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
PLXDC2	84898	broad.mit.edu	36	10	20506318	20506318	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:20506318C>G	uc001iqg.1	+	c.1035C>G	c.(1033-1035)AAC>AAG	p.N345K	PLXDC2_uc001iqh.1_Missense_Mutation_p.N296K|PLXDC2_uc009xkc.1_Non-coding_Transcript	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor	345	Extracellular (Potential).|PSI.					integral to membrane				ovary(2)|central_nervous_system(1)	3														0.337143	189.06634	193.174028	59	116	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20506318	20506318	12544	10	C	G	G	20	20	PLXDC2	G	3	3
ANK3	288	broad.mit.edu	36	10	61691713	61691713	+	Silent	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:61691713G>A	uc001jky.1	-	c.708C>T	c.(706-708)TTC>TTT	p.F236F	ANK3_uc001jkz.2_Silent_p.F230F|ANK3_uc001jlb.1_5'UTR	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	236	ANK 6.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			ovary(6)|pancreas(2)|central_nervous_system(1)|skin(1)	10														0.235294	7.487894	8.582963	4	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	61691713	61691713	625	10	G	A	A	45	45	ANK3	A	2	2
OR4X2	119764	broad.mit.edu	36	11	48223259	48223259	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48223259T>C	uc001ngs.1	+	c.28T>C	c.(28-30)TCT>CCT	p.S10P		NM_001004727	NP_001004727	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X,	10	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.089796	19.860043	61.464757	22	223	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48223259	48223259	11495	11	T	C	C	62	62	OR4X2	C	4	4
LRRC55	219527	broad.mit.edu	36	11	56706734	56706734	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56706734G>A	uc001njl.1	+	c.790_splice	c.e1+1	p.D264_splice		NM_001005210	NP_001005210			leucine rich repeat containing 55							integral to membrane					0														0.10219	8.656707	30.265989	14	123	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	56706734	56706734	9386	11	G	A	A	44	44	LRRC55	A	5	2
APLNR	187	broad.mit.edu	36	11	56760112	56760112	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56760112G>A	uc001njo.1	-	c.943C>T	c.(943-945)CGC>TGC	p.R315C	APLNR_uc001njn.2_Non-coding_Transcript	NM_005161	NP_005152	P35414	APJ_HUMAN	angiotensin II receptor-like 1	315	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0														0.469697	98.956675	99.005355	31	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56760112	56760112	788	11	G	A	A	39	39	APLNR	A	1	1
SMTNL1	219537	broad.mit.edu	36	11	57067227	57067227	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57067227C>T	uc009ymh.1	+	c.590C>T	c.(589-591)ACA>ATA	p.T197I		NM_001105565	NP_001099035	E9PPJ3	E9PPJ3_HUMAN	smoothelin-like 1	179										ovary(1)	1														0.305085	45.644854	47.63512	18	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57067227	57067227	15315	11	C	T	T	17	17	SMTNL1	T	2	2
CD248	57124	broad.mit.edu	36	11	65839340	65839340	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65839340C>T	uc001ohm.1	-	c.1735G>A	c.(1735-1737)GCC>ACC	p.A579T		NM_020404	NP_065137	Q9HCU0	CD248_HUMAN	tumor endothelial marker 1 precursor	579	Pro-rich.|Extracellular (Potential).					integral to membrane|proteinaceous extracellular matrix	calcium ion binding|sugar binding			large_intestine(3)	3					Cefalotin(DB00456)									0.333333	213.088058	218.897756	79	158	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65839340	65839340	3117	11	C	T	T	26	26	CD248	T	2	2
ACACB	32	broad.mit.edu	36	12	108164658	108164658	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:108164658C>G	uc001tob.1	+	c.5056C>G	c.(5056-5058)CCC>GCC	p.P1686A	ACACB_uc001toc.1_Missense_Mutation_p.P1686A|ACACB_uc001tod.1_Non-coding_Transcript	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1686					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|pancreas(1)	6					Biotin(DB00121)					1843				0.257426	150.64901	161.393879	52	150	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108164658	108164658	108	12	C	G	G	26	26	ACACB	G	3	3
KSR2	283455	broad.mit.edu	36	12	116782511	116782511	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:116782511G>A	uc001two.2	-	c.202C>T	c.(202-204)CGA>TGA	p.R68*		NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	97					intracellular signal transduction|protein phosphorylation	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(7)|central_nervous_system(2)|large_intestine(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)								p.R68*(SNU1-Tumor)	623				0.268657	50.222451	53.457356	18	49	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	116782511	116782511	8905	12	G	A	A	39	39	KSR2	A	5	1
