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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
ATE1	11101	broad.mit.edu	37	10	123670659	123670659	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:123670659G>A	uc001lfp.2	-	c.345C>T	c.(343-345)CCC>CCT	p.P115P	ATE1_uc001lfq.2_Silent_p.P115P|ATE1_uc010qtr.1_5'UTR|ATE1_uc010qts.1_Silent_p.P19P|ATE1_uc010qtt.1_Silent_p.P108P|ATE1_uc001lfr.2_5'UTR|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2	115					protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)												0.5625	91.729623	91.892796	27	21	KEEP	---	---	---	---	capture		Silent	SNP	123670659	123670659	1097	10	G	A	A	A	600	47	ATE1	2	2
TAF3	83860	broad.mit.edu	37	10	7860740	7860740	+	Missense_Mutation	SNP	G	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7860740G>T	uc010qbd.1	+	c.68G>T	c.(67-69)TGG>TTG	p.W23L		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	23				W->R: Loss of interaction with TAF10.|WDS -> TRP (in Ref. 4; CAB56032).	maintenance of protein location in nucleus|regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1														0.777778	23.629302	24.267765	7	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7860740	7860740	16046	10	G	T	T	T	611	47	TAF3	2	2
WAPAL	23063	broad.mit.edu	37	10	88213467	88213467	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:88213467C>G	uc001kdn.2	-	c.2890G>C	c.(2890-2892)GAG>CAG	p.E964Q	WAPAL_uc009xsv.2_Missense_Mutation_p.E241Q|WAPAL_uc001kdo.2_Missense_Mutation_p.E927Q|WAPAL_uc009xsw.2_Missense_Mutation_p.E921Q	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog	927	WAPL.				cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1														0.5	65.433074	65.433074	19	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88213467	88213467	17820	10	C	G	G	G	390	30	WAPAL	3	3
BMPR1A	657	broad.mit.edu	37	10	88677025	88677025	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:88677025C>T	uc001kdy.2	+	c.810C>T	c.(808-810)AGC>AGT	p.S270S		NM_004329	NP_004320	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	270	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|protein phosphorylation|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			stomach(1)|large_intestine(1)|lung(1)|central_nervous_system(1)|kidney(1)	5						Ovarian(190;603 2086 22044 30335 47971)				207				0.4	12.29772	12.385254	4	6	KEEP	---	---	---	---	capture		Silent	SNP	88677025	88677025	1494	10	C	T	T	T	363	28	BMPR1A	2	2
ARHGEF12	23365	broad.mit.edu	37	11	120298837	120298837	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:120298837C>T	uc001pxl.1	+	c.466C>T	c.(466-468)CTT>TTT	p.L156F	ARHGEF12_uc009zat.2_Missense_Mutation_p.L137F|ARHGEF12_uc010rzn.1_Missense_Mutation_p.L53F|ARHGEF12_uc009zau.1_Missense_Mutation_p.L53F	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	156					apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)						1000				0.343949	159.71327	163.084932	54	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120298837	120298837	911	11	C	T	T	T	260	20	ARHGEF12	2	2
VSIG2	23584	broad.mit.edu	37	11	124619682	124619682	+	Missense_Mutation	SNP	C	T	T	rs114520645	by1000genomes	TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124619682C>T	uc001qas.2	-	c.508G>A	c.(508-510)GAG>AAG	p.E170K	VSIG2_uc001qat.2_Missense_Mutation_p.E170K	NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	170	Extracellular (Potential).|Ig-like C2-type.					integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)										0.245902	39.808567	43.385367	15	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124619682	124619682	17792	11	C	T	T	T	403	31	VSIG2	1	1
SLC39A13	91252	broad.mit.edu	37	11	47431696	47431696	+	Silent	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47431696C>G	uc009ylq.2	+	c.51C>G	c.(49-51)CTC>CTG	p.L17L	SLC39A13_uc001nfd.2_Silent_p.L17L|SLC39A13_uc001nfe.1_Non-coding_Transcript|SLC39A13_uc001nff.3_Silent_p.L17L|SLC39A13_uc001nfg.3_Silent_p.L17L	NM_001128225	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter),	17	Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)										0.285714	87.226094	91.541021	30	75	KEEP	---	---	---	---	capture		Silent	SNP	47431696	47431696	15113	11	C	G	G	G	405	32	SLC39A13	3	3
