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
ANXA8	653145	broad.mit.edu	36	10	46578875	46578875	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:46578875C>T	uc001jeh.1	-	c.952G>A	c.(952-954)GCC>ACC	p.A318T	ANXA8_uc001jed.2_Intron|ANXA8_uc009xnc.1_Missense_Mutation_p.A333T	NM_001098845	NP_001092315	P13928	ANXA8_HUMAN	annexin A8-like 1	318	Annexin 4.				blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3														0.55	32.826787	32.870561	11	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46578875	46578875	732	10	C	T	T	27	27	ANXA8	T	1	1
ANO5	203859	broad.mit.edu	36	11	22248460	22248460	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22248460G>A	uc001mqi.1	+	c.1925G>A	c.(1924-1926)CGA>CAA	p.R642Q	ANO5_uc001mqj.1_Missense_Mutation_p.R641Q	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	642	Extracellular (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.12963	30.167614	51.793896	21	141	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22248460	22248460	708	11	G	A	A	37	37	ANO5	A	1	1
GDPD4	220032	broad.mit.edu	36	11	76633986	76633986	+	Silent	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:76633986G>A	uc001oyf.1	-	c.1074C>T	c.(1072-1074)ATC>ATT	p.I358I		NM_182833	NP_878253	Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain	358	GDPD.|Extracellular (Potential).				glycerol metabolic process|lipid metabolic process	integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding				0														0.314607	156.927053	162.375621	56	122	GG		KEEP	---	---	---	---	capture			Silent	SNP	76633986	76633986	6594	11	G	A	A	37	37	GDPD4	A	1	1
GRM5	2915	broad.mit.edu	36	11	87977719	87977719	+	Silent	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:87977719G>A	uc001pcq.1	-	c.1209C>T	c.(1207-1209)GCC>GCT	p.A403A	GRM5_uc001pcp.1_Silent_p.A403A|GRM5_uc009yvm.1_Silent_p.A403A	NM_000842	NP_000833	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform b	403	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(1)	5		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)									0.475904	244.403944	244.488437	79	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	87977719	87977719	7079	11	G	A	A	47	47	GRM5	A	2	2
NAALAD2	10003	broad.mit.edu	36	11	89541800	89541800	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:89541800C>G	uc001pdf.2	+	c.1334C>G	c.(1333-1335)TCT>TGT	p.S445C	NAALAD2_uc009yvx.1_Missense_Mutation_p.S412C|NAALAD2_uc009yvy.1_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	445	Extracellular (Potential).|NAALADase.				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.417582	131.435745	131.975207	38	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89541800	89541800	10523	11	C	G	G	32	32	NAALAD2	G	3	3
APOF	319	broad.mit.edu	36	12	55042019	55042019	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55042019C>G	uc001sle.1	-	c.238G>C	c.(238-240)GCC>CCC	p.A80P	STAT2_uc001slc.1_5'Flank	NM_001638	NP_001629	Q13790	APOF_HUMAN	apolipoprotein F precursor	80					cholesterol metabolic process	high-density lipoprotein particle|low-density lipoprotein particle	cholesterol binding|lipid transporter activity|receptor binding				0														0.459627	256.881107	257.114342	74	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55042019	55042019	814	12	C	G	G	26	26	APOF	G	3	3
MDM1	56890	broad.mit.edu	36	12	67003123	67003123	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:67003123C>T	uc001stz.2	-	c.798G>A	c.(796-798)AGG>AGA	p.R266R	MDM1_uc009zqv.1_5'UTR	NM_017440	NP_059136	Q8TC05	MDM1_HUMAN	mouse Mdm1 nuclear protein homolog isoform 1	266						nucleus				ovary(3)	3														0.324786	109.5072	112.695897	38	79	CC		KEEP	---	---	---	---	capture	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)	Silent	SNP	67003123	67003123	9801	12	C	T	T	30	30	MDM1	T	2	2