BCL7A	605	broad.mit.edu	36	12	120944399	120944399	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120944399C>G	uc001ubo.1	+	c.19C>G	c.(19-21)CGA>GGA	p.R7G	BCL7A_uc001ubp.1_Missense_Mutation_p.R7G	NM_020993	NP_066273	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A isoform a	7					negative regulation of transcription, DNA-dependent					ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)					GBM(17;197 467 16477 23242 44349)				51				0.375	7.321121	7.4315	3	5	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)	Missense_Mutation	SNP	120944399	120944399	1399	12	C	G	G	31	31	BCL7A	G	3	3
BCL7A	605	broad.mit.edu	36	12	120977246	120977246	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120977246C>T	uc001ubo.1	+	c.592C>T	c.(592-594)CAG>TAG	p.Q198*	BCL7A_uc001ubp.1_Intron	NM_020993	NP_066273	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A isoform a	187					negative regulation of transcription, DNA-dependent					ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)					GBM(17;197 467 16477 23242 44349)				51		OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.325843	161.386086	166.177337	58	120	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)	Nonsense_Mutation	SNP	120977246	120977246	1399	12	C	T	T	21	21	BCL7A	T	5	2
GXYLT1	283464	broad.mit.edu	36	12	40824668	40824668	+	Silent	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:40824668G>A	uc001rms.2	-	c.48C>T	c.(46-48)TTC>TTT	p.F16F	GXYLT1_uc001rmt.2_Silent_p.F16F	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3	16	Helical; Signal-anchor for type II membrane protein; (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0														0.375	7.823271	7.932867	3	5	GG		KEEP	---	---	---	---	capture			Silent	SNP	40824668	40824668	7183	12	G	A	A	33	33	GXYLT1	A	2	2
DIP2B	57609	broad.mit.edu	36	12	49408664	49408664	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:49408664C>T	uc001rwv.1	+	c.3577C>T	c.(3577-3579)CGG>TGG	p.R1193W	DIP2B_uc009zlt.1_Missense_Mutation_p.R623W	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B	1193						nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6														0.367925	111.297539	112.922786	39	67	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49408664	49408664	4707	12	C	T	T	31	31	DIP2B	T	1	1
C12orf57	113246	broad.mit.edu	36	12	6925226	6925226	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6925226C>T	uc001qrz.1	+	c.261C>T	c.(259-261)TCC>TCT	p.S87S	C12orf57_uc009zfk.1_Silent_p.S58S|PTPN6_uc001qsa.1_5'Flank	NM_138425	NP_612434	Q99622	C10_HUMAN	C10 protein	87											0														0.28125	25.760805	27.137299	9	23	CC		KEEP	---	---	---	---	capture			Silent	SNP	6925226	6925226	1745	12	C	T	T	24	24	C12orf57	T	2	2
ACSM4	341392	broad.mit.edu	36	12	7361004	7361004	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7361004G>A	uc001qsx.1	+	c.625G>A	c.(625-627)GCC>ACC	p.A209T		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member	209					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0														0.254902	31.852093	34.631091	13	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7361004	7361004	187	12	G	A	A	38	38	ACSM4	A	1	1
RBM25	58517	broad.mit.edu	36	14	72639710	72639710	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:72639710C>T	uc001xno.1	+	c.925C>T	c.(925-927)CGG>TGG	p.R309W	RBM25_uc001xnp.1_Missense_Mutation_p.R104W	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	309	Necessary for nuclear speckle localization.|Glu-rich.|Arg-rich.				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4														0.16	7.085137	9.836353	4	21	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)	Missense_Mutation	SNP	72639710	72639710	13587	14	C	T	T	19	19	RBM25	T	1	1
POTEB	339010	broad.mit.edu	36	15	19318442	19318442	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:19318442T>G	uc001ytu.1	-	c.1164A>C	c.(1162-1164)CAA>CAC	p.Q388H	POTEB_uc010axv.1_Intron	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,	388											0														0.08871	26.489933	90.064021	33	339	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19318442	19318442	12691	15	T	G	G	64	64	POTEB	G	4	4
MKRN3	7681	broad.mit.edu	36	15	21362586	21362586	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:21362586C>T	uc001ywh.2	+	c.564C>T	c.(562-564)GAC>GAT	p.D188D	MKRN3_uc010ayi.1_Silent_p.D188D|MKRN3_uc001ywi.2_Intron	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	188						ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(2)	4		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)								79				0.328767	66.276222	68.173321	24	49	CC		KEEP	---	---	---	---	capture		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)	Silent	SNP	21362586	21362586	9998	15	C	T	T	18	18	MKRN3	T	2	2
