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
CNNM1	26507	broad.mit.edu	36	10	101137653	101137653	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:101137653C>T	uc001kpp.2	+	c.2427C>T	c.(2425-2427)GAC>GAT	p.D809D	CNNM1_uc009xwf.1_Silent_p.D809D|CNNM1_uc009xwg.1_Silent_p.D209D	NM_020348	NP_065081	Q9NRU3	CNNM1_HUMAN	cyclin M1	809					ion transport	integral to membrane|plasma membrane					0		Colorectal(252;0.234)												0.709677	69.559132	70.779785	22	9	CC		KEEP	---	---	---	---	capture		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)	Silent	SNP	101137653	101137653	3750	10	C	T	T	19	19	CNNM1	T	1	1
MPP7	143098	broad.mit.edu	36	10	28385475	28385475	+	Silent	SNP	T	C	C			TCGA-27-1833-01	TCGA-27-1833-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:28385475T>C	uc001iua.1	-	c.1491A>G	c.(1489-1491)ACA>ACG	p.T497T	MPP7_uc009xkz.1_Non-coding_Transcript|MPP7_uc001iub.1_Silent_p.T497T|MPP7_uc009xla.1_Silent_p.T497T	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	497	Guanylate kinase-like.				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1														0.208333	87.790861	102.921701	40	152	TT		KEEP	---	---	---	---	capture			Silent	SNP	28385475	28385475	10131	10	T	C	C	63	63	MPP7	C	4	4
OGDHL	55753	broad.mit.edu	36	10	50613393	50613393	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:50613393G>A	uc009xog.1	-	c.3001C>T	c.(3001-3003)CGG>TGG	p.R1001W	OGDHL_uc001jie.1_Missense_Mutation_p.R974W	NM_018245	NP_060715	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like isoform a	974					glycolysis|oxidation-reduction process	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1														0.626866	140.266137	141.213338	42	25	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50613393	50613393	11245	10	G	A	A	39	39	OGDHL	A	1	1
A1CF	29974	broad.mit.edu	36	10	52266070	52266070	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:52266070C>T	uc001jjj.1	-	c.374G>A	c.(373-375)CGC>CAC	p.R125H	A1CF_uc001jji.1_Missense_Mutation_p.R125H|A1CF_uc001jjh.1_Missense_Mutation_p.R133H|A1CF_uc009xov.1_Missense_Mutation_p.R125H	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	125	RRM 1.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1														0.644068	120.863387	121.942666	38	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52266070	52266070	2	10	C	T	T	27	27	A1CF	T	1	1
OR4C6	219432	broad.mit.edu	36	11	55189343	55189343	+	Missense_Mutation	SNP	T	A	A			TCGA-27-1833-01	TCGA-27-1833-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55189343T>A	uc001nht.2	+	c.125T>A	c.(124-126)CTT>CAT	p.L42H	OR4C6_uc009ymc.1_Missense_Mutation_p.L42H	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	42	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.458564	501.405464	501.947419	166	196	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55189343	55189343	11459	11	T	A	A	56	56	OR4C6	A	4	4
DCHS1	8642	broad.mit.edu	36	11	6611422	6611422	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6611422C>T	uc001mem.1	-	c.2252G>A	c.(2251-2253)CGG>CAG	p.R751Q		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	751	Cadherin 7.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)												0.555556	28.343186	28.390769	10	8	CC		KEEP	---	---	---	---	capture		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	6611422	6611422	4458	11	C	T	T	23	23	DCHS1	T	1	1
LMO1	4004	broad.mit.edu	36	11	8205120	8205120	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:8205120C>G	uc001mgg.1	-	c.343G>C	c.(343-345)GCC>CCC	p.A115P	LMO1_uc009yfo.1_Non-coding_Transcript|LMO1_uc001mgh.1_Missense_Mutation_p.A114P	NM_002315	NP_002306	P25800	RBTN1_HUMAN	LIM domain only 1	115	LIM zinc-binding 2.				cell proliferation|multicellular organismal development|positive regulation of gene-specific transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0										78				0.4	11.347913	11.560553	8	12	CC		KEEP	---	---	---	---	capture		Epithelial(150;1.59e-07)|BRCA - Breast invasive adenocarcinoma(625;0.203)	Missense_Mutation	SNP	8205120	8205120	9180	11	C	G	G	27	27	LMO1	G	3	3
C12orf51	283450	broad.mit.edu	36	12	111134813	111134813	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1833-01	TCGA-27-1833-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:111134813T>C	uc009zwc.1	-	c.6224A>G	c.(6223-6225)GAG>GGG	p.E2075G	C12orf51_uc001ttr.1_Missense_Mutation_p.E250G	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)	1														0.46875	31.873047	31.903412	15	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111134813	111134813	1740	12	T	C	C	54	54	C12orf51	C	4	4
RPLP0	6175	broad.mit.edu	36	12	119119607	119119607	+	Nonsense_Mutation	SNP	G	T	T			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:119119607G>T	uc001txp.1	-	c.693C>A	c.(691-693)TAC>TAA	p.Y231*	GCN1L1_uc001txo.1_5'Flank|RPLP0_uc001txq.1_Nonsense_Mutation_p.Y231*|RPLP0_uc001txr.1_Nonsense_Mutation_p.Y169*	NM_053275	NP_444505	P05388	RLA0_HUMAN	ribosomal protein P0	231					endocrine pancreas development|interspecies interaction between organisms|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.180328	6.765513	12.768264	11	50	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	119119607	119119607	14083	12	G	T	T	44	44	RPLP0	T	5	3
