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
AFAP1L2	84632	broad.mit.edu	36	10	116050353	116050353	+	Silent	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:116050353G>A	uc001lbp.1	-	c.1713C>T	c.(1711-1713)GTC>GTT	p.V571V	AFAP1L2_uc001lbn.1_Silent_p.V543V|AFAP1L2_uc001lbo.1_Silent_p.V543V|AFAP1L2_uc001lbr.1_Silent_p.V543V|AFAP1L2_uc001lbm.1_Intron|AFAP1L2_uc001lbq.1_Silent_p.V65V	NM_032550	NP_115939	Q8N4X5	AF1L2_HUMAN	KIAA1914 protein isoform 2	543					inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding			ovary(1)|breast(1)	2		Colorectal(252;0.175)|Breast(234;0.231)												0.324324	29.066506	30.091236	12	25	GG		KEEP	---	---	---	---	capture		Epithelial(162;0.0219)|all cancers(201;0.0561)	Silent	SNP	116050353	116050353	356	10	G	A	A	45	45	AFAP1L2	A	2	2
ATRNL1	26033	broad.mit.edu	36	10	117597482	117597482	+	Silent	SNP	T	G	G			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:117597482T>G	uc001lcg.1	+	c.4008T>G	c.(4006-4008)CCT>CCG	p.P1336P		NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1	1336	Cytoplasmic (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)												0.428571	10.424362	10.455423	3	4	TT		KEEP	---	---	---	---	capture		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)	Silent	SNP	117597482	117597482	1226	10	T	G	G	55	55	ATRNL1	G	4	4
ERCC6	2074	broad.mit.edu	36	10	50337274	50337274	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:50337274T>C	uc001jhs.2	-	c.4075A>G	c.(4075-4077)AAA>GAA	p.K1359E	ERCC6_uc009xod.1_Missense_Mutation_p.K519E|ERCC6_uc001jhr.2_Missense_Mutation_p.K727E	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	1359					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding|transcription elongation regulator activity			breast(5)|ovary(2)|large_intestine(2)|lung(1)	10										738				0.431818	60.717131	60.895573	19	25	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50337274	50337274	5410	10	T	C	C	62	62	ERCC6	C	4	4
MMRN2	79812	broad.mit.edu	36	10	88693119	88693119	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:88693119G>C	uc001kea.1	-	c.1402C>G	c.(1402-1404)CTC>GTC	p.L468V	MMRN2_uc009xtb.1_Missense_Mutation_p.L425V	NM_024756	NP_079032	Q9H8L6	MMRN2_HUMAN	multimerin 2 precursor	468	Potential.					extracellular space				large_intestine(1)	1														0.444444	9.008384	9.030364	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88693119	88693119	10062	10	G	C	C	34	34	MMRN2	C	3	3
HTR7	3363	broad.mit.edu	36	10	92499152	92499152	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:92499152G>A	uc001kha.1	-	c.719C>T	c.(718-720)ACG>ATG	p.T240M	HTR7_uc001kgz.1_Missense_Mutation_p.T240M|HTR7_uc001khb.1_Missense_Mutation_p.T240M	NM_019859	NP_062873	P34969	5HT7R_HUMAN	5-hydroxytryptamine receptor 7 isoform d	240	Helical; Name=5; (By similarity).				blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)									0.478261	33.023921	33.033332	11	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92499152	92499152	7752	10	G	A	A	40	40	HTR7	A	1	1
MMP20	9313	broad.mit.edu	36	11	101982611	101982611	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:101982611C>T	uc001phc.1	-	c.818G>A	c.(817-819)CGG>CAG	p.R273Q		NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein	273					proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)							p.R273Q(NCIH1650-Tumor)|p.R273Q(CW2-Tumor)	637				0.230769	14.140012	15.864824	6	20	CC		KEEP	---	---	---	---	capture	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Missense_Mutation	SNP	101982611	101982611	10049	11	C	T	T	23	23	MMP20	T	1	1
CHRNA10	57053	broad.mit.edu	36	11	3644106	3644106	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:3644106C>T	uc001lyf.1	-	c.1160G>A	c.(1159-1161)CGA>CAA	p.R387Q		NM_020402	NP_065135	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10	387	Cytoplasmic (Potential).				regulation of cell proliferation|synaptic transmission, cholinergic	cell junction|postsynaptic membrane	calcium channel activity|receptor activity|receptor binding			ovary(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)			Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116)	Melanoma(153;17 1869 2949 7120 36888)								0.140351	10.888158	17.986091	8	49	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Missense_Mutation	SNP	3644106	3644106	3516	11	C	T	T	31	31	CHRNA10	T	1	1
TCN1	6947	broad.mit.edu	36	11	59386680	59386680	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59386680G>T	uc001noj.2	-	c.351C>A	c.(349-351)CAC>CAA	p.H117Q		NM_001062	NP_001053	P20061	TCO1_HUMAN	transcobalamin I precursor	117					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding			ovary(1)	1		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)									0.2	23.863679	28.889908	12	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59386680	59386680	16232	11	G	T	T	44	44	TCN1	T	3	3
BBS1	582	broad.mit.edu	36	11	66045424	66045424	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66045424G>T	uc001oii.1	+	c.941_splice	c.e9+1	p.R314_splice	ZDHHC24_uc001oim.1_Non-coding_Transcript|ZDHHC24_uc009yrg.1_3'UTR|BBS1_uc001oij.1_Splice_Site_SNP_p.R277_splice|BBS1_uc001oik.1_Splice_Site_SNP_p.R201_splice|BBS1_uc001oil.1_Intron	NM_024649	NP_078925			Bardet-Biedl syndrome 1						photoreceptor cell maintenance|response to stimulus|retina homeostasis|sensory cilium assembly	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						GBM(152;173 2612 9770 10137)								0.5	8.961551	8.961551	4	4	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	66045424	66045424	1356	11	G	T	T	44	44	BBS1	T	5	3
FAT3	120114	broad.mit.edu	36	11	92263798	92263798	+	Silent	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:92263798G>C	uc001pdj.2	+	c.13545G>C	c.(13543-13545)TCG>TCC	p.S4515S	FAT3_uc001pdi.2_Silent_p.S987S	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	4547	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.363636	12.597551	12.777293	4	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	92263798	92263798	5927	11	G	C	C	39	39	FAT3	C	3	3
GUCY2C	2984	broad.mit.edu	36	12	14718955	14718955	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:14718955G>A	uc001rcd.1	-	c.955C>T	c.(955-957)CGA>TGA	p.R319*	GUCY2C_uc009zhz.1_Nonsense_Mutation_p.R319*	NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C	319	Extracellular (Potential).				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(1)	5									p.R319*(22RV1-Tumor)	889				0.283333	43.350821	45.879978	17	43	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	14718955	14718955	7176	12	G	A	A	40	40	GUCY2C	A	5	1