RALGAPA1	253959	broad.mit.edu	36	14	35281514	35281514	+	Silent	SNP	T	C	C			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:35281514T>C	uc001wtj.1	-	c.1260A>G	c.(1258-1260)TTA>TTG	p.L420L	RALGAPA1_uc001wti.1_Silent_p.L420L|RALGAPA1_uc001wtk.1_Silent_p.L271L	NM_194301	NP_919277	Q6GYQ0	RGPA1_HUMAN	GTPase activating Rap/RanGAP domain-like 1	420					activation of Ral GTPase activity|signal transduction	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4														0.357895	116.6306	118.317232	34	61	TT		KEEP	---	---	---	---	capture			Silent	SNP	35281514	35281514	13473	14	T	C	C	49	49	RALGAPA1	C	4	4
RFX7	64864	broad.mit.edu	36	15	54222310	54222310	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:54222310G>A	uc010bfn.1	-	c.359C>T	c.(358-360)CCG>CTG	p.P120L		NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	23	RFX-type winged-helix.				regulation of transcription, DNA-dependent	nucleus	DNA binding				0														0.377049	71.412567	72.220979	23	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54222310	54222310	13740	15	G	A	A	39	39	RFX7	A	1	1
TPSD1	23430	broad.mit.edu	36	16	1247051	1247051	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1247051C>T	uc002clb.1	+	c.507C>T	c.(505-507)GAC>GAT	p.D169D	TPSD1_uc010brm.1_Silent_p.D98D	NM_012217	NP_036349	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	169	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)												0.1875	6.521971	7.980108	3	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	1247051	1247051	16969	16	C	T	T	19	19	TPSD1	T	1	1
CORO7	79585	broad.mit.edu	36	16	4331506	4331506	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:4331506G>C	uc002cwf.1	-	c.2858C>G	c.(2857-2859)GCC>GGC	p.A953G	PAM16_uc002cwd.1_Missense_Mutation_p.A30G|CORO7_uc002cwe.1_Non-coding_Transcript	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7	469						cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0														0.217391	13.265428	14.957076	5	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4331506	4331506	3897	16	G	C	C	42	42	CORO7	C	3	3
WDR90	197335	broad.mit.edu	36	16	643569	643569	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:643569C>T	uc002cii.1	+	c.1277C>T	c.(1276-1278)TCG>TTG	p.S426L	WDR90_uc002cij.1_Non-coding_Transcript|WDR90_uc002cig.1_Missense_Mutation_p.S426L|WDR90_uc002cih.1_Missense_Mutation_p.S427L|WDR90_uc002cik.1_5'Flank	NM_145294	NP_660337	Q96KV7	WDR90_HUMAN	WD repeat domain 90	426	WD 1.									ovary(1)	1		Hepatocellular(780;0.0218)												0.356757	186.103944	189.444782	66	119	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	643569	643569	17911	16	C	T	T	31	31	WDR90	T	1	1
LGALS9B	284194	broad.mit.edu	36	17	20304345	20304345	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:20304345C>T	uc002gxa.1	-	c.43G>A	c.(43-45)GTC>ATC	p.V15I	LGALS9B_uc002gwz.1_Missense_Mutation_p.V15I	NM_001042685	NP_001036150	Q3B8N2	LEG9B_HUMAN	galectin-9 like	15							sugar binding				0														0.386076	176.953341	178.744849	61	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20304345	20304345	9075	17	C	T	T	19	19	LGALS9B	T	1	1
UNC45B	146862	broad.mit.edu	36	17	30521298	30521298	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30521298G>A	uc002hja.1	+	c.1600G>A	c.(1600-1602)GGC>AGC	p.G534S	UNC45B_uc002hjb.1_Missense_Mutation_p.G534S|UNC45B_uc002hjc.1_Missense_Mutation_p.G534S|UNC45B_uc010cto.1_Intron	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	534					cell differentiation|muscle organ development		binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)												0.333333	149.264349	152.923384	50	100	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30521298	30521298	17547	17	G	A	A	43	43	UNC45B	A	2	2