SLCO1B3	28234	broad.mit.edu	36	12	21120733	21120733	+	Nonsense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21120733C>T	uc001rem.1	+	c.2011C>T	c.(2011-2013)CGA>TGA	p.R671*	LST-3TM12_uc001ren.1_Nonsense_Mutation_p.R610*|LST-3TM12_uc001rep.1_Nonsense_Mutation_p.R563*			Q9NPD5	SO1B3_HUMAN	Liver-specific organic anion transporter 3TM13 (Organic anion transporter LST-3c).	638	Helical; Name=12; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)	3	Esophageal squamous(101;0.149)													0.361111	302.978587	307.843858	104	184	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	21120733	21120733	15221	12	C	T	T	19	19	SLCO1B3	T	5	1
STAC3	246329	broad.mit.edu	36	12	55929167	55929167	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55929167G>A	uc001snp.1	-	c.258C>T	c.(256-258)AAC>AAT	p.N86N	STAC3_uc001snq.1_Silent_p.N47N|STAC3_uc009zpl.1_Intron	NM_145064	NP_659501	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	86					intracellular signal transduction		identical protein binding|metal ion binding			ovary(2)	2														0.286624	116.611412	123.023698	45	112	GG		KEEP	---	---	---	---	capture			Silent	SNP	55929167	55929167	15759	12	G	A	A	40	40	STAC3	A	1	1
SACS	26278	broad.mit.edu	36	13	22806788	22806788	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:22806788G>T	uc001uon.2	-	c.9227C>A	c.(9226-9228)ACT>AAT	p.T3076N	SACS_uc001uoo.2_Missense_Mutation_p.T2929N|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	3076					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)|skin(1)	11		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)								738				0.436364	143.682789	144.071269	48	62	GG		KEEP	---	---	---	---	capture		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)	Missense_Mutation	SNP	22806788	22806788	14284	13	G	T	T	36	36	SACS	T	3	3
WBP4	11193	broad.mit.edu	36	13	40537425	40537425	+	Splice_Site_SNP	SNP	T	A	A			TCGA-27-1833-01	TCGA-27-1833-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:40537425T>A	uc001uxt.1	+	c.262_splice	c.e4+2	p.E88_splice		NM_007187	NP_009118			WW domain-containing binding protein 4						nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)								133				0.230769	12.050475	13.769475	6	20	TT		KEEP	---	---	---	---	capture		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)	Splice_Site_SNP	SNP	40537425	40537425	17833	13	T	A	A	57	57	WBP4	A	5	4
SPTB	6710	broad.mit.edu	36	14	64340085	64340085	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:64340085C>T	uc001xhr.1	-	c.467G>A	c.(466-468)CGC>CAC	p.R156H	SPTB_uc001xhs.1_Missense_Mutation_p.R156H|SPTB_uc001xht.1_Missense_Mutation_p.R156H|SPTB_uc001xhu.1_Missense_Mutation_p.R156H	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a	156	CH 1.|Actin-binding.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|lung(1)|central_nervous_system(1)	9		all_lung(585;4.15e-09)												0.387755	163.340102	164.96317	57	90	CC		KEEP	---	---	---	---	capture		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)	Missense_Mutation	SNP	64340085	64340085	15632	14	C	T	T	27	27	SPTB	T	1	1
WDR72	256764	broad.mit.edu	36	15	51779352	51779352	+	Missense_Mutation	SNP	A	T	T			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:51779352A>T	uc002acj.2	-	c.1652T>A	c.(1651-1653)CTG>CAG	p.L551Q	WDR72_uc010bfi.1_Missense_Mutation_p.L551Q	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	551	WD 7.									lung(1)	1														0.365546	262.763591	266.546774	87	151	AA		KEEP	---	---	---	---	capture		all cancers(107;0.0511)	Missense_Mutation	SNP	51779352	51779352	17895	15	A	T	T	7	7	WDR72	T	4	4
MEF2A	4205	broad.mit.edu	36	15	98048020	98048020	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:98048020G>A	uc002bvh.2	+	c.728G>A	c.(727-729)GGT>GAT	p.G243D	MEF2A_uc002bve.1_Missense_Mutation_p.G241D|MEF2A_uc002bvf.1_Missense_Mutation_p.G243D|MEF2A_uc002bvg.1_Missense_Mutation_p.G241D|MEF2A_uc010bos.1_Missense_Mutation_p.G241D|MEF2A_uc002bvi.1_Missense_Mutation_p.G241D|MEF2A_uc010bot.1_Missense_Mutation_p.G173D	NM_005587	NP_005578	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A isoform 1	243					apoptosis|innate immune response|muscle cell differentiation|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|nervous system development|positive regulation of muscle cell differentiation|regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nuclear chromatin|nucleoplasm	sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)									195				0.414634	51.667826	51.928686	17	24	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(32;0.00085)		Missense_Mutation	SNP	98048020	98048020	9844	15	G	A	A	44	44	MEF2A	A	2	2
CACNA1H	8912	broad.mit.edu	36	16	1195219	1195219	+	Nonsense_Mutation	SNP	C	A	A			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1195219C>A	uc002cks.1	+	c.2556C>A	c.(2554-2556)TAC>TAA	p.Y852*	CACNA1H_uc002ckt.1_Nonsense_Mutation_p.Y852*	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	852	II.|Cytoplasmic (Potential).				axon guidance|muscle contraction|muscle organ development|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)									0.350649	79.401107	80.91657	27	50	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	1195219	1195219	2661	16	C	A	A	17	17	CACNA1H	A	5	3