ARHGAP9	64333	broad.mit.edu	36	12	56154927	56154927	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56154927C>T	uc001sod.1	-	c.1919G>A	c.(1918-1920)AGA>AAA	p.R640K	ARHGAP9_uc001sny.1_Non-coding_Transcript|ARHGAP9_uc001snz.1_Missense_Mutation_p.R366K|ARHGAP9_uc001soa.1_Missense_Mutation_p.R239K|ARHGAP9_uc001sob.1_Missense_Mutation_p.R550K|ARHGAP9_uc001soc.1_Missense_Mutation_p.R550K|ARHGAP9_uc001soe.1_Missense_Mutation_p.R629K	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	569	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1														0.473684	53.245134	53.268176	18	20	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(3;3.37e-34)		Missense_Mutation	SNP	56154927	56154927	903	12	C	T	T	32	32	ARHGAP9	T	2	2
TINF2	26277	broad.mit.edu	36	14	23778922	23778922	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23778922C>T	uc001woa.2	-	c.1277G>A	c.(1276-1278)TGT>TAT	p.C426Y	TINF2_uc010alm.1_3'UTR|TINF2_uc001wob.2_3'UTR|TINF2_uc001woc.2_3'UTR	NM_001099274	NP_001092744	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	426					negative regulation of epithelial cell proliferation|negative regulation of protein ADP-ribosylation|negative regulation of telomere maintenance via telomerase|positive regulation of telomere maintenance|protein localization to chromosome, telomeric region|telomere assembly|telomere maintenance via telomere lengthening	nuclear telomere cap complex|nucleoplasm|perinucleolar chromocenter	protein binding|protein binding|telomeric DNA binding				0														0.371429	35.164192	35.67315	13	22	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0185)	Missense_Mutation	SNP	23778922	23778922	16452	14	C	T	T	17	17	TINF2	T	2	2
ZBTB25	7597	broad.mit.edu	36	14	64023650	64023650	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:64023650C>T	uc001xhf.1	-	c.1052G>A	c.(1051-1053)TGT>TAT	p.C351Y	ZBTB25_uc001xhc.2_Intron|ZBTB25_uc001xhg.1_Missense_Mutation_p.C351Y	NM_006977	NP_008908	P24278	ZBT25_HUMAN	zinc finger protein 46	351	C2H2-type 2.				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.377358	54.984318	55.684866	20	33	CC		KEEP	---	---	---	---	capture		all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)	Missense_Mutation	SNP	64023650	64023650	18118	14	C	T	T	17	17	ZBTB25	T	2	2
LTBP2	4053	broad.mit.edu	36	14	74087670	74087670	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74087670C>T	uc001xqa.1	-	c.1536G>A	c.(1534-1536)CCG>CCA	p.P512P		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	512					protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)	1														0.285714	10.199341	10.773183	4	10	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)	Silent	SNP	74087670	74087670	9450	14	C	T	T	27	27	LTBP2	T	1	1
SERPINA3	12	broad.mit.edu	36	14	94155411	94155411	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:94155411A>T	uc001ydo.2	+	c.845A>T	c.(844-846)GAG>GTG	p.E282V	SERPINA3_uc001ydr.1_Intron|SERPINA3_uc001ydq.1_Missense_Mutation_p.E257V|SERPINA3_uc001ydp.1_Missense_Mutation_p.E257V|SERPINA3_uc001yds.1_Missense_Mutation_p.E257V|SERPINA3_uc010avg.1_Missense_Mutation_p.E257V	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	257					acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)	5		all_cancers(154;0.0525)|all_epithelial(191;0.179)												0.222222	8.691252	9.968558	4	14	AA		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)	Missense_Mutation	SNP	94155411	94155411	14578	14	A	T	T	11	11	SERPINA3	T	4	4
CYLD	1540	broad.mit.edu	36	16	49341401	49341401	+	Silent	SNP	A	G	G			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49341401A>G	uc002egp.1	+	c.291A>G	c.(289-291)ACA>ACG	p.T97T	CYLD_uc002egn.1_Silent_p.T97T|CYLD_uc002ego.2_Silent_p.T97T|CYLD_uc010cbs.1_Silent_p.T97T|CYLD_uc002egq.1_Silent_p.T97T|CYLD_uc002egr.1_Silent_p.T97T|CYLD_uc002egs.1_Silent_p.T97T	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD	97					cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)								247				0.315789	50.229396	51.949912	18	39	AA		KEEP	---	---	---	---	capture			Silent	SNP	49341401	49341401	4308	16	A	G	G	7	7	CYLD	G	4	4
ACCN1	40	broad.mit.edu	36	17	29507544	29507544	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:29507544G>A	uc002hhu.1	-	c.121C>T	c.(121-123)CGG>TGG	p.R41W		NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal	41	Helical; (Potential).				central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)			Amiloride(DB00594)									0.3	23.664338	24.735929	9	21	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Missense_Mutation	SNP	29507544	29507544	129	17	G	A	A	39	39	ACCN1	A	1	1
KRT222	125113	broad.mit.edu	36	17	36066304	36066304	+	Nonsense_Mutation	SNP	A	C	C			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36066304A>C	uc002hvc.2	-	c.764T>G	c.(763-765)TTA>TGA	p.L255*	KRT222_uc002hvb.2_Nonsense_Mutation_p.L215*	NM_152349	NP_689562	Q8N1A0	KT222_HUMAN	truncated type I keratin KA21	255						intermediate filament	structural molecule activity			central_nervous_system(1)	1														0.138889	8.852178	13.387844	5	31	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	36066304	36066304	8774	17	A	C	C	13	13	KRT222	C	5	4
BRCA1	672	broad.mit.edu	36	17	38498129	38498129	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38498129G>A	uc002ict.1	-	c.2945C>T	c.(2944-2946)CCA>CTA	p.P982L	BRCA1_uc002ico.1_Missense_Mutation_p.P982L|BRCA1_uc002icp.2_Missense_Mutation_p.P911L|BRCA1_uc002icq.1_Missense_Mutation_p.P982L|BRCA1_uc002icr.1_Missense_Mutation_p.P982L|BRCA1_uc002ics.1_Missense_Mutation_p.P686L|BRCA1_uc002icu.1_Intron|BRCA1_uc010cyx.1_Missense_Mutation_p.P935L|BRCA1_uc002icw.1_Missense_Mutation_p.P982L|BRCA1_uc002icv.1_Intron|BRCA1_uc002icx.1_Intron|BRCA1_uc002icy.1_Missense_Mutation_p.P941L|BRCA1_uc002icz.1_Intron|BRCA1_uc002ida.1_Intron|BRCA1_uc002idb.1_Missense_Mutation_p.P982L|BRCA1_uc002idc.1_Intron|BRCA1_uc002idd.2_Missense_Mutation_p.P982L|BRCA1_uc002ide.1_Missense_Mutation_p.P813L|BRCA1_uc010cyy.1_Missense_Mutation_p.P982L|BRCA1_uc010cyz.1_Missense_Mutation_p.P935L|BRCA1_uc010cza.1_Missense_Mutation_p.P956L	NM_007296	NP_009227	P38398	BRCA1_HUMAN	breast cancer 1, early onset isoform 1	982					androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of protein ubiquitination|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription activator activity|transcription coactivator activity|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(17)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)|lung(1)	45		Breast(137;0.000717)								296	TCGA Ovarian(2;0.000030)			0.333333	64.603313	66.3001	23	46	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.126)	Missense_Mutation	SNP	38498129	38498129	1529	17	G	A	A	47	47	BRCA1	A	2	2
LRRC46	90506	broad.mit.edu	36	17	43268714	43268714	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:43268714G>C	uc002ima.1	+	c.469G>C	c.(469-471)GCC>CCC	p.A157P	LRRC46_uc002imb.1_Missense_Mutation_p.A110P	NM_033413	NP_219481	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	157	LRRCT.									ovary(1)	1														0.217391	7.966787	9.660218	5	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43268714	43268714	9378	17	G	C	C	34	34	LRRC46	C	3	3