GABRA5	2558	broad.mit.edu	36	15	24775973	24775973	+	Silent	SNP	T	A	A			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:24775973T>A	uc001zbd.1	+	c.1236T>A	c.(1234-1236)ACT>ACA	p.T412T	GABRA5_uc001zbe.1_Non-coding_Transcript	NM_000810	NP_000801	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	412	Cytoplasmic (Potential).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)			Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.259259	18.111867	19.529564	7	20	TT		KEEP	---	---	---	---	capture		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Silent	SNP	24775973	24775973	6415	15	T	A	A	56	56	GABRA5	A	4	4
DNAJA4	55466	broad.mit.edu	36	15	76355005	76355005	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:76355005C>G	uc002bdi.1	+	c.757C>G	c.(757-759)CAG>GAG	p.Q253E	DNAJA4_uc002bdj.1_Missense_Mutation_p.Q253E|DNAJA4_uc002bdk.1_Missense_Mutation_p.Q226E|DNAJA4_uc002bdm.1_Missense_Mutation_p.Q37E	NM_018602	NP_061072	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	253					protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding			skin(1)	1														0.308333	121.93005	125.858907	37	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76355005	76355005	4797	15	C	G	G	29	29	DNAJA4	G	3	3
LRRC28	123355	broad.mit.edu	36	15	97719234	97719234	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:97719234T>A	uc002bva.1	+	c.866T>A	c.(865-867)CTG>CAG	p.L289Q	LRRC28_uc002bvb.1_Missense_Mutation_p.L135Q|LRRC28_uc002bvc.1_Missense_Mutation_p.L289Q|LRRC28_uc002bvd.1_Intron	NM_144598	NP_653199	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	289											0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)											OREG0023509	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.350575	186.827562	190.252857	61	113	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(32;0.00106)		Missense_Mutation	SNP	97719234	97719234	9357	15	T	A	A	55	55	LRRC28	A	4	4
PITPNA	5306	broad.mit.edu	36	17	1403167	1403167	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1403167C>T	uc002fst.2	-	c.78G>A	c.(76-78)GTG>GTA	p.V26V	PITPNA_uc010cjt.1_5'UTR|PITPNA_uc010cju.1_5'UTR	NM_006224	NP_006215	Q00169	PIPNA_HUMAN	phosphatidylinositol transfer protein, alpha	26					axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1														0.176	41.465699	53.843638	22	103	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)	Silent	SNP	1403167	1403167	12371	17	C	T	T	21	21	PITPNA	T	2	2
SLC47A1	55244	broad.mit.edu	36	17	19399926	19399926	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19399926G>A	uc002gvx.2	+	c.880G>A	c.(880-882)GCT>ACT	p.A294T	SLC47A1_uc002gvy.1_Missense_Mutation_p.A294T|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Missense_Mutation_p.A99T|SNORA59B_uc002gvz.1_5'Flank	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1	294	Extracellular (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)													0.366197	72.235437	73.351081	26	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19399926	19399926	15144	17	G	A	A	38	38	SLC47A1	A	1	1
KSR1	8844	broad.mit.edu	36	17	22933993	22933993	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:22933993C>T	uc010crg.1	+	c.304C>T	c.(304-306)CCC>TCC	p.P102S	KSR1_uc002gzj.1_Intron	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras	237					protein phosphorylation|Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)					Esophageal Squamous(88;1120 1336 6324 10502 16832)				1488				0.35	39.555388	40.341421	14	26	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)	Missense_Mutation	SNP	22933993	22933993	8904	17	C	T	T	22	22	KSR1	T	2	2
NF1	4763	broad.mit.edu	36	17	26678919	26678919	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26678919G>A	uc002hgg.1	+	c.5545G>A	c.(5545-5547)GAT>AAT	p.D1849N	NF1_uc002hgh.1_Missense_Mutation_p.D1828N|NF1_uc002hgi.1_Missense_Mutation_p.D861N|NF1_uc010cso.1_Missense_Mutation_p.D37N	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1849					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.D1849N(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)			0.273381	105.486271	111.920402	38	101	GG		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)	Missense_Mutation	SNP	26678919	26678919	10756	17	G	A	A	33	33	NF1	A	2	2
CALCOCO2	10241	broad.mit.edu	36	17	44292755	44292755	+	Silent	SNP	A	G	G			TCGA-06-0214-01	TCGA-06-0214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44292755A>G	uc002iof.1	+	c.1089A>G	c.(1087-1089)TCA>TCG	p.S363S		NM_005831	NP_005822	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	363					response to interferon-gamma|viral reproduction	cytoskeleton|Golgi apparatus|nucleus|perinuclear region of cytoplasm|soluble fraction	protein homodimerization activity			ovary(1)	1														0.316514	212.197838	218.724043	69	149	AA		KEEP	---	---	---	---	capture			Silent	SNP	44292755	44292755	2694	17	A	G	G	7	7	CALCOCO2	G	4	4