MAPK8IP3	23162	broad.mit.edu	36	16	1756094	1756094	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1756094G>A	uc002cmk.1	+	c.2576G>A	c.(2575-2577)CGG>CAG	p.R859Q	MAPK8IP3_uc002cml.1_Missense_Mutation_p.R853Q	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	859					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			central_nervous_system(1)	1														0.328767	68.778792	70.674563	24	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1756094	1756094	9669	16	G	A	A	39	39	MAPK8IP3	A	1	1
SCNN1G	6340	broad.mit.edu	36	16	23108285	23108285	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23108285G>A	uc002dlm.1	+	c.410G>A	c.(409-411)CGC>CAC	p.R137H		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	137	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|large_intestine(1)|pancreas(1)	4					Amiloride(DB00594)|Triamterene(DB00384)									0.458746	404.064124	404.514773	139	164	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0366)	Missense_Mutation	SNP	23108285	23108285	14412	16	G	A	A	38	38	SCNN1G	A	1	1
IL4R	3566	broad.mit.edu	36	16	27265290	27265290	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27265290G>A	uc002don.1	+	c.363G>A	c.(361-363)GTG>GTA	p.V121V	IL4R_uc002dom.1_Silent_p.V121V|IL4R_uc010bxy.1_Silent_p.V121V|IL4R_uc002doo.1_5'UTR	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	121	Extracellular (Potential).				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2														0.311688	62.083802	64.508787	24	53	GG		KEEP	---	---	---	---	capture			Silent	SNP	27265290	27265290	7999	16	G	A	A	45	45	IL4R	A	2	2
DNAH9	1770	broad.mit.edu	36	17	11625084	11625084	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:11625084G>A	uc002gne.1	+	c.7586G>A	c.(7585-7587)GGC>GAC	p.G2529D	DNAH9_uc010coo.1_Missense_Mutation_p.G1823D	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	2529	AAA 3 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)												0.38961	85.632103	86.45405	30	47	GG		KEEP	---	---	---	---	capture		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	Missense_Mutation	SNP	11625084	11625084	4791	17	G	A	A	42	42	DNAH9	A	2	2
CDRT15	146822	broad.mit.edu	36	17	14080797	14080797	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:14080797G>A	uc002gog.1	-	c.79C>T	c.(79-81)CGA>TGA	p.R27*	CDRT15_uc010coq.1_Non-coding_Transcript	NM_001007530	NP_001007531	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	27											0														0.364865	79.807464	80.995135	27	47	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)	Nonsense_Mutation	SNP	14080797	14080797	3304	17	G	A	A	39	39	CDRT15	A	5	1
CCL3	6348	broad.mit.edu	36	17	31440208	31440208	+	Nonsense_Mutation	SNP	G	A	A	rs5029409	unknown	TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31440208G>A	uc002hkv.1	-	c.202C>T	c.(202-204)CGA>TGA	p.R68*		NM_002983	NP_002974	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	68		Involved in GAG binding.		R->A: Strongly reduces heparin binding.	cell-cell signaling|cellular calcium ion homeostasis|cellular component movement|cytoskeleton organization|exocytosis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|regulation of viral genome replication	extracellular space|soluble fraction	chemoattractant activity|chemokine activity|signal transducer activity				0		Ovarian(249;0.17)								50				0.092	6.366266	48.253848	23	227	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Nonsense_Mutation	SNP	31440208	31440208	3026	17	G	A	A	38	38	CCL3	A	5	1
KRT19	3880	broad.mit.edu	36	17	36933975	36933975	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36933975G>T	uc002hxd.2	-	c.894C>A	c.(892-894)GAC>GAA	p.D298E	KRT15_uc002hxb.1_5'Flank	NM_002276	NP_002267	P08727	K1C19_HUMAN	keratin 19	298	Coil 2.|Rod.|Necessary for interaction with PNN.				interspecies interaction between organisms|response to estrogen stimulus|sarcomere organization	costamere|intermediate filament	protein binding|structural constituent of cytoskeleton|structural constituent of muscle				0		Breast(137;0.00038)												0.376623	81.662802	82.68871	29	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36933975	36933975	8771	17	G	T	T	44	44	KRT19	T	3	3
EPB41L3	23136	broad.mit.edu	36	18	5396824	5396824	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:5396824G>A	uc002kmt.1	-	c.2301C>T	c.(2299-2301)GCC>GCT	p.A767A	EPB41L3_uc002kmu.1_Silent_p.A586A|EPB41L3_uc010dkq.1_Silent_p.A477A|EPB41L3_uc002kms.1_Silent_p.A39A|EPB41L3_uc010dkr.1_Silent_p.A159A	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	767	Spectrin--actin-binding (Potential).				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5														0.358025	168.916239	171.787084	58	104	GG		KEEP	---	---	---	---	capture			Silent	SNP	5396824	5396824	5347	18	G	A	A	39	39	EPB41L3	A	1	1
SERPINB2	5055	broad.mit.edu	36	18	59720652	59720652	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59720652G>A	uc002ljo.1	+	c.713G>A	c.(712-714)CGT>CAT	p.R238H	SERPINB2_uc010dqh.1_Missense_Mutation_p.R168H|SERPINB2_uc002ljp.1_Missense_Mutation_p.R43H|SERPINB2_uc002ljq.1_Missense_Mutation_p.R43H	NM_002575	NP_002566	P05120	PAI2_HUMAN	serine (or cysteine) proteinase inhibitor, clade	238					anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)									0.342857	137.261063	140.313589	48	92	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59720652	59720652	14589	18	G	A	A	40	40	SERPINB2	A	1	1