MGAT5B	146664	broad.mit.edu	36	17	72412019	72412019	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:72412019G>A	uc002jti.1	+	c.643G>A	c.(643-645)GTC>ATC	p.V215I	MGAT5B_uc002jth.1_Missense_Mutation_p.V204I	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	beta(1,6)-N-acetylglucosaminyltransferase V	204	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)	2														0.5	10.597303	10.597303	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72412019	72412019	9939	17	G	A	A	44	44	MGAT5B	A	2	2
ENGASE	64772	broad.mit.edu	36	17	74593411	74593411	+	Silent	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:74593411G>A	uc002jwv.1	+	c.1815G>A	c.(1813-1815)CAG>CAA	p.Q605Q	ENGASE_uc002jww.1_Silent_p.Q310Q	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	605						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity				0														0.3	8.321237	8.67853	3	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	74593411	74593411	5311	17	G	A	A	35	35	ENGASE	A	2	2
DSC1	1823	broad.mit.edu	36	18	26964544	26964544	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:26964544C>T	uc002kwn.1	-	c.2616G>A	c.(2614-2616)GAG>GAA	p.E872E	DSC1_uc002kwm.1_3'UTR	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein	872	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)	3														0.375	61.860443	62.6288	21	35	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00778)		Silent	SNP	26964544	26964544	4949	18	C	T	T	24	24	DSC1	T	2	2
DOK6	220164	broad.mit.edu	36	18	65496058	65496058	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:65496058G>A	uc002lkl.1	+	c.398G>A	c.(397-399)CGG>CAG	p.R133Q		NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6	133	IRS-type PTB.						insulin receptor binding			central_nervous_system(1)	1		Colorectal(73;0.083)|Esophageal squamous(42;0.131)												0.2	9.288281	10.962545	4	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65496058	65496058	4885	18	G	A	A	39	39	DOK6	A	1	1
EEF2	1938	broad.mit.edu	36	19	3930828	3930828	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3930828G>C	uc002lze.1	-	c.1583C>G	c.(1582-1584)GCC>GGC	p.A528G		NM_001961	NP_001952	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	528						cytosol|ribonucleoprotein complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0		Hepatocellular(1079;0.137)				Colon(165;1804 1908 4071 6587 18799)								0.2	7.72078	9.372402	4	16	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3930828	3930828	5116	19	G	C	C	42	42	EEF2	C	3	3
CATSPERG	57828	broad.mit.edu	36	19	43553029	43553029	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43553029C>T	uc002oih.2	+	c.3237C>T	c.(3235-3237)GGC>GGT	p.G1079G	CATSPERG_uc002oig.2_Silent_p.G1039G|CATSPERG_uc002oif.2_Silent_p.G719G|CATSPERG_uc010efw.1_Non-coding_Transcript	NM_021185	NP_067008	Q6ZRH7	CTSRG_HUMAN	hypothetical protein LOC57828	1079	Helical; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)	1														0.15	8.353594	13.032467	6	34	CC		KEEP	---	---	---	---	capture			Silent	SNP	43553029	43553029	2811	19	C	T	T	26	26	CATSPERG	T	2	2
ZNF28	7576	broad.mit.edu	36	19	57995014	57995014	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:57995014C>G	uc002qad.1	-	c.1896G>C	c.(1894-1896)GAG>GAC	p.E632D	ZNF28_uc002qac.1_Missense_Mutation_p.E579D|ZNF28_uc010eqe.1_Missense_Mutation_p.E578D|ZNF28_uc010eqf.1_Missense_Mutation_p.E579D	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	632					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1														0.284483	91.027729	95.864864	33	83	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)	Missense_Mutation	SNP	57995014	57995014	18405	19	C	G	G	32	32	ZNF28	G	3	3
ZNF28	7576	broad.mit.edu	36	19	57996027	57996027	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:57996027C>T	uc002qad.1	-	c.883G>A	c.(883-885)GCA>ACA	p.A295T	ZNF28_uc002qac.1_Missense_Mutation_p.A242T|ZNF28_uc010eqe.1_Missense_Mutation_p.A241T|ZNF28_uc010eqf.1_Missense_Mutation_p.A242T	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	295					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1														0.303571	42.852319	44.781607	17	39	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)	Missense_Mutation	SNP	57996027	57996027	18405	19	C	T	T	25	25	ZNF28	T	2	2
ZNF28	7576	broad.mit.edu	36	19	57996111	57996111	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:57996111C>G	uc002qad.1	-	c.799G>C	c.(799-801)GAT>CAT	p.D267H	ZNF28_uc002qac.1_Missense_Mutation_p.D214H|ZNF28_uc010eqe.1_Missense_Mutation_p.D213H|ZNF28_uc010eqf.1_Missense_Mutation_p.D214H	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	267					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1														0.34375	70.631139	72.011089	22	42	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)	Missense_Mutation	SNP	57996111	57996111	18405	19	C	G	G	29	29	ZNF28	G	3	3
LILRB3	11025	broad.mit.edu	36	19	59438407	59438407	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59438407C>T	uc010erh.1	-	c.6G>A	c.(4-6)ACG>ACA	p.T2T	LILRB3_uc002qes.1_Silent_p.T2T|LILRB3_uc002qeg.1_Non-coding_Transcript|LILRB3_uc002qeh.1_Silent_p.T2T|LILRB3_uc002qei.1_Silent_p.T2T|LILRB3_uc002qej.1_Non-coding_Transcript|LILRA6_uc002qek.1_Silent_p.T2T|LILRA6_uc002qel.1_Silent_p.T2T|LILRA6_uc002qem.1_Non-coding_Transcript|LILRB3_uc002qen.1_Non-coding_Transcript|LILRB3_uc002qeo.1_Silent_p.T2T|LILRB3_uc002qep.1_Silent_p.T2T|LILRB3_uc002qeq.1_Silent_p.T2T|LILRB3_uc002qer.1_Non-coding_Transcript|LILRA6_uc002qet.2_Non-coding_Transcript|LILRA6_uc002qeu.1_Silent_p.T2T|LILRA6_uc002qev.1_5'Flank|LILRA6_uc002qew.1_Intron	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,	2					cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			ovary(1)	1	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)													0.2	6.717184	7.972206	3	12	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.105)	Silent	SNP	59438407	59438407	9118	19	C	T	T	27	27	LILRB3	T	1	1
NLRP7	199713	broad.mit.edu	36	19	60141400	60141400	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60141400C>T	uc010esl.1	-	c.2037G>A	c.(2035-2037)CCG>CCA	p.P679P	NLRP7_uc002qig.2_Intron|NLRP7_uc002qii.2_Silent_p.P651P|NLRP7_uc002qih.2_Silent_p.P651P|NLRP7_uc010esk.1_Silent_p.P651P	NM_001127255	NP_001120727	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	651			P -> S (in HYDM).				ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3														0.170732	13.105451	17.305063	7	34	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0325)	Silent	SNP	60141400	60141400	10885	19	C	T	T	31	31	NLRP7	T	1	1