SLC25A11	8402	broad.mit.edu	36	17	4782995	4782995	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:4782995C>T	uc002fzo.1	-	c.269G>A	c.(268-270)CGT>CAT	p.R90H	SLC25A11_uc002fzp.1_Missense_Mutation_p.R86H|RNF167_uc002fzq.1_5'Flank|RNF167_uc002fzr.1_5'Flank|RNF167_uc002fzs.1_5'Flank|RNF167_uc002fzt.1_5'Flank|RNF167_uc002fzu.1_5'Flank|RNF167_uc002fzv.1_5'Flank|RNF167_uc002fzw.1_5'Flank|RNF167_uc002fzx.1_5'Flank	NM_003562	NP_003553	Q02978	M2OM_HUMAN	solute carrier family 25 (mitochondrial carrier;	90	Helical; Name=2; (Potential).|Solcar 1.				gluconeogenesis	integral to plasma membrane|mitochondrial inner membrane	oxoglutarate:malate antiporter activity				0						Esophageal Squamous(144;1178 2388 18010 48797)								0.391667	127.21799	128.443869	47	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4782995	4782995	14970	17	C	T	T	19	19	SLC25A11	T	1	1
TMEM102	284114	broad.mit.edu	36	17	7280937	7280937	+	Silent	SNP	T	A	A			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7280937T>A	uc002ggx.1	+	c.915T>A	c.(913-915)GCT>GCA	p.A305A	TMEM102_uc002ggy.1_Silent_p.A305A|FGF11_uc010cmh.1_5'Flank|FGF11_uc010cmi.1_5'Flank|FGF11_uc002ggz.1_5'Flank	NM_178518	NP_848613	Q8N9M5	TM102_HUMAN	transmembrane protein 102	305					regulation of apoptosis|response to cytokine stimulus|signal transduction	cell surface|integral to membrane|intracellular	protein binding				0		Prostate(122;0.173)												0.357143	81.231084	82.738783	30	54	TT		KEEP	---	---	---	---	capture			Silent	SNP	7280937	7280937	16547	17	T	A	A	53	53	TMEM102	A	4	4
TMC6	11322	broad.mit.edu	36	17	73631671	73631671	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0158-01	TCGA-06-0158-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:73631671A>C	uc002juj.1	-	c.1076T>G	c.(1075-1077)GTG>GGG	p.V359G	TMC6_uc002jui.1_5'Flank|TMC6_uc010dhf.1_Missense_Mutation_p.V192G|TMC6_uc002juk.2_Missense_Mutation_p.V359G|TMC6_uc010dhg.1_Missense_Mutation_p.V359G|TMC6_uc002jul.1_Missense_Mutation_p.V359G|TMC6_uc002jum.2_Missense_Mutation_p.V150G|TMC6_uc002jun.2_Missense_Mutation_p.V359G|TMC6_uc002juo.2_Missense_Mutation_p.V132G	NM_007267	NP_009198	Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	359	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane					0														0.403846	143.93411	144.773515	42	62	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)		Missense_Mutation	SNP	73631671	73631671	16519	17	A	C	C	6	6	TMC6	C	4	4
CANT1	124583	broad.mit.edu	36	17	74501239	74501239	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:74501239G>C	uc002jwj.1	-	c.1194C>G	c.(1192-1194)ATC>ATG	p.I398M	CANT1_uc002jwk.1_Missense_Mutation_p.I398M|CANT1_uc002jwl.1_Intron|CANT1_uc002jwm.1_Non-coding_Transcript|CANT1_uc002jwn.1_Missense_Mutation_p.I398M	NM_138793	NP_620148	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	398	Lumenal (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to membrane	calcium ion binding|nucleoside-diphosphatase activity|signal transducer activity				0												OREG0024788	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.387755	130.447399	131.522359	38	60	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)		Missense_Mutation	SNP	74501239	74501239	2734	17	G	C	C	37	37	CANT1	C	3	3
RPTOR	57521	broad.mit.edu	36	17	76411595	76411595	+	Silent	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:76411595G>A	uc002jyt.1	+	c.1113G>A	c.(1111-1113)CCG>CCA	p.P371P	RPTOR_uc002jys.2_Silent_p.P371P	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor	371					cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)	5										1368				0.373444	246.691559	250.07964	90	151	GG		KEEP	---	---	---	---	capture			Silent	SNP	76411595	76411595	14145	17	G	A	A	38	38	RPTOR	A	1	1
KRBA2	124751	broad.mit.edu	36	17	8215427	8215427	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:8215427T>G	uc002glf.1	-	c.151A>C	c.(151-153)AAT>CAT	p.N51H	KRBA2_uc002glg.1_Intron	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	51	KRAB.				DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0														0.165289	91.151716	116.873377	40	202	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8215427	8215427	8755	17	T	G	G	62	62	KRBA2	G	4	4