CACNA1A	773	broad.mit.edu	36	19	13271023	13271023	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13271023C>T	uc010dzd.1	-	c.2436G>A	c.(2434-2436)ACG>ACA	p.T812T	CACNA1A_uc010dzc.1_Silent_p.T334T|CACNA1A_uc002mwz.2_Silent_p.T812T|CACNA1A_uc002mwy.2_Silent_p.T808T|CACNA1A_uc010dze.1_Silent_p.T809T	NM_023035	NP_075461	O00555	CAC1A_HUMAN	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage- gated calcium channel subunit alpha Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI).	809	Cytoplasmic (Potential).				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2					Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)									0.23622	68.619285	76.683502	30	97	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Silent	SNP	13271023	13271023	2654	19	C	T	T	27	27	CACNA1A	T	1	1
GPR4	2828	broad.mit.edu	36	19	50786523	50786523	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50786523C>T	uc002pcl.1	-	c.442G>A	c.(442-444)GCC>ACC	p.A148T	GPR4_uc002pcm.1_Missense_Mutation_p.A148T	NM_005282	NP_005273	P46093	GPR4_HUMAN	G protein-coupled receptor 4	148	Helical; Name=4; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(2)	2						Esophageal Squamous(117;181 1612 1673 14956 42937)								0.30303	227.738379	238.026221	90	207	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)	Missense_Mutation	SNP	50786523	50786523	6969	19	C	T	T	27	27	GPR4	T	1	1
GPR4	2828	broad.mit.edu	36	19	50786665	50786665	+	Silent	SNP	A	G	G			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50786665A>G	uc002pcl.1	-	c.300T>C	c.(298-300)AAT>AAC	p.N100N	GPR4_uc002pcm.1_Silent_p.N100N	NM_005282	NP_005273	P46093	GPR4_HUMAN	G protein-coupled receptor 4	100	Helical; Name=3; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(2)	2						Esophageal Squamous(117;181 1612 1673 14956 42937)								0.232558	162.586073	179.406225	60	198	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)	Silent	SNP	50786665	50786665	6969	19	A	G	G	16	16	GPR4	G	4	4
CCDC114	93233	broad.mit.edu	36	19	53498833	53498833	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53498833C>T	uc002pir.1	-	c.763G>A	c.(763-765)GTC>ATC	p.V255I	CCDC114_uc002pip.1_Missense_Mutation_p.V48I|CCDC114_uc002piq.1_Missense_Mutation_p.V48I|CCDC114_uc002pio.2_Missense_Mutation_p.V292I|CCDC114_uc002pis.1_5'Flank|CCDC114_uc002pit.1_Missense_Mutation_p.V292I|CCDC114_uc002piu.1_Missense_Mutation_p.V292I	NM_144577	NP_653178	Q96M63	CC114_HUMAN	coiled-coil domain containing 114 isoform 2	255										ovary(1)	1		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)												0.286932	253.863115	268.182293	101	251	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)	Missense_Mutation	SNP	53498833	53498833	2871	19	C	T	T	19	19	CCDC114	T	1	1
CD33	945	broad.mit.edu	36	19	56421143	56421143	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56421143G>A	uc002pwa.2	+	c.691G>A	c.(691-693)GTC>ATC	p.V231I	CD33_uc010eos.1_Missense_Mutation_p.V231I|CD33_uc010eot.1_Missense_Mutation_p.V104I|CD33_uc010eou.1_Non-coding_Transcript	NM_001772	NP_001763	P20138	CD33_HUMAN	CD33 antigen isoform 1 precursor	231	Extracellular (Potential).				cell adhesion|cell-cell signaling|negative regulation of cell proliferation	integral to plasma membrane	receptor activity|sugar binding				0		all_neural(266;0.0199)			Gemtuzumab ozogamicin(DB00056)									0.232558	44.852723	50.48852	20	66	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Missense_Mutation	SNP	56421143	56421143	3133	19	G	A	A	40	40	CD33	A	1	1
PLEKHM2	23207	broad.mit.edu	36	1	15927761	15927761	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:15927761G>A	uc001axa.2	+	c.2241G>A	c.(2239-2241)GAG>GAA	p.E747E		NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M	644					Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)												0.222222	6.690182	7.971088	4	14	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)	Silent	SNP	15927761	15927761	12507	1	G	A	A	33	33	PLEKHM2	A	2	2
ILDR2	387597	broad.mit.edu	36	1	165171208	165171208	+	Missense_Mutation	SNP	A	T	T			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165171208A>T	uc001gdx.1	-	c.834T>A	c.(832-834)CAT>CAA	p.H278Q		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	278	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1														0.355932	121.316038	123.474004	42	76	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165171208	165171208	8011	1	A	T	T	12	12	ILDR2	T	4	4
EPHA10	284656	broad.mit.edu	36	1	37999696	37999696	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:37999696G>A	uc009vvi.1	-	c.818C>T	c.(817-819)GCG>GTG	p.A273V	EPHA10_uc001cbw.2_Missense_Mutation_p.A273V	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	273	Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(3)|stomach(1)	4	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)								328				0.410256	83.971684	84.52335	32	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37999696	37999696	5359	1	G	A	A	38	38	EPHA10	A	1	1