ACE	1636	broad.mit.edu	36	17	58914224	58914224	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:58914224G>A	uc002jau.1	+	c.1445G>A	c.(1444-1446)CGT>CAT	p.R482H	ACE_uc010ddu.1_Missense_Mutation_p.R299H|ACE_uc002jav.1_5'Flank|ACE_uc010ddv.1_5'Flank|ACE_uc002jaw.1_5'Flank	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme isoform 1	482	Extracellular (Potential).|Peptidase M2 1.				angiotensin catabolic process in blood|arachidonic acid secretion|blood vessel remodeling|hemopoietic stem cell differentiation|hormone catabolic process|kidney development|mononuclear cell proliferation|peptide catabolic process|regulation of renal output by angiotensin|regulation of smooth muscle cell migration|regulation of vasoconstriction|regulation of vasodilation	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)									0.300836	259.19402	271.901178	108	251	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58914224	58914224	137	17	G	A	A	40	40	ACE	A	1	1
SLC38A10	124565	broad.mit.edu	36	17	76834689	76834689	+	Silent	SNP	G	C	C			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:76834689G>C	uc002jzz.1	-	c.2622C>G	c.(2620-2622)CTC>CTG	p.L874L	SLC38A10_uc002jzy.1_Silent_p.L792L	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a	874					amino acid transport|sodium ion transport	integral to membrane				pancreas(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)													0.081301	12.125792	56.029824	20	226	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)		Silent	SNP	76834689	76834689	15099	17	G	C	C	37	37	SLC38A10	C	3	3
HGS	9146	broad.mit.edu	36	17	77271189	77271189	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77271189T>G	uc002kbg.1	+	c.840_splice	c.e10+2	p.L280_splice		NM_004712	NP_004703			hepatocyte growth factor-regulated tyrosine						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	protein domain specific binding|zinc ion binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)													0.714286	7.448719	7.693029	5	2	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Splice_Site_SNP	SNP	77271189	77271189	7371	17	T	G	G	57	57	HGS	G	5	4
CLPTM1	1209	broad.mit.edu	36	19	50186028	50186028	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50186028C>T	uc002pai.1	+	c.1404C>T	c.(1402-1404)ACC>ACT	p.T468T		NM_001294	NP_001285	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane	468	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|regulation of T cell differentiation in thymus	external side of plasma membrane|integral to plasma membrane				ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)								199				0.296296	40.475305	42.48161	16	38	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)	Silent	SNP	50186028	50186028	3692	19	C	T	T	21	21	CLPTM1	T	2	2
ERCC1	2067	broad.mit.edu	36	19	50615494	50615494	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50615494T>C	uc002pbv.1	-	c.353A>G	c.(352-354)AAT>AGT	p.N118S	ERCC1_uc002pbs.1_Missense_Mutation_p.N118S|ERCC1_uc002pbt.1_Missense_Mutation_p.N118S|ERCC1_uc002pbu.1_Missense_Mutation_p.N46S	NM_202001	NP_973730	P07992	ERCC1_HUMAN	excision repair cross-complementing 1 isoform 1	118					mitotic recombination|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|response to oxidative stress|transcription-coupled nucleotide-excision repair	cytoplasm|nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair complex	damaged DNA binding|endonuclease activity|protein C-terminus binding|protein domain specific binding|single-stranded DNA binding				0		Ovarian(192;0.051)|all_neural(266;0.112)												0.354167	52.063438	52.962104	17	31	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.0247)	Missense_Mutation	SNP	50615494	50615494	5405	19	T	C	C	52	52	ERCC1	C	4	4
PRR12	57479	broad.mit.edu	36	19	54791179	54791179	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54791179C>T	uc002poo.2	+	c.1775C>T	c.(1774-1776)TCA>TTA	p.S592L		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	356	A.T hook 1.|Pro-rich.						DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)												0.371901	122.027161	123.777363	45	76	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	Missense_Mutation	SNP	54791179	54791179	13027	19	C	T	T	29	29	PRR12	T	2	2
ZNF552	79818	broad.mit.edu	36	19	63011229	63011229	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63011229C>T	uc002qqg.1	-	c.1215G>A	c.(1213-1215)AAG>AAA	p.K405K	ZNF587_uc002qqb.1_Intron	NM_024762	NP_079038	Q9H707	ZN552_HUMAN	zinc finger protein 552	405					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)												0.290323	161.983234	169.30498	54	132	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)	Silent	SNP	63011229	63011229	18579	19	C	T	T	24	24	ZNF552	T	2	2
HRNR	388697	broad.mit.edu	36	1	150459017	150459017	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150459017C>T	uc001ezt.1	-	c.1712G>A	c.(1711-1713)CGT>CAT	p.R571H		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	571					keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.309446	245.13406	255.054784	95	212	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150459017	150459017	7653	1	C	T	T	19	19	HRNR	T	1	1