RTTN	25914	broad.mit.edu	36	18	65869670	65869670	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:65869670C>T	uc002lkp.1	-	c.5280G>A	c.(5278-5280)CCG>CCA	p.P1760P	RTTN_uc002lko.1_Non-coding_Transcript|RTTN_uc010dqp.1_Silent_p.P12P	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1760							binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Esophageal squamous(42;0.129)												0.275556	164.561848	174.762009	62	163	CC		KEEP	---	---	---	---	capture			Silent	SNP	65869670	65869670	14217	18	C	T	T	19	19	RTTN	T	1	1
RGL3	57139	broad.mit.edu	36	19	11387629	11387629	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11387629C>T	uc002mrp.1	-	c.621G>A	c.(619-621)CCG>CCA	p.P207P	RGL3_uc002mrm.1_5'UTR|RGL3_uc002mrn.1_5'UTR	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation	207					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1						GBM(174;751 2067 17998 27979 33959)				120				0.224913	293.046296	333.241158	130	448	CC		KEEP	---	---	---	---	capture			Silent	SNP	11387629	11387629	13751	19	C	T	T	27	27	RGL3	T	1	1
ZNF91	7644	broad.mit.edu	36	19	23336878	23336878	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:23336878T>C	uc002nre.1	-	c.743A>G	c.(742-744)AAG>AGG	p.K248R		NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	248	C2H2-type 4.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)												0.139194	82.459774	116.795487	38	235	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23336878	23336878	18804	19	T	C	C	56	56	ZNF91	C	4	4
ODF3L2	284451	broad.mit.edu	36	19	414966	414966	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:414966C>T	uc002lor.1	-	c.748G>A	c.(748-750)GTG>ATG	p.V250M	SHC2_uc002loq.2_5'Flank|ODF3L2_uc010drp.1_Missense_Mutation_p.V214M	NM_182577	NP_872383	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	250	DUF1309 3.										0														0.26087	45.122368	48.691661	18	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	414966	414966	11237	19	C	T	T	19	19	ODF3L2	T	1	1
HIPK4	147746	broad.mit.edu	36	19	45578622	45578622	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45578622C>T	uc002onp.1	-	c.1116G>A	c.(1114-1116)TCG>TCA	p.S372S		NM_144685	NP_653286	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	372					protein phosphorylation	cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)	1										108				0.202381	104.877627	125.626309	51	201	CC		KEEP	---	---	---	---	capture	Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)		Silent	SNP	45578622	45578622	7404	19	C	T	T	27	27	HIPK4	T	1	1
NLRP11	204801	broad.mit.edu	36	19	61012601	61012601	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61012601C>T	uc002qma.1	-	c.1187G>A	c.(1186-1188)CGT>CAT	p.R396H	NLRP11_uc002qlz.1_Missense_Mutation_p.R297H|NLRP11_uc002qmb.1_Missense_Mutation_p.R297H|NLRP11_uc002qmc.1_Non-coding_Transcript|NLRP11_uc010ete.1_Non-coding_Transcript	NM_145007	NP_659444	P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	396	NACHT.						ATP binding			ovary(3)|central_nervous_system(1)	4		Colorectal(82;0.0002)												0.27459	166.710304	177.884593	67	177	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0325)	Missense_Mutation	SNP	61012601	61012601	10876	19	C	T	T	19	19	NLRP11	T	1	1
TDRD10	126668	broad.mit.edu	36	1	152783561	152783561	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152783561C>T	uc009wow.1	+	c.741C>T	c.(739-741)CGC>CGT	p.R247R	TDRD10_uc001ffd.1_Silent_p.R247R|TDRD10_uc001ffe.1_Silent_p.R168R	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a	247	Tudor.						nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)													0.413793	35.89501	36.083132	12	17	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.185)		Silent	SNP	152783561	152783561	16257	1	C	T	T	27	27	TDRD10	T	1	1