LRRIQ3	127255	broad.mit.edu	36	1	74279951	74279951	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:74279951G>A	uc001dfy.2	-	c.1252C>T	c.(1252-1254)CGA>TGA	p.R418*	LRRIQ3_uc001dfz.2_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	418										ovary(2)	2										2				0.373563	194.222654	196.668101	65	109	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	74279951	74279951	9406	1	G	A	A	39	39	LRRIQ3	A	5	1
SEMG2	6407	broad.mit.edu	36	20	43285035	43285035	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43285035G>A	uc010ggz.1	+	c.1348G>A	c.(1348-1350)GTA>ATA	p.V450I	SEMG2_uc002xnk.1_Missense_Mutation_p.V450I|SEMG2_uc002xnl.1_Intron	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	450	Repeat-rich region.|4 X 60 AA tandem repeats, type I.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity				0		Myeloproliferative disorder(115;0.0122)												0.317073	141.938646	146.819661	52	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43285035	43285035	14531	20	G	A	A	44	44	SEMG2	A	2	2
SULF2	55959	broad.mit.edu	36	20	45725621	45725621	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:45725621G>A	uc002xto.1	-	c.2210C>T	c.(2209-2211)ACG>ATG	p.T737M	SULF2_uc002xtp.1_Missense_Mutation_p.T737M|SULF2_uc002xtq.1_Missense_Mutation_p.T737M|SULF2_uc002xtr.1_Missense_Mutation_p.T737M	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	737					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)	5										709		OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.308176	256.512777	266.89848	98	220	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45725621	45725621	15891	20	G	A	A	40	40	SULF2	A	1	1
ZFP64	55734	broad.mit.edu	36	20	50237001	50237001	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:50237001C>T	uc002xwl.1	-	c.63G>A	c.(61-63)ACG>ACA	p.T21T	ZFP64_uc002xwk.1_Silent_p.T21T|ZFP64_uc002xwm.1_Silent_p.T19T|ZFP64_uc002xwn.1_Silent_p.T21T	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform a	21					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.105882	8.215818	21.32898	9	76	CC		KEEP	---	---	---	---	capture			Silent	SNP	50237001	50237001	18241	20	C	T	T	23	23	ZFP64	T	1	1
TMPRSS15	5651	broad.mit.edu	36	21	18692093	18692093	+	Silent	SNP	A	G	G			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:18692093A>G	uc002ykw.1	-	c.318T>C	c.(316-318)TAT>TAC	p.Y106Y		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	106	Extracellular (Potential).|SEA.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|breast(1)	6														0.545455	63.953553	64.012987	18	15	AA		KEEP	---	---	---	---	capture			Silent	SNP	18692093	18692093	16787	21	A	G	G	16	16	TMPRSS15	G	4	4
RIPK4	54101	broad.mit.edu	36	21	42034588	42034588	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42034588C>T	uc002yzn.1	-	c.1834G>A	c.(1834-1836)GCA>ACA	p.A612T		NM_020639	NP_065690	Q9H4D1	Q9H4D1_HUMAN	ankyrin repeat domain 3	612					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7										268				0.423077	214.955293	215.890614	77	105	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42034588	42034588	13860	21	C	T	T	27	27	RIPK4	T	1	1
COMT	1312	broad.mit.edu	36	22	18330164	18330164	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:18330164A>G	uc002zqu.1	+	c.115A>G	c.(115-117)AAC>GAC	p.N39D	COMT_uc002zqt.1_Missense_Mutation_p.N39D|COMT_uc002zqv.1_Missense_Mutation_p.N39D|COMT_uc002zqw.1_Missense_Mutation_p.N39D|COMT_uc002zqx.1_Missense_Mutation_p.N39D	NM_000754	NP_009294	P21964	COMT_HUMAN	catechol-O-methyltransferase isoform MB-COMT	39					neurotransmitter biosynthetic process|neurotransmitter catabolic process|xenobiotic metabolic process	cytosol|integral to membrane|intracellular membrane-bounded organelle|microsome|plasma membrane|soluble fraction	catechol O-methyltransferase activity|magnesium ion binding|protein binding			ovary(1)	1	Colorectal(54;0.0993)				Carbidopa(DB00190)|Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Folic Acid(DB00158)|L-Valine(DB00161)|Levodopa(DB01235)|Methyldopa(DB00968)|Modafinil(DB00745)|Morphine(DB00295)|S-Adenosylmethionine(DB00118)|Tolcapone(DB00323)									0.294118	11.112851	11.732581	5	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18330164	18330164	3863	22	A	G	G	9	9	COMT	G	4	4
A4GALT	53947	broad.mit.edu	36	22	41419374	41419374	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:41419374G>A	uc003bdb.1	-	c.528C>T	c.(526-528)GAC>GAT	p.D176D	A4GALT_uc010gzd.1_Silent_p.D176D|A4GALT_uc010gze.1_Silent_p.D176D	NM_017436	NP_059132	Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	176	Lumenal (Potential).				glycosphingolipid biosynthetic process|plasma membrane organization	Golgi stack|integral to Golgi membrane|membrane fraction	lactosylceramide 4-alpha-galactosyltransferase activity			central_nervous_system(1)	1														0.47929	241.864118	241.927071	81	88	GG		KEEP	---	---	---	---	capture			Silent	SNP	41419374	41419374	7	22	G	A	A	40	40	A4GALT	A	1	1
SHANK3	85358	broad.mit.edu	36	22	49506495	49506495	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49506495C>T	uc003bne.1	+	c.3416C>T	c.(3415-3417)GCG>GTG	p.A1139V	SHANK3_uc003bnf.1_Missense_Mutation_p.A586V|SHANK3_uc010hbg.1_Missense_Mutation_p.A321V	NM_001080420	NP_001073889			SH3 and multiple ankyrin repeat domains 3											central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)												0.5	35.445283	35.445283	12	12	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.22)	Missense_Mutation	SNP	49506495	49506495	14758	22	C	T	T	27	27	SHANK3	T	1	1