PRMT6	55170	broad.mit.edu	36	1	107401838	107401838	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:107401838C>G	uc001dvb.1	+	c.801C>G	c.(799-801)AAC>AAG	p.N267K		NM_018137	NP_060607	Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	326					base-excision repair|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|histone methyltransferase activity (H2A-R3 specific)|histone methyltransferase activity (H3-R2 specific)|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity				0		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)												0.272727	7.622035	8.133049	3	8	CC		KEEP	---	---	---	---	capture		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)	Missense_Mutation	SNP	107401838	107401838	12983	1	C	G	G	19	19	PRMT6	G	3	3
SLAMF8	56833	broad.mit.edu	36	1	158069415	158069415	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158069415C>T	uc001fue.2	+	c.493C>T	c.(493-495)CGA>TGA	p.R165*		NM_020125	NP_064510	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	165	Ig-like C2-type.|Extracellular (Potential).					integral to membrane					0	all_hematologic(112;0.0597)													0.217391	18.642633	22.021853	10	36	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	158069415	158069415	14865	1	C	T	T	27	27	SLAMF8	T	5	1
SOAT1	6646	broad.mit.edu	36	1	177576889	177576889	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:177576889T>G	uc001gml.1	+	c.601T>G	c.(601-603)TTT>GTT	p.F201V	SOAT1_uc001gmm.1_Missense_Mutation_p.F143V	NM_003101	NP_003092	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	201					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)	1					Ezetimibe(DB00973)|Hesperetin(DB01094)									0.20202	51.44455	59.610515	20	79	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	177576889	177576889	15410	1	T	G	G	64	64	SOAT1	G	4	4
HMCN1	83872	broad.mit.edu	36	1	184355549	184355549	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184355549C>T	uc001grq.1	+	c.12006C>T	c.(12004-12006)AAC>AAT	p.N4002N		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	4002	Ig-like C2-type 39.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.451613	38.842996	38.906576	14	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	184355549	184355549	7511	1	C	T	T	17	17	HMCN1	T	2	2
ZNF683	257101	broad.mit.edu	36	1	26563834	26563834	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:26563834C>T	uc001bmg.1	-	c.790G>A	c.(790-792)GGC>AGC	p.G264S	ZNF683_uc001bmh.1_Missense_Mutation_p.G264S|ZNF683_uc009vsj.1_Missense_Mutation_p.G264S	NM_173574	NP_775845	Q8IZ20	ZN683_HUMAN	zinc finger protein 683	264					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)												0.266667	28.277319	30.49237	12	33	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)	Missense_Mutation	SNP	26563834	26563834	18685	1	C	T	T	21	21	ZNF683	T	2	2
GJB4	127534	broad.mit.edu	36	1	35000234	35000234	+	Silent	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:35000234G>T	uc001bxv.1	+	c.792G>T	c.(790-792)GGG>GGT	p.G264G	GJB4_uc001bxw.2_Silent_p.G264G	NM_153212	NP_694944	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4	264	Cytoplasmic (Potential).				cell communication	connexon complex|integral to membrane	gap junction channel activity			ovary(2)|central_nervous_system(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)												0.357143	7.755078	8.011929	5	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	35000234	35000234	6678	1	G	T	T	44	44	GJB4	T	3	3
PTCH2	8643	broad.mit.edu	36	1	45080258	45080258	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:45080258G>C	uc001cms.1	-	c.113C>G	c.(112-114)GCT>GGT	p.A38G		NM_003738	NP_003729	Q9Y6C5	PTC2_HUMAN	patched 2	38	Cytoplasmic (Potential).				protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(4)|breast(3)|central_nervous_system(3)|ovary(1)|skin(1)	12	Acute lymphoblastic leukemia(166;0.155)									193				0.19697	28.136058	33.784209	13	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45080258	45080258	13185	1	G	C	C	34	34	PTCH2	C	3	3
ID1	3397	broad.mit.edu	36	20	29656872	29656872	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:29656872C>G	uc002wwg.1	+	c.21C>G	c.(19-21)AGC>AGG	p.S7R	ID1_uc002wwh.1_Missense_Mutation_p.S7R	NM_002165	NP_002156	P41134	ID1_HUMAN	inhibitor of DNA binding 1 isoform a	7					angiogenesis|blood vessel endothelial cell migration|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by transcription factor localization|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein binding|transcription repressor activity			ovary(1)	1	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)					NSCLC(123;1618 1779 21803 28680 33854)				46				0.6	7.1226	7.165802	3	2	CC		KEEP	---	---	---	---	capture	Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)		Missense_Mutation	SNP	29656872	29656872	7789	20	C	G	G	25	25	ID1	G	3	3
CXADR	1525	broad.mit.edu	36	21	17855600	17855600	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:17855600C>T	uc002yki.1	+	c.768C>T	c.(766-768)ATC>ATT	p.I256I	CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron|CXADR_uc002ykj.1_Silent_p.I229I	NM_001338	NP_001329	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	256	Helical; (Potential).				blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1														0.357143	13.669916	13.922069	5	9	CC		KEEP	---	---	---	---	capture		Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)	Silent	SNP	17855600	17855600	4236	21	C	T	T	29	29	CXADR	T	2	2
UMODL1	89766	broad.mit.edu	36	21	42392204	42392204	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42392204T>G	uc002zag.1	+	c.1031T>G	c.(1030-1032)GTC>GGC	p.V344G	UMODL1_uc002zad.1_Missense_Mutation_p.V272G|UMODL1_uc002zae.1_Missense_Mutation_p.V272G|UMODL1_uc002zaf.1_Missense_Mutation_p.V344G|UMODL1_uc010gow.1_Missense_Mutation_p.V136G|UMODL1_uc002zai.1_Non-coding_Transcript|UMODL1_uc010gox.1_Non-coding_Transcript|UMODL1_uc010goy.1_5'UTR|UMODL1_uc002zaj.1_Non-coding_Transcript|UMODL1_uc010goz.1_Missense_Mutation_p.V89G	NM_173568	NP_775839	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 2 precursor	344	Extracellular (Potential).|Fibronectin type-III 1.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)	2						Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)								0.308642	73.248238	75.889767	25	56	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42392204	42392204	17538	21	T	G	G	58	58	UMODL1	G	4	4
DGCR2	9993	broad.mit.edu	36	22	17424577	17424577	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:17424577G>C	uc002zoq.1	-	c.724C>G	c.(724-726)CCC>GCC	p.P242A	DGCR2_uc002zor.1_Missense_Mutation_p.P18A	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2	242	Extracellular (Potential).				cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)													0.428571	7.838808	7.86621	3	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17424577	17424577	4640	22	G	C	C	43	43	DGCR2	C	3	3