LY9	4063	broad.mit.edu	36	1	159050951	159050951	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159050951T>G	uc001fwu.1	+	c.848T>G	c.(847-849)TTG>TGG	p.L283W	LY9_uc001fwv.1_Missense_Mutation_p.L283W|LY9_uc001fww.1_Missense_Mutation_p.L283W|LY9_uc001fwx.1_Missense_Mutation_p.L283W|LY9_uc001fwy.1_Missense_Mutation_p.L185W|LY9_uc001fwz.1_5'UTR	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	283	Extracellular (Potential).|Ig-like V-type 2.				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)													0.422078	218.451666	219.26696	65	89	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00737)		Missense_Mutation	SNP	159050951	159050951	9478	1	T	G	G	63	63	LY9	G	4	4
CR2	1380	broad.mit.edu	36	1	205713838	205713838	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205713838C>T	uc001hfv.1	+	c.2225C>T	c.(2224-2226)ACG>ATG	p.T742M	CR2_uc001hfw.1_Missense_Mutation_p.T683M|CR2_uc009xch.1_Missense_Mutation_p.T683M	NM_001006658	NP_001006659	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	814	Sushi 13.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(1)|urinary_tract(1)|ovary(1)	3														0.385057	194.088862	196.102174	67	107	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205713838	205713838	3981	1	C	T	T	19	19	CR2	T	1	1
ACBD3	64746	broad.mit.edu	36	1	224413633	224413633	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:224413633G>C	uc001hpy.1	-	c.778C>G	c.(778-780)CAG>GAG	p.Q260E		NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3	260	Gln-rich.				steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)													0.333333	153.307017	156.993631	50	100	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.121)	Missense_Mutation	SNP	224413633	224413633	124	1	G	C	C	46	46	ACBD3	C	3	3
OR13G1	441933	broad.mit.edu	36	1	245902752	245902752	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245902752G>T	uc001idi.1	-	c.215C>A	c.(214-216)ACA>AAA	p.T72K		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	72	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)													0.37037	88.931325	90.126435	30	51	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.017)		Missense_Mutation	SNP	245902752	245902752	11348	1	G	T	T	48	48	OR13G1	T	3	3
OR2L8	391190	broad.mit.edu	36	1	246179288	246179288	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246179288G>A	uc001idt.1	+	c.506G>A	c.(505-507)CGA>CAA	p.R169Q	OR2L13_uc001ids.1_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	169	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.265537	121.247683	130.03881	47	130	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0152)		Missense_Mutation	SNP	246179288	246179288	11415	1	G	A	A	37	37	OR2L8	A	1	1
SEMG1	6406	broad.mit.edu	36	20	43269704	43269704	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0158-01	TCGA-06-0158-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43269704A>G	uc002xni.1	+	c.352A>G	c.(352-354)AAA>GAA	p.K118E	SEMG1_uc002xnh.1_Missense_Mutation_p.K118E|SEMG1_uc002xnj.1_Missense_Mutation_p.K118E|SEMG2_uc010ggz.1_Intron	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I isoform a preproprotein	118					insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity				0		Myeloproliferative disorder(115;0.0122)												0.268657	171.168732	180.871858	54	147	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43269704	43269704	14530	20	A	G	G	13	13	SEMG1	G	4	4
MC3R	4159	broad.mit.edu	36	20	54257736	54257736	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:54257736G>A	uc002xxb.2	+	c.541G>A	c.(541-543)GTC>ATC	p.V181I		NM_019888	NP_063941	P41968	MC3R_HUMAN	melanocortin 3 receptor	181	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)	2														0.267857	185.505549	199.127144	75	205	GG		KEEP	---	---	---	---	capture	Colorectal(105;0.202)		Missense_Mutation	SNP	54257736	54257736	9754	20	G	A	A	40	40	MC3R	A	1	1