CPS1	1373	broad.mit.edu	36	2	211189467	211189467	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:211189467C>T	uc010fur.1	+	c.2662C>T	c.(2662-2664)CGT>TGT	p.R888C	CPS1_uc002vee.2_Missense_Mutation_p.R882C|CPS1_uc010fus.1_Missense_Mutation_p.R431C|CPS1IT_uc002vef.1_5'Flank	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a	882					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)	12														0.477987	230.98922	231.056257	76	83	CC		KEEP	---	---	---	---	capture		Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Missense_Mutation	SNP	211189467	211189467	3961	2	C	T	T	27	27	CPS1	T	1	1
SH3BP4	23677	broad.mit.edu	36	2	235615502	235615502	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:235615502C>T	uc002vvp.1	+	c.1350C>T	c.(1348-1350)TAC>TAT	p.Y450Y	SH3BP4_uc010fym.1_Silent_p.Y450Y|SH3BP4_uc002vvq.1_Silent_p.Y450Y	NM_014521	NP_055336	Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	450					endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			ovary(1)|skin(1)	2		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)												0.388889	97.258655	98.212604	35	55	CC		KEEP	---	---	---	---	capture		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)	Silent	SNP	235615502	235615502	14737	2	C	T	T	19	19	SH3BP4	T	1	1
GPC1	2817	broad.mit.edu	36	2	241054167	241054167	+	Silent	SNP	G	C	C			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241054167G>C	uc002vyw.2	+	c.1464G>C	c.(1462-1464)TCG>TCC	p.S488S		NM_002081	NP_002072	P35052	GPC1_HUMAN	glypican 1 precursor	488					axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)												0.315789	11.539533	12.176423	6	13	GG		KEEP	---	---	---	---	capture		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)	Silent	SNP	241054167	241054167	6871	2	G	C	C	39	39	GPC1	C	3	3
CNTN6	27255	broad.mit.edu	36	3	1393745	1393745	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:1393745G>A	uc003boz.1	+	c.2152G>A	c.(2152-2154)GTC>ATC	p.V718I	CNTN6_uc003bpa.1_Missense_Mutation_p.V718I	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6	718	Fibronectin type-III 2.				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane		p.V718I(1)		lung(2)|breast(2)|pancreas(1)	5		all_cancers(2;0.000164)|all_epithelial(2;0.107)							p.V718L(ES2-Tumor)	1038				0.403409	204.988447	206.4243	71	105	GG		KEEP	---	---	---	---	capture		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)	Missense_Mutation	SNP	1393745	1393745	3783	3	G	A	A	40	40	CNTN6	A	1	1
CYP8B1	1582	broad.mit.edu	36	3	42891831	42891831	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42891831G>A	uc003cmh.1	-	c.482C>T	c.(481-483)GCC>GTC	p.A161V	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CCBP2_uc010hie.1_Intron|CYP8B1_uc010hif.1_Missense_Mutation_p.A161V	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,	161					bile acid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2														0.331169	133.675249	137.563768	51	103	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)	Missense_Mutation	SNP	42891831	42891831	4363	3	G	A	A	42	42	CYP8B1	A	2	2
WHSC1	7468	broad.mit.edu	36	4	1924907	1924907	+	Silent	SNP	A	G	G			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:1924907A>G	uc003gdz.2	+	c.2196A>G	c.(2194-2196)GTA>GTG	p.V732V	WHSC1_uc003geb.2_Silent_p.V732V|WHSC1_uc003gec.2_Silent_p.V732V|WHSC1_uc003ged.2_Silent_p.V732V|WHSC1_uc003gee.2_Non-coding_Transcript|WHSC1_uc003gef.2_Non-coding_Transcript|WHSC1_uc003gei.2_5'UTR|WHSC1_uc010icf.1_Silent_p.V80V	NM_001042424	NP_579890	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein	732	PHD-type 2.				anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		all_epithelial(65;1.34e-05)								355				0.422222	518.33899	520.238007	152	208	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)	Silent	SNP	1924907	1924907	17936	4	A	G	G	13	13	WHSC1	G	4	4
TRAF3IP2	10758	broad.mit.edu	36	6	112019253	112019253	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1833-01	TCGA-27-1833-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:112019253A>G	uc003pve.1	-	c.757T>C	c.(757-759)TAT>CAT	p.Y253H	TRAF3IP2_uc003pvf.1_Missense_Mutation_p.Y244H|TRAF3IP2_uc003pvg.1_Missense_Mutation_p.Y244H|TRAF3IP2_uc010kdw.1_Missense_Mutation_p.Y244H|TRAF3IP2_uc010kdx.1_Missense_Mutation_p.Y244H	NM_147200	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 1	253					intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade					ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)												0.341667	132.249432	134.902582	41	79	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)	Missense_Mutation	SNP	112019253	112019253	16985	6	A	G	G	14	14	TRAF3IP2	G	4	4
IFNGR1	3459	broad.mit.edu	36	6	137569812	137569812	+	Missense_Mutation	SNP	C	T	T	rs17175322	unknown	TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:137569812C>T	uc003qho.2	-	c.181G>A	c.(181-183)GTA>ATA	p.V61I		NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor	61	Extracellular (Potential).				regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity				0	Colorectal(23;0.24)				Interferon gamma-1b(DB00033)									0.694118	190.252591	193.108611	59	26	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Missense_Mutation	SNP	137569812	137569812	7850	6	C	T	T	19	19	IFNGR1	T	1	1