CACNA1I	8911	broad.mit.edu	36	22	38296867	38296867	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38296867C>T	uc003ayc.1	+	c.164C>T	c.(163-165)GCG>GTG	p.A55V	CACNA1I_uc003ayd.1_Missense_Mutation_p.A55V	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	55	Cytoplasmic (Potential).				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)									0.173077	15.542085	20.792715	9	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38296867	38296867	2662	22	C	T	T	27	27	CACNA1I	T	1	1
SLC9A2	6549	broad.mit.edu	36	2	102691088	102691088	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102691088C>A	uc002tca.1	+	c.2147C>A	c.(2146-2148)CCA>CAA	p.P716Q		NM_003048	NP_003039	Q9UBY0	SL9A2_HUMAN	solute carrier family 9 (sodium/hydrogen	716	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			central_nervous_system(3)|breast(2)	5														0.262295	40.570825	43.689982	16	45	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102691088	102691088	15209	2	C	A	A	21	21	SLC9A2	A	3	3
UGGT1	56886	broad.mit.edu	36	2	128583741	128583741	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128583741A>G	uc002tps.1	+	c.472A>G	c.(472-474)ACT>GCT	p.T158A	UGGT1_uc010fme.1_Missense_Mutation_p.T33A|UGGT1_uc002tpr.1_Missense_Mutation_p.T134A	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	158					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1														0.269231	18.51576	19.763826	7	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128583741	128583741	17499	2	A	G	G	10	10	UGGT1	G	4	4
PTH2R	5746	broad.mit.edu	36	2	209016424	209016424	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:209016424G>C	uc002vdb.1	+	c.616G>C	c.(616-618)GGA>CGA	p.G206R		NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	206	Extracellular (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)	1														0.181818	12.228764	15.368694	6	27	GG		KEEP	---	---	---	---	capture		Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Missense_Mutation	SNP	209016424	209016424	13215	2	G	C	C	35	35	PTH2R	C	3	3
COL6A3	1293	broad.mit.edu	36	2	237948193	237948193	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237948193C>T	uc002vwl.2	-	c.3280G>A	c.(3280-3282)GCT>ACT	p.A1094T	COL6A3_uc002vwk.2_Missense_Mutation_p.A1094T|COL6A3_uc002vwm.2_Missense_Mutation_p.A893T|COL6A3_uc002vwn.2_Missense_Mutation_p.A894T|COL6A3_uc002vwo.2_Missense_Mutation_p.A888T|COL6A3_uc002vwq.2_Missense_Mutation_p.A888T|COL6A3_uc002vwr.2_Missense_Mutation_p.A687T	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1094	Nonhelical region.|VWFA 6.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.269231	16.013504	17.263401	7	19	CC		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Missense_Mutation	SNP	237948193	237948193	3839	2	C	T	T	27	27	COL6A3	T	1	1
KBTBD5	131377	broad.mit.edu	36	3	42704724	42704724	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42704724C>T	uc003clv.1	+	c.1239C>T	c.(1237-1239)TCC>TCT	p.S413S		NM_152393	NP_689606	Q2TBA0	KBTB5_HUMAN	kelch repeat and BTB (POZ) domain containing 5	413	Kelch 2.									ovary(1)	1														0.289474	27.108113	28.618719	11	27	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.214)	Silent	SNP	42704724	42704724	8301	3	C	T	T	21	21	KBTBD5	T	2	2
FBXL5	26234	broad.mit.edu	36	4	15241437	15241437	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:15241437T>G	uc003goc.1	-	c.842A>C	c.(841-843)GAA>GCA	p.E281A	FBXL5_uc010idw.1_Missense_Mutation_p.E194A|FBXL5_uc003gob.1_Missense_Mutation_p.E155A|FBXL5_uc010idx.1_Missense_Mutation_p.E280A|FBXL5_uc003god.1_Missense_Mutation_p.E264A|FBXL5_uc010idy.1_Missense_Mutation_p.E281A	NM_012161	NP_277077	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5 isoform	281					iron ion homeostasis|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|SCF ubiquitin ligase complex	iron ion binding|protein binding|ubiquitin-protein ligase activity				0														0.153846	12.528716	16.992916	6	33	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15241437	15241437	5959	4	T	G	G	62	62	FBXL5	G	4	4
CLOCK	9575	broad.mit.edu	36	4	56031663	56031663	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:56031663G>T	uc003haz.1	-	c.416C>A	c.(415-417)ACT>AAT	p.T139N	CLOCK_uc003hba.1_Missense_Mutation_p.T139N	NM_004898	NP_004889	O15516	CLOCK_HUMAN	clock	139	PAS 1.				circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)													0.209677	26.538205	31.378111	13	49	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)		Missense_Mutation	SNP	56031663	56031663	3687	4	G	T	T	36	36	CLOCK	T	3	3
UGT2B7	7364	broad.mit.edu	36	4	69997231	69997231	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:69997231A>T	uc003heg.2	+	c.404A>T	c.(403-405)AAA>ATA	p.K135I	UGT2B7_uc010ihq.1_Missense_Mutation_p.K135I	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family,	135					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)	1														0.32	20.489837	21.21025	8	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69997231	69997231	17520	4	A	T	T	1	1	UGT2B7	T	4	4
UGT2B4	7363	broad.mit.edu	36	4	70385695	70385695	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70385695G>T	uc003hek.2	-	c.1130C>A	c.(1129-1131)GCC>GAC	p.A377D	UGT2B4_uc003hel.2_Intron	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family,	377					estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0														0.226804	48.271422	54.950194	22	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70385695	70385695	17519	4	G	T	T	42	42	UGT2B4	T	3	3
CTNND2	1501	broad.mit.edu	36	5	11289806	11289806	+	Silent	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:11289806G>A	uc003jfa.1	-	c.1758C>T	c.(1756-1758)GCC>GCT	p.A586A	CTNND2_uc010itt.1_Silent_p.A495A|CTNND2_uc010itu.1_Non-coding_Transcript	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	586	ARM 3.				multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|pancreas(1)|lung(1)|skin(1)	7														0.133333	12.222666	19.997735	8	52	GG		KEEP	---	---	---	---	capture			Silent	SNP	11289806	11289806	4179	5	G	A	A	39	39	CTNND2	A	1	1
SLIT3	6586	broad.mit.edu	36	5	168030800	168030800	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168030800C>T	uc010jjg.1	-	c.4129G>A	c.(4129-4131)GAC>AAC	p.D1377N	SLIT3_uc003mab.1_Missense_Mutation_p.D1370N	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	1370	EGF-like 8.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)				Ovarian(29;311 847 10864 17279 24903)								0.26087	13.338069	14.529886	6	17	CC		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	168030800	168030800	15239	5	C	T	T	30	30	SLIT3	T	2	2