SPTA1	6708	broad.mit.edu	36	1	156905932	156905932	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156905932G>A	uc001fst.1	-	c.1723C>T	c.(1723-1725)CGT>TGT	p.R575C		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	575	Spectrin 6.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.325714	304.330376	313.762477	114	236	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156905932	156905932	15630	1	G	A	A	40	40	SPTA1	A	1	1
USH2A	7399	broad.mit.edu	36	1	214210618	214210618	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:214210618G>A	uc001hku.1	-	c.6929C>T	c.(6928-6930)ACG>ATG	p.T2310M		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2310	Fibronectin type-III 9.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22														0.31875	139.766718	144.439131	51	109	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	Missense_Mutation	SNP	214210618	214210618	17598	1	G	A	A	40	40	USH2A	A	1	1
CLIC4	25932	broad.mit.edu	36	1	24996853	24996853	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24996853C>T	uc001bjo.1	+	c.106C>T	c.(106-108)CCC>TCC	p.P36S	CLIC4_uc001bjn.1_Non-coding_Transcript|CLIC4_uc001bjp.1_Intron	NM_013943	NP_039234	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4	36	Required for insertion into the membrane (Probable).				cellular response to calcium ion|establishment or maintenance of apical/basal cell polarity|keratinocyte differentiation|negative regulation of cell migration|regulation of cytoskeleton organization	actin cytoskeleton|apical part of cell|cell surface|cell-cell junction|centrosome|chloride channel complex|cytoplasmic vesicle membrane|cytosol|microvillus|midbody|mitochondrion|nuclear matrix|perinuclear region of cytoplasm|soluble fraction	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)												0.25641	83.497756	89.790246	30	87	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)	Missense_Mutation	SNP	24996853	24996853	3666	1	C	T	T	22	22	CLIC4	T	2	2
IL12RB2	3595	broad.mit.edu	36	1	67559890	67559890	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:67559890G>A	uc001ddu.1	+	c.94G>A	c.(94-96)GAT>AAT	p.D32N		NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor	32	Extracellular (Potential).				positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3														0.282869	193.523721	204.150224	71	180	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67559890	67559890	7928	1	G	A	A	37	37	IL12RB2	A	1	1
GBP3	2635	broad.mit.edu	36	1	89253616	89253616	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:89253616T>C	uc001dmt.1	-	c.260A>G	c.(259-261)AAA>AGA	p.K87R	GBP3_uc001dmu.1_5'UTR|GBP3_uc001dmv.1_Non-coding_Transcript	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	87						integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)												0.103053	37.842177	78.94211	27	235	TT		KEEP	---	---	---	---	capture		all cancers(265;0.0103)|Epithelial(280;0.0293)	Missense_Mutation	SNP	89253616	89253616	6541	1	T	C	C	64	64	GBP3	C	4	4
TSHZ2	128553	broad.mit.edu	36	20	51305774	51305774	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:51305774C>T	uc002xwo.2	+	c.2370C>T	c.(2368-2370)CAC>CAT	p.H790H		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	790					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4														0.328042	168.489796	173.443217	62	127	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(23;0.1)		Silent	SNP	51305774	51305774	17175	20	C	T	T	19	19	TSHZ2	T	1	1
ADRM1	11047	broad.mit.edu	36	20	60316075	60316075	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60316075C>T	uc002ycn.1	+	c.652C>T	c.(652-654)CCG>TCG	p.P218S	ADRM1_uc002yco.1_Missense_Mutation_p.P218S	NM_007002	NP_783163	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1 precursor	218	Ser-rich.				proteasome assembly|transcription elongation from RNA polymerase II promoter	cytoplasm|integral to plasma membrane|membrane fraction|nucleus|proteasome complex	endopeptidase activator activity|protease binding|proteasome binding				0	Breast(26;7.76e-09)													0.384615	42.808131	43.265576	15	24	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(19;2.51e-06)		Missense_Mutation	SNP	60316075	60316075	346	20	C	T	T	22	22	ADRM1	T	2	2
OSBP2	23762	broad.mit.edu	36	22	29467177	29467177	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29467177G>A	uc003aiy.1	+	c.674G>A	c.(673-675)CGT>CAT	p.R225H	OSBP2_uc010gwc.1_Missense_Mutation_p.R52H|OSBP2_uc003aix.1_Missense_Mutation_p.R225H|OSBP2_uc003aiz.1_Missense_Mutation_p.R225H	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a	225	PH.				lipid transport	membrane	lipid binding			breast(1)	1														0.134021	17.907646	30.51303	13	84	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29467177	29467177	11685	22	G	A	A	40	40	OSBP2	A	1	1