AARS2	57505	broad.mit.edu	36	6	44389019	44389019	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:44389019G>C	uc010jza.1	-	c.20C>G	c.(19-21)GCT>GGT	p.A7G	SPATS1_uc003oxg.1_Intron	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial	7					alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)				L-Alanine(DB00160)							OREG0017474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.333333	7.99179	8.289104	4	8	GG		KEEP	---	---	---	---	capture	Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Missense_Mutation	SNP	44389019	44389019	21	6	G	C	C	34	34	AARS2	C	3	3
PKHD1	5314	broad.mit.edu	36	6	51631876	51631876	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:51631876C>T	uc003pah.1	-	c.11007G>A	c.(11005-11007)TCG>TCA	p.S3669S		NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3669	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)								p.S3669S(NCIH1793-Tumor)|p.S3669S(TE9-Tumor)	1537				0.116592	26.695826	58.970387	26	197	CC		KEEP	---	---	---	---	capture			Silent	SNP	51631876	51631876	12396	6	C	T	T	27	27	PKHD1	T	1	1
PIK3CG	5294	broad.mit.edu	36	7	106300522	106300522	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106300522C>T	uc003vdv.2	+	c.2190C>T	c.(2188-2190)CAC>CAT	p.H730H	PIK3CG_uc003vdu.1_Silent_p.H730H|PIK3CG_uc003vdw.1_Silent_p.H730H	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	730					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.366071	233.119163	236.64028	82	142	CC		KEEP	---	---	---	---	capture			Silent	SNP	106300522	106300522	12340	7	C	T	T	19	19	PIK3CG	T	1	1
MLL3	58508	broad.mit.edu	36	7	151508779	151508779	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1833-01	TCGA-27-1833-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:151508779T>C	uc003wla.1	-	c.7099A>G	c.(7099-7101)ACA>GCA	p.T2367A	MLL3_uc003wkz.1_Missense_Mutation_p.T1428A|MLL3_uc003wky.2_5'Flank	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	2367					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			pancreas(12)|ovary(7)|large_intestine(6)|central_nervous_system(4)|urinary_tract(1)|skin(1)	31	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)				Colon(68;14 1149 1884 27689 34759)				1780				0.202247	97.909713	112.559198	36	142	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)	Missense_Mutation	SNP	151508779	151508779	10012	7	T	C	C	57	57	MLL3	C	4	4
PON1	5444	broad.mit.edu	36	7	94791693	94791693	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:94791693C>A	uc003uns.1	-	c.31G>T	c.(31-33)GGG>TGG	p.G11W		NM_000446	NP_000437	P27169	PON1_HUMAN	paraoxonase 1 precursor	11					aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)				Atorvastatin(DB01076)|Cefazolin(DB01327)	GBM(119;715 1622 17358 22490 33240)								0.148649	17.085137	25.845307	11	63	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0031)		Missense_Mutation	SNP	94791693	94791693	12677	7	C	A	A	22	22	PON1	A	3	3
FLJ43860	389690	broad.mit.edu	36	8	142545768	142545768	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:142545768G>A	uc003ywi.2	-	c.2400C>T	c.(2398-2400)CAC>CAT	p.H800H	FLJ43860_uc010meu.1_Non-coding_Transcript	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	800							binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)													0.357143	39.912002	40.667406	15	27	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0493)		Silent	SNP	142545768	142545768	6170	8	G	A	A	40	40	FLJ43860	A	1	1
RAD23B	5887	broad.mit.edu	36	9	109124173	109124173	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:109124173C>G	uc004bde.1	+	c.770C>G	c.(769-771)GCA>GGA	p.A257G		NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B	257	Poly-Ala.				nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1														0.222222	6.77888	8.071278	4	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109124173	109124173	13443	9	C	G	G	25	25	RAD23B	G	3	3
EXD3	54932	broad.mit.edu	36	9	139321436	139321436	+	Silent	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139321436G>A	uc004cmp.2	-	c.2418C>T	c.(2416-2418)GCC>GCT	p.A806A	EXD3_uc010ncf.1_Silent_p.A444A	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	hypothetical protein LOC54932	806					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0														0.416667	14.973526	15.046094	5	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	139321436	139321436	5492	9	G	A	A	39	39	EXD3	A	1	1
NXF3	56000	broad.mit.edu	36	X	102221454	102221454	+	Silent	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:102221454C>T	uc004eju.1	-	c.1053G>A	c.(1051-1053)CAG>CAA	p.Q351Q	NXF3_uc010noi.1_Silent_p.Q201Q	NM_022052	NP_071335	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	351	NTF2.					cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3														0.468165	372.942858	373.179111	125	142	CC		KEEP	---	---	---	---	capture			Silent	SNP	102221454	102221454	11190	23	C	T	T	18	18	NXF3	T	2	2
MAGEB4	4115	broad.mit.edu	36	X	30170390	30170390	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30170390G>A	uc004dcb.1	+	c.217G>A	c.(217-219)GCA>ACA	p.A73T	MAGEB1_uc004dcc.1_5'Flank|MAGEB1_uc004dcd.1_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	73										ovary(1)	1														0.469388	65.818107	65.858268	23	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30170390	30170390	9559	23	G	A	A	46	46	MAGEB4	A	2	2
