Y1364*	RIMS2_uc003ylp.2_Nonsense_Mutation_p.Y1346*|RIMS2_uc003ylq.2_Nonsense_Mutation_p.Y1160*|RIMS2_uc003ylr.2_Nonsense_Mutation_p.Y1185*	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1408					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14										728				0.338889	160.610822	164.746164	61	119	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		Nonsense_Mutation	SNP	105333212	105333212	13845	8	C	A	A	20	20	RIMS2	A	5	3
ADAM7	8756	broad.mit.edu	36	8	24420901	24420902	+	Missense_Mutation	DNP	TC	AA	AA			TCGA-06-0124-01	TCGA-06-0124-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:24420901_24420902TC>AA	uc003xeb.1	+	c.2227_2228TC>AA	c.(2227-2229)TCA>AAA	p.S743K	ADAM7_uc003xec.2_Intron	NM_003817	NP_003808	Q9H2U9	ADAM7_HUMAN	a disintegrin and metalloproteinase domain 7	743	Cytoplasmic (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			kidney(1)	1		Prostate(55;0.0181)												0.333333	109.821106	112.914265	42	84	TT		KEEP	---	---	---	---	capture		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)	Missense_Mutation	DNP	24420901	24420902	252	8	TC	AA	AA	62	62	ADAM7	AA	4	4
DOCK5	80005	broad.mit.edu	36	8	25214089	25214089	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25214089C>G	uc003xeg.1	+	c.845C>G	c.(844-846)ACA>AGA	p.T282R	DOCK5_uc003xef.2_Missense_Mutation_p.T282R|DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Intron	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	282						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.176471	6.514209	8.191327	3	14	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Missense_Mutation	SNP	25214089	25214089	4874	8	C	G	G	17	17	DOCK5	G	3	3
EBF2	64641	broad.mit.edu	36	8	25771907	25771907	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25771907G>A	uc003xes.1	-	c.1373C>T	c.(1372-1374)CCG>CTG	p.P458L	PPP2R2A_uc003xek.1_Intron|EBF2_uc010lug.1_Non-coding_Transcript	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	458	Pro/Ser/Thr-rich.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|transcription regulator activity			ovary(3)	3		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)				Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)								0.326733	92.942907	95.63116	33	68	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)	Missense_Mutation	SNP	25771907	25771907	5067	8	G	A	A	39	39	EBF2	A	1	1
TRPA1	8989	broad.mit.edu	36	8	73111205	73111205	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:73111205C>A	uc003xza.1	-	c.2427G>T	c.(2425-2427)TGG>TGT	p.W809C		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	809	Helical; Name=3; (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6					Menthol(DB00825)									0.307692	59.574305	62.14408	24	54	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.223)		Missense_Mutation	SNP	73111205	73111205	17128	8	C	A	A	30	30	TRPA1	A	3	3
DAB2IP	153090	broad.mit.edu	36	9	123575078	123575078	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:123575078C>T	uc004bln.1	+	c.2366C>T	c.(2365-2367)CCA>CTA	p.P789L	DAB2IP_uc004blo.1_Missense_Mutation_p.P693L|DAB2IP_uc004blp.1_Missense_Mutation_p.P222L	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	817					activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of Ras protein signal transduction|positive regulation of apoptosis|positive regulation of gene-specific transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2														0.2625	49.035435	53.121177	21	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123575078	123575078	4385	9	C	T	T	21	21	DAB2IP	T	2	2
ABCA2	20	broad.mit.edu	36	9	139028201	139028201	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0124-01	TCGA-06-0124-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139028201C>G	uc004ckm.1	-	c.4441G>C	c.(4441-4443)GCC>CCC	p.A1481P	ABCA2_uc010nby.1_Missense_Mutation_p.A1381P|ABCA2_uc010nbz.1_Missense_Mutation_p.A1451P|ABCA2_uc004ckl.1_Missense_Mutation_p.A1381P|ABCA2_uc004ckn.1_Non-coding_Transcript	NM_212533	NP_997698	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	1450					cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|lysosomal membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)												0.3	7.334623	8.122965	6	14	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)	Missense_Mutation	SNP	139028201	139028201	33	9	C	G	G	27	27	ABCA2	G	3	3
SMARCA2	6595	broad.mit.edu	36	9	2029586	2029586	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:2029586G>A	uc003zhc.1	+	c.476G>A	c.(475-477)GGT>GAT	p.G159D	SMARCA2_uc003zhd.1_Missense_Mutation_p.G159D|SMARCA2_uc010mha.1_Missense_Mutation_p.G150D	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	159					chromatin remodeling|negative regulation of gene-specific transcription from RNA polymerase II promoter|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein binding|transcription activator activity|transcription coactivator activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)												0.358491	100.574101	102.420055	38	68	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;0.0475)	Missense_Mutation	SNP	2029586	2029586	15267	9	G	A	A	44	44	SMARCA2	A	2	2
AQP3	360	broad.mit.edu	36	9	33437465	33437465	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0124-01	TCGA-06-0124-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:33437465G>C	uc003zsx.1	-	c.64C>G	c.(64-66)CTC>GTC	p.L22V	SUGT1P1_uc010mjq.1_Intron|AQP3_uc003zsv.1_Missense_Mutation_p.L22V|AQP3_uc010mju.1_Missense_Mutation_p.L22V	NM_004925	NP_004916	Q92482	AQP3_HUMAN	aquaporin 3	22	Cytoplasmic (Potential).				excretion|odontogenesis|positive regulation of immune system process|regulation of keratinocyte differentiation|response to calcium ion|response to retinoic acid|response to vitamin D	basolateral plasma membrane|cell-cell junction|cytoplasm|integral to membrane	glycerol channel activity|water channel activity				0														0.4	7.37967	7.471734	4	6	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)	Missense_Mutation	SNP	33437465	33437465	838	9	G	C	C	34	34	AQP3	C	3	3