C20orf135	140701	broad.mit.edu	36	20	61964076	61964076	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61964076T>G	uc002ygx.1	+	c.739T>G	c.(739-741)TCT>GCT	p.S247A	TPD52L2_uc002ygy.1_5'Flank|TPD52L2_uc002ygz.1_5'Flank|TPD52L2_uc002yha.1_5'Flank|TPD52L2_uc002yhb.1_5'Flank|TPD52L2_uc002yhc.1_5'Flank|TPD52L2_uc002yhd.1_5'Flank	NM_080622	NP_542189	Q9H3Z7	ABHGB_HUMAN	hypothetical protein LOC140701	247		Charge relay system (By similarity).					hydrolase activity				0	all_cancers(38;1.77e-12)|all_epithelial(29;3.12e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)													0.2	6.405208	8.070418	4	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61964076	61964076	2165	20	T	G	G	58	58	C20orf135	G	4	4
ITGB2	3689	broad.mit.edu	36	21	45144662	45144662	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45144662C>T	uc002zgd.1	-	c.897_splice	c.e6+1	p.F299_splice	ITGB2_uc002zge.1_Splice_Site_SNP_p.F299_splice|ITGB2_uc002zgf.2_Splice_Site_SNP_p.F299_splice|ITGB2_uc010gpw.1_Splice_Site_SNP_p.F242_splice|ITGB2_uc002zgg.1_Splice_Site_SNP_p.F299_splice	NM_001127491	NP_001120963			integrin, beta 2 precursor						apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity	p.?(1)		ovary(3)|central_nervous_system(3)|breast(2)	8					Simvastatin(DB00641)									0.345455	103.10106	105.428088	38	72	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0669)	Splice_Site_SNP	SNP	45144662	45144662	8198	21	C	T	T	19	19	ITGB2	T	5	1
C2orf62	375307	broad.mit.edu	36	2	218930537	218930537	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:218930537C>T	uc002vhr.1	+	c.155C>T	c.(154-156)ACG>ATG	p.T52M	C2orf62_uc002vhs.1_Non-coding_Transcript	NM_198559	NP_940961	Q7Z7H3	CB062_HUMAN	hypothetical protein LOC375307	52											0		Renal(207;0.0915)												0.396552	67.31441	67.856961	23	35	CC		KEEP	---	---	---	---	capture		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	218930537	218930537	2269	2	C	T	T	19	19	C2orf62	T	1	1
TSPYL6	388951	broad.mit.edu	36	2	54336649	54336649	+	Silent	SNP	C	G	G			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:54336649C>G	uc002rxr.2	-	c.144G>C	c.(142-144)GTG>GTC	p.V48V	ACYP2_uc002rxq.2_Intron	NM_001003937	NP_001003937	Q8N831	TSYL6_HUMAN	TSPY-like 6	48					nucleosome assembly	nucleus					0														0.367876	230.480549	233.439898	71	122	CC		KEEP	---	---	---	---	capture			Silent	SNP	54336649	54336649	17216	2	C	G	G	17	17	TSPYL6	G	3	3
COL6A6	131873	broad.mit.edu	36	3	131766846	131766846	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:131766846G>A	uc010htl.1	+	c.980G>A	c.(979-981)CGG>CAG	p.R327Q		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6	327	Nonhelical region.|VWFA 2.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.099042	19.936142	70.227293	31	282	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131766846	131766846	3841	3	G	A	A	39	39	COL6A6	A	1	1
KCNH8	131096	broad.mit.edu	36	3	19550125	19550125	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0158-01	TCGA-06-0158-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:19550125A>T	uc003cbk.1	+	c.2854A>T	c.(2854-2856)AGT>TGT	p.S952C	KCNH8_uc010hex.1_Missense_Mutation_p.S413C	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	952	Ser-rich.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity			ovary(1)	1						NSCLC(124;1625 1765 8018 24930 42026)								0.390374	223.940715	225.906543	73	114	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19550125	19550125	8343	3	A	T	T	7	7	KCNH8	T	4	4
CCR8	1237	broad.mit.edu	36	3	39349307	39349307	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:39349307G>A	uc003cjn.1	+	c.481G>A	c.(481-483)GCC>ACC	p.A161T	CCR8_uc003cjm.1_Missense_Mutation_p.A78T|CCR8_uc010hhr.1_Missense_Mutation_p.A161T	NM_005201	NP_005192	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	161	Helical; Name=4; (Potential).				cell adhesion|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane	coreceptor activity			ovary(1)	1														0.454286	460.486526	461.105419	159	191	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)	Missense_Mutation	SNP	39349307	39349307	3074	3	G	A	A	38	38	CCR8	A	1	1