CCDC120	90060	broad.mit.edu	36	X	48810021	48810021	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1833-01	TCGA-27-1833-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48810021C>T	uc010nik.1	+	c.775C>T	c.(775-777)CGG>TGG	p.R259W	CCDC120_uc004dmf.1_Missense_Mutation_p.R259W|CCDC120_uc010nil.1_Missense_Mutation_p.R259W	NM_033626	NP_296375	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	259							protein binding			pancreas(1)	1														0.425926	63.847798	64.097956	23	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48810021	48810021	2876	23	C	T	T	27	27	CCDC120	T	1	1
BRWD3	254065	broad.mit.edu	36	X	79824765	79824765	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1833-01	TCGA-27-1833-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:79824765G>A	uc004edt.2	-	c.4252C>T	c.(4252-4254)CGA>TGA	p.R1418*	BRWD3_uc010nmi.1_Non-coding_Transcript|BRWD3_uc004edo.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edp.2_Nonsense_Mutation_p.R1247*|BRWD3_uc004edq.2_Nonsense_Mutation_p.R1014*|BRWD3_uc010nmj.1_Nonsense_Mutation_p.R1014*|BRWD3_uc004edr.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004eds.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edu.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004edv.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edw.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edx.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edy.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edz.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004eea.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004eeb.2_Nonsense_Mutation_p.R1014*	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1418										ovary(4)	4														0.541872	332.750724	333.05916	110	93	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	79824765	79824765	1557	23	G	A	A	38	38	BRWD3	A	5	1
KRTAP5-5	439915	broad.mit.edu	36	11	1607767	1607775	+	In_Frame_Del	DEL	GGCTGTGGA	-	-			TCGA-27-1833-01	TCGA-27-1833-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1607767_1607775delGGCTGTGGA	uc001lty.1	+	c.121_129delGGCTGTGGA	c.(121-129)GGCTGTGGAdel	p.GCG47del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47_49						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)										0.57			34	26				---	---	---	---	capture_indel			In_Frame_Del	DEL	1607767	1607775	8886	11	GGCTGTGGA	-	-	39	39	KRTAP5-5	-	5	5
MAP4K2	5871	broad.mit.edu	36	11	64316023	64316024	+	Frame_Shift_Ins	INS	-	G	G			TCGA-27-1833-01	TCGA-27-1833-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64316023_64316024insG	uc001obh.1	-	c.2025_2026insC	c.(2023-2028)GGCTGCfs	p.G675fs	MAP4K2_uc001obg.1_Non-coding_Transcript|MAP4K2_uc001obi.1_Frame_Shift_Ins_p.G667fs	NM_004579	NP_004570	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase	675_676	CNH.				immune response|JNK cascade|protein phosphorylation|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2										392				0.33			7	14				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	64316023	64316024	9643	11	-	G	G	7	7	MAP4K2	G	5	5
PLA2G4E	123745	broad.mit.edu	36	15	40089630	40089630	+	Frame_Shift_Del	DEL	A	-	-	rs28736629	unknown	TCGA-27-1833-01	TCGA-27-1833-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40089630_40089630delA	uc001zow.1	-	c.108_108delT	c.(106-108)GGTfs	p.G36fs		NM_001080490	NP_001073959	C9JK77	C9JK77_HUMAN	phospholipase A2, group IVE	36					phospholipid catabolic process						0		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)										0.49			22	23				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	40089630	40089630	12431	15	A	-	-	6	6	PLA2G4E	-	5	5
PAM	5066	broad.mit.edu	36	5	102388809	102388810	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-27-1833-01	TCGA-27-1833-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:102388809_102388810delAG	uc003knt.1	+	c.2561_2562delAG	c.(2560-2562)CAGfs	p.Q854fs	PAM_uc003kns.1_Frame_Shift_Del_p.Q747fs|PAM_uc003knu.1_Intron|PAM_uc003knv.1_Intron|PAM_uc003knw.1_Frame_Shift_Del_p.Q854fs|PAM_uc003knz.1_Frame_Shift_Del_p.Q94fs	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	854	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)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)									0.39			73	116				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	102388809	102388810	11829	5	AG	-	-	7	7	PAM	-	5	5
PHF2	5253	broad.mit.edu	36	9	95478825	95478826	+	In_Frame_Ins	INS	-	CCTGCCTCCACCACA	CCTGCCTCCACCACA			TCGA-27-1833-01	TCGA-27-1833-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:95478825_95478826insCCTGCCTCCACCACA	uc004aub.1	+	c.2961_2962insCCTGCCTCCACCACA	c.(2959-2964)insCCTGCCTCCACCACA	p.992_993insPASTT	PHF2_uc004auc.2_In_Frame_Ins_p.412_413insPASTT	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	992_993	Ser/Thr-rich.				negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	methylated histone residue binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)										0.50			3	3				---	---	---	---	capture_indel			In_Frame_Ins	INS	95478825	95478826	12253	9	-	CCTGCCTCCACCACA	CCTGCCTCCACCACA	22	22	PHF2	CCTGCCTCCACCACA	5	5