ARID1B	57492	broad.mit.edu	36	6	157495867	157495867	+	Silent	SNP	C	G	G			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:157495867C>G	uc003qqn.1	+	c.2172C>G	c.(2170-2172)GGC>GGG	p.G724G	ARID1B_uc003qqo.1_Silent_p.G737G|ARID1B_uc003qqp.1_Silent_p.G724G|ARID1B_uc003qqq.1_Silent_p.G166G	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	782					chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			breast(1)	1		Breast(66;0.000162)|Ovarian(120;0.0265)												0.4	8.807199	8.891266	4	6	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)	Silent	SNP	157495867	157495867	929	6	C	G	G	25	25	ARID1B	G	3	3
PLG	5340	broad.mit.edu	36	6	161047522	161047522	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:161047522A>G	uc003qtm.2	+	c.143A>G	c.(142-144)GAA>GGA	p.E48G		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	48	PAN.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			ovary(1)	1					Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)									0.296296	44.878065	46.882792	16	38	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Missense_Mutation	SNP	161047522	161047522	12512	6	A	G	G	9	9	PLG	G	4	4
KIF13A	63971	broad.mit.edu	36	6	17934272	17934272	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:17934272A>G	uc003ncg.2	-	c.1595T>C	c.(1594-1596)CTA>CCA	p.L532P	KIF13A_uc003ncf.2_Missense_Mutation_p.L532P|KIF13A_uc003nch.2_Missense_Mutation_p.L532P|KIF13A_uc003nci.2_Missense_Mutation_p.L532P|KIF13A_uc003ncj.2_Missense_Mutation_p.L208P	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	532					cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)												0.128205	8.148594	13.400718	5	34	AA		KEEP	---	---	---	---	capture	all cancers(50;0.0865)|Epithelial(50;0.0974)		Missense_Mutation	SNP	17934272	17934272	8585	6	A	G	G	15	15	KIF13A	G	4	4
BTNL2	56244	broad.mit.edu	36	6	32480700	32480700	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32480700C>T	uc003obg.1	-	c.421G>A	c.(421-423)GTA>ATA	p.V141I	BTNL2_uc010jty.1_Intron|BTNL2_uc010jtz.1_Intron|BTNL2_uc010jua.1_Intron	NM_019602	NP_062548	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2	141	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1														0.230769	19.953362	22.545422	9	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32480700	32480700	1599	6	C	T	T	20	20	BTNL2	T	2	2
CGA	1081	broad.mit.edu	36	6	87852731	87852731	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:87852731C>T	uc003plj.1	-	c.229G>A	c.(229-231)GTC>ATC	p.V77I		NM_000735	NP_000726	P01215	GLHA_HUMAN	glycoprotein hormones, alpha polypeptide	77					hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity			ovary(1)	1		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)												0.282051	55.81845	59.146772	22	56	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0484)	Missense_Mutation	SNP	87852731	87852731	3428	6	C	T	T	19	19	CGA	T	1	1
GIMAP4	55303	broad.mit.edu	36	7	149900724	149900724	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149900724C>T	uc003whl.1	+	c.633C>T	c.(631-633)CGC>CGT	p.R211R		NM_018326	NP_060796	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	211	Potential.						GTP binding			ovary(1)	1														0.240741	30.651825	33.96146	13	41	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Silent	SNP	149900724	149900724	6649	7	C	T	T	27	27	GIMAP4	T	1	1
PDE1C	5137	broad.mit.edu	36	7	31822113	31822113	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:31822113C>T	uc003tco.1	-	c.1943G>A	c.(1942-1944)CGT>CAT	p.R648H	PDE1C_uc003tcm.1_Missense_Mutation_p.R588H|PDE1C_uc003tcn.1_Missense_Mutation_p.R588H|PDE1C_uc003tcr.1_Missense_Mutation_p.R588H|PDE1C_uc003tcs.1_Missense_Mutation_p.R588H	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent	588					activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			central_nervous_system(1)	1														0.253333	93.119093	101.379378	38	112	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(11;0.216)		Missense_Mutation	SNP	31822113	31822113	12056	7	C	T	T	19	19	PDE1C	T	1	1
C7orf10	79783	broad.mit.edu	36	7	40194637	40194637	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:40194637G>A	uc003thn.1	+	c.245G>A	c.(244-246)CGA>CAA	p.R82Q	C7orf10_uc003thm.1_Missense_Mutation_p.R89Q|C7orf10_uc003tho.1_Missense_Mutation_p.R82Q	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	hypothetical protein LOC79783	89							transferase activity			ovary(2)	2														0.227273	11.565161	13.06596	5	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40194637	40194637	2483	7	G	A	A	37	37	C7orf10	A	1	1
POM121	9883	broad.mit.edu	36	7	72051179	72051179	+	Missense_Mutation	SNP	A	C	C	rs437678	by-frequency	TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72051179A>C	uc003twk.2	+	c.2711A>C	c.(2710-2712)CAC>CCC	p.H904P	POM121_uc003twj.1_Missense_Mutation_p.H639P|POM121_uc010lam.1_Missense_Mutation_p.H639P	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	904	Thr-rich.|Pore side (Potential).			H -> P (in Ref. 3; BAB14097).	carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)												0.106383	6.343085	13.570047	5	42	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72051179	72051179	12667	7	A	C	C	6	6	POM121	C	4	4
PCLO	27445	broad.mit.edu	36	7	82419405	82419405	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82419405C>T	uc003uhx.2	-	c.8800G>A	c.(8800-8802)GCA>ACA	p.A2934T	PCLO_uc003uhv.2_Missense_Mutation_p.A2934T|PCLO_uc010lec.1_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2865					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														0.179487	26.102345	33.642191	14	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82419405	82419405	12003	7	C	T	T	27	27	PCLO	T	1	1
SAMD9L	219285	broad.mit.edu	36	7	92599236	92599236	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92599236T>C	uc003umh.1	-	c.3985A>G	c.(3985-3987)AGG>GGG	p.R1329G	SAMD9L_uc003umj.1_Missense_Mutation_p.R1329G|SAMD9L_uc003umi.1_Missense_Mutation_p.R1329G|SAMD9L_uc010lfb.1_Missense_Mutation_p.R1329G|SAMD9L_uc003umk.1_Missense_Mutation_p.R1329G|SAMD9L_uc010lfc.1_Missense_Mutation_p.R1329G|SAMD9L_uc010lfd.1_Missense_Mutation_p.R1329G|SAMD9L_uc010lfe.1_Missense_Mutation_p.R1329G	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1329										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)													0.242857	40.03731	44.260145	17	53	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000302)		Missense_Mutation	SNP	92599236	92599236	14307	7	T	C	C	55	55	SAMD9L	C	4	4
HEPACAM2	253012	broad.mit.edu	36	7	92686532	92686532	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92686532G>A	uc003umm.1	-	c.248C>T	c.(247-249)TCT>TTT	p.S83F	HEPACAM2_uc003uml.1_Missense_Mutation_p.S71F|HEPACAM2_uc010lff.1_Missense_Mutation_p.S71F	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	83	Extracellular (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.235294	27.972483	31.243003	12	39	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92686532	92686532	7336	7	G	A	A	33	33	HEPACAM2	A	2	2