IL1F6	27179	broad.mit.edu	36	2	113480758	113480758	+	Silent	SNP	C	T	T	rs2289934	by-frequency	TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113480758C>T	uc002tip.1	+	c.237C>T	c.(235-237)GTC>GTT	p.V79V		NM_014440	NP_055255	Q9UHA7	IL1F6_HUMAN	interleukin 1 family, member 6 (epsilon)	79					immune response|inflammatory response	extracellular space	cytokine activity|interleukin-1 receptor binding			ovary(2)	2														0.293286	212.67896	223.481664	83	200	CC		KEEP	---	---	---	---	capture			Silent	SNP	113480758	113480758	7955	2	C	T	T	31	31	IL1F6	T	1	1
APOB	338	broad.mit.edu	36	2	21103275	21103275	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21103275G>A	uc002red.1	-	c.2134C>T	c.(2134-2136)CCA>TCA	p.P712S		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	712					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)									0.352564	168.479426	171.469464	55	101	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21103275	21103275	796	2	G	A	A	43	43	APOB	A	2	2
SEMA4F	10505	broad.mit.edu	36	2	74754397	74754397	+	Silent	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74754397G>A	uc002sna.1	+	c.756G>A	c.(754-756)ACG>ACA	p.T252T	SEMA4F_uc010ffq.1_Silent_p.T219T|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W	252	Sema.|Extracellular (Potential).				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)	3														0.289256	188.458098	198.088375	70	172	GG		KEEP	---	---	---	---	capture			Silent	SNP	74754397	74754397	14521	2	G	A	A	39	39	SEMA4F	A	1	1
C3orf67	200844	broad.mit.edu	36	3	58845424	58845424	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:58845424C>T	uc003dkt.1	-	c.227G>A	c.(226-228)CGA>CAA	p.R76Q	C3orf67_uc003dkv.1_5'UTR|C3orf67_uc003dkw.2_5'UTR	NM_198463	NP_940865	Q6ZVT6	CC067_HUMAN	hypothetical protein LOC200844	76											0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)												0.326772	234.641801	241.400477	83	171	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)	Missense_Mutation	SNP	58845424	58845424	2334	3	C	T	T	31	31	C3orf67	T	1	1
SGMS2	166929	broad.mit.edu	36	4	109040282	109040282	+	Silent	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:109040282C>T	uc003hyl.2	+	c.558C>T	c.(556-558)TTC>TTT	p.F186F	SGMS2_uc003hyn.1_Silent_p.F186F|SGMS2_uc003hyo.1_Silent_p.F186F	NM_152621	NP_689834	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	186					sphingomyelin biosynthetic process	integral to Golgi membrane|integral to plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			lung(1)	1					Choline(DB00122)									0.144105	55.216795	83.14576	33	196	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)	Silent	SNP	109040282	109040282	14706	4	C	T	T	30	30	SGMS2	T	2	2
GPR125	166647	broad.mit.edu	36	4	22024037	22024037	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:22024037C>T	uc003gqm.1	-	c.2098G>A	c.(2098-2100)GTT>ATT	p.V700I	GPR125_uc010ieo.1_Missense_Mutation_p.V556I	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	700	Extracellular (Potential).|GPS.				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity				0		Breast(46;0.198)												0.333333	202.703288	208.383509	77	154	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22024037	22024037	6913	4	C	T	T	17	17	GPR125	T	2	2
PDGFRA	5156	broad.mit.edu	36	4	54825899	54825899	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:54825899G>A	uc003han.2	+	c.685G>A	c.(685-687)GAA>AAA	p.E229K	PDGFRA_uc003haa.1_Intron|PDGFRA_uc003hal.2_3'UTR|PDGFRA_uc010igq.1_Missense_Mutation_p.E123K|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	229	Ig-like C2-type 3.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)				Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.11041	107.040887	249.794102	105	846	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Missense_Mutation	SNP	54825899	54825899	12082	4	G	A	A	41	41	PDGFRA	A	2	2
PAM	5066	broad.mit.edu	36	5	102312027	102312027	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:102312027G>C	uc003knt.1	+	c.622G>C	c.(622-624)GTT>CTT	p.V208L	PAM_uc003kns.1_Missense_Mutation_p.V208L|PAM_uc003knu.1_Missense_Mutation_p.V208L|PAM_uc003knv.1_Missense_Mutation_p.V208L|PAM_uc003knw.1_Missense_Mutation_p.V208L	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	208	Peptidylglycine alpha-hydroxylating monooxygenase (By similarity).|Intragranular (Potential).				oxidation-reduction process|peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)			Vitamin C(DB00126)									0.342308	306.931141	312.627314	89	171	GG		KEEP	---	---	---	---	capture		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Missense_Mutation	SNP	102312027	102312027	11829	5	G	C	C	48	48	PAM	C	3	3