AMBN	258	broad.mit.edu	36	4	71501848	71501848	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0158-01	TCGA-06-0158-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71501848T>A	uc003hfl.1	+	c.419T>A	c.(418-420)CTG>CAG	p.L140Q		NM_016519	NP_057603	Q9NP70	AMBN_HUMAN	ameloblastin precursor	140					bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)	3												OREG0016218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.411576	403.571816	405.687198	128	183	TT		KEEP	---	---	---	---	capture	Lung(101;0.235)		Missense_Mutation	SNP	71501848	71501848	566	4	T	A	A	55	55	AMBN	A	4	4
PCDHGA10	56106	broad.mit.edu	36	5	140774691	140774691	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140774691G>A	uc003lkl.1	+	c.1765G>A	c.(1765-1767)GGC>AGC	p.G589S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkk.1_Missense_Mutation_p.G589S|PCDHGB7_uc003lkm.1_5'Flank|PCDHGB7_uc003lkn.1_5'Flank	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1	589	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.345238	250.767779	256.088641	87	165	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140774691	140774691	11971	5	G	A	A	39	39	PCDHGA10	A	1	1
EDIL3	10085	broad.mit.edu	36	5	83468927	83468927	+	Silent	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:83468927G>A	uc003kio.1	-	c.357C>T	c.(355-357)AAC>AAT	p.N119N	EDIL3_uc003kip.1_Silent_p.N109N	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	119	EGF-like 3.				cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)												0.35122	200.832468	204.837944	72	133	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)	Silent	SNP	83468927	83468927	5102	5	G	A	A	48	48	EDIL3	A	2	2
TRIM38	10475	broad.mit.edu	36	6	26074943	26074943	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:26074943C>T	uc003nfm.1	+	c.214C>T	c.(214-216)CGA>TGA	p.R72*	TRIM38_uc003nfn.1_Nonsense_Mutation_p.R72*	NM_006355	NP_006346	O00635	TRI38_HUMAN	tripartite motif-containing 38	72					positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular	signal transducer activity|zinc ion binding				0														0.316832	86.970687	89.980285	32	69	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	26074943	26074943	17056	6	C	T	T	23	23	TRIM38	T	5	1
HLA-F	3134	broad.mit.edu	36	6	29802655	29802655	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29802655C>T	uc003nno.2	+	c.1053C>T	c.(1051-1053)AGC>AGT	p.S351S	LOC285830_uc003nnp.1_Non-coding_Transcript	NM_001098479	NP_001091949	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	Error:Variant_position_missing_in_P30511_after_alignment					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0														0.161826	67.712433	93.896946	39	202	CC		KEEP	---	---	---	---	capture			Silent	SNP	29802655	29802655	7502	6	C	T	T	27	27	HLA-F	T	1	1
CRISP3	10321	broad.mit.edu	36	6	49812177	49812177	+	Silent	SNP	A	G	G			TCGA-06-0158-01	TCGA-06-0158-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:49812177A>G	uc003ozs.1	-	c.75T>C	c.(73-75)GAT>GAC	p.D25D	CRISP3_uc003ozt.2_Silent_p.D25D	NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	25					innate immune response	proteinaceous extracellular matrix|specific granule				skin(1)	1	Lung NSC(77;0.0161)													0.386628	448.711397	452.613329	133	211	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)		Silent	SNP	49812177	49812177	4020	6	A	G	G	12	12	CRISP3	G	4	4