KIAA0196	9897	broad.mit.edu	36	8	126125302	126125302	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:126125302C>T	uc003yrt.1	-	c.2797G>A	c.(2797-2799)GCC>ACC	p.A933T	KIAA0196_uc003yru.1_Missense_Mutation_p.A507T	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin	933					cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)													0.296296	19.7892	20.791476	8	19	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Missense_Mutation	SNP	126125302	126125302	8468	8	C	T	T	27	27	KIAA0196	T	1	1
GPR20	2843	broad.mit.edu	36	8	142436411	142436411	+	Silent	SNP	C	A	A			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:142436411C>A	uc003ywf.1	-	c.795G>T	c.(793-795)GCG>GCT	p.A265A	GPR20_uc010mer.1_Silent_p.A265A	NM_005293	NP_005284	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	265	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)													0.357143	26.846262	27.347656	10	18	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0415)		Silent	SNP	142436411	142436411	6955	8	C	A	A	27	27	GPR20	A	3	3
FAM83H	286077	broad.mit.edu	36	8	144882286	144882286	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144882286T>G	uc003yzk.1	-	c.1333A>C	c.(1333-1335)ACC>CCC	p.T445P	FAM83H_uc010mfk.1_Non-coding_Transcript	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	hypothetical protein LOC286077	445					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.6	6.495497	6.533948	3	2	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)		Missense_Mutation	SNP	144882286	144882286	5866	8	T	G	G	58	58	FAM83H	G	4	4
TRIM35	23087	broad.mit.edu	36	8	27224367	27224367	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:27224367G>C	uc003xfl.1	-	c.303C>G	c.(301-303)TGC>TGG	p.C101W	PTK2B_uc003xfn.1_5'Flank|PTK2B_uc003xfo.1_5'Flank|TRIM35_uc010lup.1_Missense_Mutation_p.C101W|TRIM35_uc003xfm.1_Non-coding_Transcript	NM_171982	NP_741983	Q9UPQ4	TRI35_HUMAN	tripartite motif-containing 35 isoform 2	101	B box-type.				apoptosis|induction of apoptosis|negative regulation of mitotic cell cycle	cytoplasm|nucleus	zinc ion binding				0		Ovarian(32;2.61e-05)												0.363636	8.594356	8.775235	4	7	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)	Missense_Mutation	SNP	27224367	27224367	17053	8	G	C	C	42	42	TRIM35	C	3	3
KCNU1	157855	broad.mit.edu	36	8	36813016	36813016	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0649-01	TCGA-06-0649-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:36813016T>A	uc010lvw.1	+	c.1340T>A	c.(1339-1341)ATA>AAA	p.I447K	KCNU1_uc003xjw.2_Non-coding_Transcript	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	447	RCK N-terminal.|Cytoplasmic (Potential).					voltage-gated potassium channel complex	binding|catalytic activity|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.205882	15.40491	18.134203	7	27	TT		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)	Missense_Mutation	SNP	36813016	36813016	8398	8	T	A	A	49	49	KCNU1	A	4	4
JPH1	56704	broad.mit.edu	36	8	75319703	75319703	+	Missense_Mutation	SNP	G	A	A	rs16938829	by-frequency,by-hapmap	TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:75319703G>A	uc003yae.1	-	c.1520C>T	c.(1519-1521)ACG>ATG	p.T507M	JPH1_uc003yaf.2_Missense_Mutation_p.T507M|JPH1_uc003yag.1_Missense_Mutation_p.T371M	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	507	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)													0.298246	44.491715	46.543581	17	40	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)		Missense_Mutation	SNP	75319703	75319703	8264	8	G	A	A	40	40	JPH1	A	1	1
TTC16	158248	broad.mit.edu	36	9	129529108	129529108	+	Silent	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:129529108G>T	uc004brq.1	+	c.1464G>T	c.(1462-1464)TCG>TCT	p.S488S	PTRH1_uc004brp.1_5'Flank|TTC16_uc004brr.1_Intron|TTC16_uc010mxn.1_Silent_p.S84S	NM_144965	NP_659402	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	488							binding				0														0.24	42.619444	47.242638	18	57	GG		KEEP	---	---	---	---	capture			Silent	SNP	129529108	129529108	17237	9	G	T	T	39	39	TTC16	T	3	3
RXRA	6256	broad.mit.edu	36	9	136448960	136448960	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:136448960A>T	uc004cfb.1	+	c.746A>T	c.(745-747)TAC>TTC	p.Y249F	RXRA_uc004cfc.1_Missense_Mutation_p.Y152F|RXRA_uc004cfd.1_Missense_Mutation_p.Y20F	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha	249	Ligand-binding.				cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of gene-specific transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			ovary(1)	1					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)					303				0.444444	32.991126	33.064281	12	15	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Missense_Mutation	SNP	136448960	136448960	14243	9	A	T	T	14	14	RXRA	T	4	4
SMARCA2	6595	broad.mit.edu	36	9	2094169	2094169	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:2094169G>A	uc003zhc.1	+	c.3292G>A	c.(3292-3294)GGC>AGC	p.G1098S	SMARCA2_uc003zhd.1_Missense_Mutation_p.G1098S|SMARCA2_uc010mha.1_Missense_Mutation_p.G1031S	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	1098	Helicase C-terminal.				chromatin remodeling|negative regulation of gene-specific transcription from RNA polymerase II promoter|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein binding|transcription activator activity|transcription coactivator activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)												0.285714	16.144472	17.007908	6	15	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;0.0475)	Missense_Mutation	SNP	2094169	2094169	15267	9	G	A	A	47	47	SMARCA2	A	2	2
DOCK8	81704	broad.mit.edu	36	9	408102	408102	+	Silent	SNP	G	C	C			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:408102G>C	uc003zgf.1	+	c.3735G>C	c.(3733-3735)TCG>TCC	p.S1245S	DOCK8_uc003zgi.1_Silent_p.S1177S|DOCK8_uc010mgu.1_Silent_p.S547S|DOCK8_uc010mgv.1_Silent_p.S1145S|DOCK8_uc003zgk.1_Silent_p.S703S	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1245					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)												0.291667	8.305296	9.320319	7	17	GG		KEEP	---	---	---	---	capture		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)	Silent	SNP	408102	408102	4877	9	G	C	C	39	39	DOCK8	C	3	3
TRPM6	140803	broad.mit.edu	36	9	76567768	76567768	+	Silent	SNP	A	G	G			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:76567768A>G	uc004ajl.1	-	c.3639T>C	c.(3637-3639)GAT>GAC	p.D1213D	TRPM6_uc004ajj.1_Silent_p.D169D|TRPM6_uc004ajk.1_Silent_p.D1208D|TRPM6_uc010mpb.1_Non-coding_Transcript|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	1213	Cytoplasmic (Potential).				protein phosphorylation|response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4										879				0.2	21.138322	25.313247	10	40	AA		KEEP	---	---	---	---	capture			Silent	SNP	76567768	76567768	17141	9	A	G	G	12	12	TRPM6	G	4	4