GRM6	2916	broad.mit.edu	36	5	178348701	178348701	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178348701C>T	uc003mjr.1	-	c.1195G>A	c.(1195-1197)GGC>AGC	p.G399S	GRM6_uc010jla.1_Intron|GRM6_uc003mjs.1_Missense_Mutation_p.G19S	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor	399	Extracellular (Potential).				detection of visible light|visual perception	integral to plasma membrane				ovary(2)|breast(1)|pancreas(1)	4	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)												0.211538	24.800932	28.798718	11	41	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)	Missense_Mutation	SNP	178348701	178348701	7080	5	C	T	T	22	22	GRM6	T	2	2
THBS4	7060	broad.mit.edu	36	5	79367185	79367185	+	Silent	SNP	C	G	G			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79367185C>G	uc003kgh.1	+	c.69C>G	c.(67-69)GGC>GGG	p.G23G		NM_003248	NP_003239	P35443	TSP4_HUMAN	thrombospondin 4 precursor	23					endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity				0		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)												0.375	6.718616	6.829732	3	5	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)	Silent	SNP	79367185	79367185	16384	5	C	G	G	27	27	THBS4	G	3	3
BTBD9	114781	broad.mit.edu	36	6	38332166	38332166	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:38332166C>A	uc003ooa.2	-	c.1559G>T	c.(1558-1560)TGC>TTC	p.C520F	BTBD9_uc003ony.2_Missense_Mutation_p.C452F|BTBD9_uc010jwv.1_Missense_Mutation_p.C481F|BTBD9_uc010jww.1_Non-coding_Transcript|BTBD9_uc010jwx.1_Missense_Mutation_p.C520F	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a	520					cell adhesion						0														0.324675	71.246451	73.347909	25	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38332166	38332166	1582	6	C	A	A	25	25	BTBD9	A	3	3
EMID2	136227	broad.mit.edu	36	7	100850035	100850035	+	Silent	SNP	G	C	C			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100850035G>C	uc010lhy.1	+	c.216G>C	c.(214-216)TCG>TCC	p.S72S	EMID2_uc003uyo.1_Silent_p.S72S	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2	72	EMI.					collagen				ovary(1)	1	Lung NSC(181;0.215)													0.269231	8.076078	9.456586	7	19	GG		KEEP	---	---	---	---	capture			Silent	SNP	100850035	100850035	5284	7	G	C	C	39	39	EMID2	C	3	3
FOXP2	93986	broad.mit.edu	36	7	114091645	114091645	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:114091645G>A	uc003vgz.2	+	c.1996G>A	c.(1996-1998)GTC>ATC	p.V666I	FOXP2_uc003vgu.2_Non-coding_Transcript|FOXP2_uc003vha.2_Missense_Mutation_p.V549I|FOXP2_uc003vhb.2_Missense_Mutation_p.V641I|FOXP2_uc010ljz.1_Missense_Mutation_p.V456I	NM_148898	NP_683697	O15409	FOXP2_HUMAN	forkhead box P2 isoform II	641					camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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|zinc ion binding			ovary(4)|lung(1)|breast(1)|pancreas(1)	7														0.191176	53.568839	65.692782	26	110	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114091645	114091645	6273	7	G	A	A	40	40	FOXP2	A	1	1
WDR91	29062	broad.mit.edu	36	7	134528589	134528589	+	Silent	SNP	G	T	T			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:134528589G>T	uc003vsp.1	-	c.1593C>A	c.(1591-1593)GGC>GGA	p.G531G	WDR91_uc010lmq.1_Silent_p.G120G|WDR91_uc010lmr.1_Non-coding_Transcript	NM_014149	NP_054868	A4D1P6	WDR91_HUMAN	WD repeat domain 91	531	WD 3.									breast(2)|ovary(1)	3														0.213836	77.457492	89.488693	34	125	GG		KEEP	---	---	---	---	capture			Silent	SNP	134528589	134528589	17912	7	G	T	T	46	46	WDR91	T	3	3
HTR5A	3361	broad.mit.edu	36	7	154494030	154494030	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:154494030C>T	uc003wlu.1	+	c.488C>T	c.(487-489)GCG>GTG	p.A163V		NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	163	Helical; Name=4; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)												0.215054	41.64033	48.62354	20	73	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Missense_Mutation	SNP	154494030	154494030	7750	7	C	T	T	27	27	HTR5A	T	1	1
PKD1L1	168507	broad.mit.edu	36	7	47833581	47833581	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47833581G>C	uc003tny.1	-	c.6746C>G	c.(6745-6747)GCC>GGC	p.A2249G	C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'UTR	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2249	Cytoplasmic (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.172414	6.856932	9.80353	5	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47833581	47833581	12388	7	G	C	C	42	42	PKD1L1	C	3	3
PCLO	27445	broad.mit.edu	36	7	82419523	82419523	+	Silent	SNP	A	G	G			TCGA-06-0214-01	TCGA-06-0214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82419523A>G	uc003uhx.2	-	c.8682T>C	c.(8680-8682)GAT>GAC	p.D2894D	PCLO_uc003uhv.2_Silent_p.D2894D|PCLO_uc010lec.1_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2825					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														0.229064	252.27737	279.597224	93	313	AA		KEEP	---	---	---	---	capture			Silent	SNP	82419523	82419523	12003	7	A	G	G	8	8	PCLO	G	4	4