ASB15	142685	broad.mit.edu	36	7	123064100	123064100	+	Silent	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:123064100G>A	uc003vku.1	+	c.1596G>A	c.(1594-1596)GAG>GAA	p.E532E	ASB15_uc003vkw.1_Silent_p.E532E	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box-containing 15	532	SOCS box.				intracellular signal transduction					lung(1)	1														0.388571	214.192863	216.085237	68	107	GG		KEEP	---	---	---	---	capture			Silent	SNP	123064100	123064100	1037	7	G	A	A	33	33	ASB15	A	2	2
NUP205	23165	broad.mit.edu	36	7	134951285	134951285	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:134951285G>A	uc003vsw.1	+	c.3392G>A	c.(3391-3393)CGT>CAT	p.R1131H		NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1131					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6														0.369427	166.207024	168.560109	58	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134951285	134951285	11164	7	G	A	A	40	40	NUP205	A	1	1
POM121L12	285877	broad.mit.edu	36	7	53070885	53070885	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:53070885C>T	uc003tpz.1	+	c.27C>T	c.(25-27)TCC>TCT	p.S9S		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	hypothetical protein LOC285877	9											0														0.277778	27.734611	29.334094	10	26	CC		KEEP	---	---	---	---	capture			Silent	SNP	53070885	53070885	12669	7	C	T	T	23	23	POM121L12	T	1	1
PCLO	27445	broad.mit.edu	36	7	82602840	82602840	+	Silent	SNP	C	T	T			TCGA-06-0158-01	TCGA-06-0158-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82602840C>T	uc003uhx.2	-	c.1962G>A	c.(1960-1962)CCG>CCA	p.P654P	PCLO_uc003uhv.2_Silent_p.P654P	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	600	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.440476	108.86372	109.122525	37	47	CC		KEEP	---	---	---	---	capture			Silent	SNP	82602840	82602840	12003	7	C	T	T	19	19	PCLO	T	1	1
TRPA1	8989	broad.mit.edu	36	8	73111194	73111194	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:73111194G>A	uc003xza.1	-	c.2438C>T	c.(2437-2439)ACG>ATG	p.T813M		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	813	Helical; Name=3; (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6					Menthol(DB00825)									0.333333	110.759793	113.711971	40	80	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.223)		Missense_Mutation	SNP	73111194	73111194	17128	8	G	A	A	40	40	TRPA1	A	1	1
C9orf171	389799	broad.mit.edu	36	9	134364693	134364693	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0158-01	TCGA-06-0158-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134364693G>C	uc004cbn.1	+	c.517G>C	c.(517-519)GAG>CAG	p.E173Q	C9orf171_uc004cbo.1_Missense_Mutation_p.E137Q	NM_207417	NP_997300	Q6ZQR2	CI171_HUMAN	hypothetical protein LOC389799	173										ovary(4)|large_intestine(1)	5														0.393939	255.155439	257.088556	78	120	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134364693	134364693	2585	9	G	C	C	41	41	C9orf171	C	3	3
FAM46D	169966	broad.mit.edu	36	X	79585772	79585772	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0158-01	TCGA-06-0158-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:79585772A>T	uc004edl.1	+	c.1078A>T	c.(1078-1080)AGG>TGG	p.R360W	FAM46D_uc004edm.1_Missense_Mutation_p.R360W|FAM46D_uc010nmh.1_Missense_Mutation_p.R360W	NM_152630	NP_689843	Q8NEK8	FA46D_HUMAN	hypothetical protein LOC169966	360										lung(2)	2														0.831169	210.747303	218.754414	64	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79585772	79585772	5789	23	A	T	T	3	3	FAM46D	T	4	4
MST1	4485	broad.mit.edu	36	3	49699145	49699148	+	Frame_Shift_Del	DEL	CTCG	-	-			TCGA-06-0158-01	TCGA-06-0158-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49699145_49699148delCTCG	uc003cxg.1	-	c.778_781delCGAG	c.(778-783)CGAGAGfs	p.R260fs	MST1_uc010hkx.1_Frame_Shift_Del_p.R195fs|RNF123_uc003cxh.1_5'Flank	NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth	260_261	Kringle 2.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GBM(110;181 1524 8005 22865 46297)								0.37			10	17				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	49699145	49699148	10283	3	CTCG	-	-	32	32	MST1	-	5	5