SLC25A14	9016	broad.mit.edu	36	X	129334582	129334582	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:129334582C>A	uc004evr.1	+	c.1039C>A	c.(1039-1041)CAG>AAG	p.Q347K	SLC25A14_uc004evn.1_Missense_Mutation_p.Q319K|SLC25A14_uc004evo.1_Missense_Mutation_p.Q140K|SLC25A14_uc004evp.1_Missense_Mutation_p.Q319K|SLC25A14_uc004evq.1_Missense_Mutation_p.Q316K	NM_022810	NP_073721	O95258	UCP5_HUMAN	solute carrier family 25, member 14 isoform	319	Solcar 3.				aerobic respiration|mitochondrial transport	integral to plasma membrane|mitochondrial inner membrane	binding			ovary(1)	1														0.197531	68.100233	81.908958	32	130	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129334582	129334582	14973	23	C	A	A	25	25	SLC25A14	A	3	3
SPANXN3	139067	broad.mit.edu	36	X	142424520	142424520	+	Silent	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142424520C>T	uc004fbw.1	-	c.216G>A	c.(214-216)CAG>CAA	p.Q72Q		NM_001009609	NP_001009609	Q5MJ09	SPXN3_HUMAN	SPANX-N3 protein	72										ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.239437	41.136415	45.540071	17	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	142424520	142424520	15500	23	C	T	T	20	20	SPANXN3	T	2	2
UBE2NL	389898	broad.mit.edu	36	X	142795032	142795032	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142795032G>A	uc004fca.1	+	c.164G>A	c.(163-165)CGT>CAT	p.R55H		NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like	55					post-translational protein modification		acid-amino acid ligase activity				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.273684	64.108163	68.49327	26	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142795032	142795032	17424	23	G	A	A	40	40	UBE2NL	A	1	1
UBE2NL	389898	broad.mit.edu	36	X	142795094	142795094	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142795094A>G	uc004fca.1	+	c.226A>G	c.(226-228)ATT>GTT	p.I76V		NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like	76					post-translational protein modification		acid-amino acid ligase activity				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.291667	55.838286	58.643049	21	51	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142795094	142795094	17424	23	A	G	G	4	4	UBE2NL	G	4	4
IRAK1	3654	broad.mit.edu	36	X	152932039	152932039	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0649-01	TCGA-06-0649-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152932039C>T	uc004fjs.1	-	c.1579G>A	c.(1579-1581)GGG>AGG	p.G527R	IRAK1_uc004fjr.1_Intron|IRAK1_uc004fjt.1_Missense_Mutation_p.G448R|IRAK1_uc010nur.1_Intron	NM_001569	NP_001560	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	527					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|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|transmembrane receptor protein serine/threonine kinase signaling pathway	cytosol|endosome membrane|interleukin-1 receptor complex	ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|transcription activator activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|breast(1)|central_nervous_system(1)	8	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)									83				0.3	15.592147	16.279037	6	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152932039	152932039	8124	23	C	T	T	22	22	IRAK1	T	2	2
F8	2157	broad.mit.edu	36	X	153878486	153878486	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0649-01	TCGA-06-0649-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153878486A>T	uc004fmt.1	-	c.344T>A	c.(343-345)GTC>GAC	p.V115D		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	115	Plastocyanin-like 1.|F5/8 type A 1.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)					359				0.258427	51.780628	56.490164	23	66	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153878486	153878486	5544	23	A	T	T	10	10	F8	T	4	4
DDX53	168400	broad.mit.edu	36	X	22929373	22929373	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:22929373G>T	uc004daj.1	+	c.1278G>T	c.(1276-1278)ATG>ATT	p.M426I		NM_182699	NP_874358	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	426	Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			large_intestine(1)|kidney(1)	2														0.244681	52.273783	57.860522	23	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22929373	22929373	4542	23	G	T	T	45	45	DDX53	T	3	3
PIM2	11040	broad.mit.edu	36	X	48660765	48660765	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0649-01	TCGA-06-0649-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48660765G>A	uc004dls.1	-	c.163C>T	c.(163-165)CGA>TGA	p.R55*		NM_006875	NP_006866	Q9P1W9	PIM2_HUMAN	pim-2 oncogene	55	Protein kinase.				anti-apoptosis|cell proliferation|male meiosis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein phosphorylation|response to virus		ATP binding|protein serine/threonine kinase activity			lung(2)|stomach(1)	3										33				0.275862	19.991146	21.300664	8	21	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	48660765	48660765	12352	23	G	A	A	37	37	PIM2	A	5	1
MTFMT	123263	broad.mit.edu	36	15	63099597	63099597	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0649-01	TCGA-06-0649-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:63099597_63099597delC	uc002aof.2	-	c.712_712delG	c.(712-714)GCGfs	p.A238fs		NM_139242	NP_640335	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	238						mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)									0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	63099597	63099597	10317	15	C	-	-	26	26	MTFMT	-	5	5
RFC4	5984	broad.mit.edu	36	3	187990865	187990867	+	In_Frame_Del	DEL	CAT	-	-			TCGA-06-0649-01	TCGA-06-0649-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:187990865_187990867delCAT	uc003fqy.1	-	c.824_826delATG	c.(823-828)GATGGA>GGA	p.D275del	RFC4_uc003fqz.1_In_Frame_Del_p.D275del	NM_181573	NP_853551	P35249	RFC4_HUMAN	replication factor C 4	275					cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)						599				0.33			13	26				---	---	---	---	capture_indel			In_Frame_Del	DEL	187990865	187990867	13718	3	CAT	-	-	21	21	RFC4	-	5	5
TRIM50	135892	broad.mit.edu	36	7	72365285	72365286	+	Frame_Shift_Ins	INS	-	GGAA	GGAA			TCGA-06-0649-01	TCGA-06-0649-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:72365285_72365286insGGAA	uc010lbd.1	-	c.1031_1032insTTCC	c.(1030-1032)TTCfs	p.F344fs	FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Frame_Shift_Ins_p.F344fs|TRIM50_uc003txz.1_Frame_Shift_Ins_p.F343fs	NM_178125	NP_835226	Q86XT4	TRI50_HUMAN	tripartite motif protein 50A	344	B30.2/SPRY.					cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding				0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	72365285	72365286	17072	7	-	GGAA	GGAA	33	33	TRIM50	GGAA	5	5