TEX15	56154	broad.mit.edu	36	8	30825521	30825521	+	Silent	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:30825521G>A	uc003xil.1	-	c.555C>T	c.(553-555)TCC>TCT	p.S185S		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	185										ovary(3)	3														0.295302	125.042854	130.627265	44	105	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)	Silent	SNP	30825521	30825521	16306	8	G	A	A	39	39	TEX15	A	1	1
C9orf91	203197	broad.mit.edu	36	9	116435928	116435928	+	Silent	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116435928G>A	uc004bjd.2	+	c.534G>A	c.(532-534)CGG>CGA	p.R178R	C9orf91_uc004bje.2_Silent_p.R157R|C9orf91_uc004bjf.2_Silent_p.R77R	NM_153045	NP_694590	Q5VZI3	CI091_HUMAN	hypothetical protein LOC203197	178						integral to membrane				pancreas(1)	1														0.3125	99.677046	103.187267	35	77	GG		KEEP	---	---	---	---	capture			Silent	SNP	116435928	116435928	2621	9	G	A	A	43	43	C9orf91	A	2	2
SEC16A	9919	broad.mit.edu	36	9	138477997	138477997	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0214-01	TCGA-06-0214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138477997G>A	uc004chx.1	-	c.4463C>T	c.(4462-4464)ACG>ATG	p.T1488M	SEC16A_uc004chv.2_Missense_Mutation_p.T878M|SEC16A_uc004chw.1_Missense_Mutation_p.T1488M|SEC16A_uc010nbn.1_Missense_Mutation_p.T1488M	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	1310					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)												0.330709	114.004576	117.231328	42	85	GG		KEEP	---	---	---	---	capture		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)	Missense_Mutation	SNP	138477997	138477997	14472	9	G	A	A	40	40	SEC16A	A	1	1
RRAGA	10670	broad.mit.edu	36	9	19040150	19040150	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:19040150T>A	uc003znj.1	+	c.493T>A	c.(493-495)TGG>AGG	p.W165R		NM_006570	NP_006561	Q7L523	RRAGA_HUMAN	Ras-related GTP binding A	165					apoptosis|cellular protein localization|cellular response to amino acid stimulus|positive regulation of cytolysis|positive regulation of TOR signaling cascade|virus-host interaction	Golgi apparatus|lysosome|nucleus	GTP binding|phosphoprotein binding|protein heterodimerization activity|protein homodimerization activity				0														0.147059	7.954459	12.022198	5	29	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19040150	19040150	14152	9	T	A	A	55	55	RRAGA	A	4	4
CCL19	6363	broad.mit.edu	36	9	34680006	34680006	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0214-01	TCGA-06-0214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:34680006C>T	uc003zvn.1	-	c.197G>A	c.(196-198)AGG>AAG	p.R66K	CCL19_uc010mkf.1_Intron	NM_006274	NP_006265	Q99731	CCL19_HUMAN	small inducible cytokine A19 precursor	66					activation of JUN kinase activity|cell communication|cell maturation|establishment of T cell polarity|immune response|immunological synapse formation|inflammatory response|interleukin-12 secretion|myeloid dendritic cell chemotaxis|negative regulation of leukocyte apoptosis|positive regulation of Cdc42 GTPase activity|positive regulation of dendritic cell antigen processing and presentation|positive regulation of ERK1 and ERK2 cascade|positive regulation of glycoprotein biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of neutrophil chemotaxis|positive regulation of NF-kappaB import into nucleus|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of receptor-mediated endocytosis|positive regulation of T cell proliferation|positive regulation of T-helper 1 cell differentiation|positive regulation of tumor necrosis factor production|regulation of cell projection assembly|release of sequestered calcium ion into cytosol|response to nitric oxide|response to prostaglandin E stimulus|response to virus|T cell costimulation	extracellular space	CCR10 chemokine receptor binding|CCR7 chemokine receptor binding|chemokine activity				0	all_epithelial(49;0.102)					Melanoma(129;177 1723 4710 11020 27705)								0.37931	101.072421	102.17717	33	54	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)	Missense_Mutation	SNP	34680006	34680006	3015	9	C	T	T	24	24	CCL19	T	2	2
PAX5	5079	broad.mit.edu	36	9	36836902	36836902	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0214-01	TCGA-06-0214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:36836902T>C	uc003zzo.1	-	c.1037A>G	c.(1036-1038)TAC>TGC	p.Y346C	PAX5_uc010mlo.1_Missense_Mutation_p.Y312C|PAX5_uc010mlp.1_Intron|PAX5_uc010mlq.1_Non-coding_Transcript|PAX5_uc010mlr.1_Missense_Mutation_p.T269A|PAX5_uc010mls.1_Intron	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5	346					cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(4)|p.Y346C(1)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(139)|central_nervous_system(2)	141		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)								323				0.184211	35.610967	42.715274	14	62	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(29;0.0108)	Missense_Mutation	SNP	36836902	36836902	11902	9	T	C	C	57	57	PAX5	C	4	4