OR4C3	256144	broad.mit.edu	37	11	48346598	48346598	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48346598G>C	uc010rhv.1	+	c.106G>C	c.(106-108)GAA>CAA	p.E36Q		NM_001004702	NP_001004702	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C,	9	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.25	67.462119	72.71185	23	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48346598	48346598	11456	11	G	C	C	C	429	33	OR4C3	3	3
UBQLNL	143630	broad.mit.edu	37	11	5536678	5536678	+	Missense_Mutation	SNP	T	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5536678T>G	uc001maz.3	-	c.994A>C	c.(994-996)ATC>CTC	p.I332L	HBG2_uc001mak.1_Intron	NM_145053	NP_659490	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	332										large_intestine(2)	2		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)										0.348837	90.423171	92.157629	30	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5536678	5536678	17458	11	T	G	G	G	663	51	UBQLNL	4	4
OR4D6	219983	broad.mit.edu	37	11	59224646	59224646	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59224646C>T	uc010rku.1	+	c.213C>T	c.(211-213)ATC>ATT	p.I71I		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	71	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.256757	50.262085	54.18622	19	55	KEEP	---	---	---	---	capture		Silent	SNP	59224646	59224646	11465	11	C	T	T	T	395	31	OR4D6	1	1
CCDC83	220047	broad.mit.edu	37	11	85626533	85626533	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:85626533C>T	uc001pbg.1	+	c.959C>T	c.(958-960)ACA>ATA	p.T320I	CCDC83_uc001pbh.1_Missense_Mutation_p.T289I|CCDC83_uc001pbi.1_Non-coding_Transcript|CCDC83_uc001pbj.1_Missense_Mutation_p.T190I	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	289											0		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)												0.25	33.121345	36.304762	14	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85626533	85626533	2981	11	C	T	T	T	221	17	CCDC83	2	2
TMEM132D	121256	broad.mit.edu	37	12	129558864	129558864	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:129558864G>C	uc009zyl.1	-	c.2856C>G	c.(2854-2856)TTC>TTG	p.F952L	TMEM132D_uc001uia.2_Missense_Mutation_p.F490L	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	952	Cytoplasmic (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.351648	100.579169	102.342046	32	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129558864	129558864	16579	12	G	C	C	C	477	37	TMEM132D	3	3
PDZRN4	29951	broad.mit.edu	37	12	41967475	41967475	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:41967475G>A	uc010skn.1	+	c.2297G>A	c.(2296-2298)CGA>CAA	p.R766Q	PDZRN4_uc001rmq.3_Missense_Mutation_p.R707Q|PDZRN4_uc009zjz.2_Missense_Mutation_p.R705Q|PDZRN4_uc001rmr.2_Missense_Mutation_p.R592Q	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	965							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	8	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)								467				0.238095	13.2646	14.580186	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41967475	41967475	12131	12	G	A	A	A	481	37	PDZRN4	1	1
PUS7L	83448	broad.mit.edu	37	12	44124206	44124206	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:44124206C>T	uc001rnq.3	-	c.2079G>A	c.(2077-2079)CTG>CTA	p.L693L	PUS7L_uc001rnr.3_Silent_p.L693L|PUS7L_uc001rns.3_Silent_p.L693L|PUS7L_uc009zkb.2_Silent_p.L380L	NM_001098615	NP_001092085	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S.	693					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			pancreas(1)	1	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)										0.306122	40.673453	42.338793	15	34	KEEP	---	---	---	---	capture		Silent	SNP	44124206	44124206	13292	12	C	T	T	T	366	29	PUS7L	2	2
HDAC7	51564	broad.mit.edu	37	12	48179570	48179570	+	Missense_Mutation	SNP	A	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:48179570A>G	uc010slo.1	-	c.2671T>C	c.(2671-2673)TCT>CCT	p.S891P	HDAC7_uc009zku.2_Non-coding_Transcript|HDAC7_uc001rqe.2_Missense_Mutation_p.S325P|HDAC7_uc001rqj.3_Missense_Mutation_p.S854P|HDAC7_uc001rqk.3_Missense_Mutation_p.S874P|HDAC7_uc010slp.1_Missense_Mutation_p.S135P	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a	852	Histone deacetylase.				negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)										0.428571	8.124204	8.155213	3	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48179570	48179570	7295	12	A	G	G	G	143	11	HDAC7	4	4
SUOX	6821	broad.mit.edu	37	12	56398128	56398128	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56398128G>C	uc001six.2	+	c.955G>C	c.(955-957)GAG>CAG	p.E319Q	SUOX_uc001siy.2_Missense_Mutation_p.E319Q|SUOX_uc001siz.2_Missense_Mutation_p.E319Q|SUOX_uc001sja.2_Missense_Mutation_p.E319Q	NM_000456	NP_000447	P51687	SUOX_HUMAN	sulfite oxidase precursor	319	Molybdenum-pterin domain (By similarity).				oxidation-reduction process	mitochondrial intermembrane space	electron carrier activity|molybdenum ion binding|sulfite oxidase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)											0.435897	54.367471	54.507448	17	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56398128	56398128	15915	12	G	C	C	C	585	45	SUOX	3	3
CAND1	55832	broad.mit.edu	37	12	67699360	67699360	+	Missense_Mutation	SNP	T	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:67699360T>C	uc001stn.2	+	c.1912T>C	c.(1912-1914)TCA>CCA	p.S638P	CAND1_uc001sto.2_Missense_Mutation_p.S148P	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	638	HEAT 14.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)	1			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)										0.282258	94.205187	99.62081	35	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67699360	67699360	2732	12	T	C	C	C	754	58	CAND1	4	4
C1R	715	broad.mit.edu	37	12	7188187	7188187	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7188187C>G	uc010sfy.1	-	c.1767G>C	c.(1765-1767)TTG>TTC	p.L589F		NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	589	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)									0.258065	23.587391	25.230205	8	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7188187	7188187	2039	12	C	G	G	G	376	29	C1R	3	3
DUSP6	1848	broad.mit.edu	37	12	89743067	89743067	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:89743067C>G	uc001tay.2	-	c.1110G>C	c.(1108-1110)CAG>CAC	p.Q370H	DUSP6_uc001taz.2_Missense_Mutation_p.Q224H	NM_001946	NP_001937	Q16828	DUS6_HUMAN	dual specificity phosphatase 6 isoform a	370	Tyrosine-protein phosphatase.				dorsal/ventral pattern formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|nerve growth factor receptor signaling pathway|positive regulation of apoptosis|regulation of endodermal cell fate specification|regulation of fibroblast growth factor receptor signaling pathway|regulation of heart growth|response to nitrosative stress|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	cytosol|nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0						Colon(132;3456 5224)				159				0.348837	91.758109	93.522006	30	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89743067	89743067	5014	12	C	G	G	G	415	32	DUSP6	3	3
OR4Q3	441669	broad.mit.edu	37	14	20216038	20216038	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20216038G>A	uc010tkt.1	+	c.452G>A	c.(451-453)TGT>TAT	p.C151Y		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.225806	30.915378	35.199489	14	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20216038	20216038	11491	14	G	A	A	A	624	48	OR4Q3	2	2
OR4K13	390433	broad.mit.edu	37	14	20502887	20502887	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20502887C>T	uc010tkz.1	-	c.31G>A	c.(31-33)GAA>AAA	p.E11K		NM_001004714	NP_001004714	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K,	11	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)										0.210526	20.179476	23.124497	8	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20502887	20502887	11478	14	C	T	T	T	390	30	OR4K13	2	2
KIAA0391	9692	broad.mit.edu	37	14	35739633	35739633	+	Missense_Mutation	SNP	A	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:35739633A>G	uc001wsy.1	+	c.1451A>G	c.(1450-1452)TAT>TGT	p.Y484C	KIAA0391_uc010tps.1_Missense_Mutation_p.Y389C|KIAA0391_uc001wsz.1_Missense_Mutation_p.Y468C|KIAA0391_uc001wta.2_Non-coding_Transcript|KIAA0391_uc001wtb.1_Missense_Mutation_p.Y468C|KIAA0391_uc001wtc.1_Missense_Mutation_p.Y112C	NM_014672	NP_055487	O15091	MRRP3_HUMAN	mitochondrial RNase P protein 3 precursor	484					tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)										0.292308	54.914932	57.417464	19	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35739633	35739633	8479	14	A	G	G	G	208	16	KIAA0391	4	4
NKX2-1	7080	broad.mit.edu	37	14	36988447	36988447	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:36988447G>A	uc001wtu.2	-	c.206C>T	c.(205-207)GCG>GTG	p.A69V	SFTA3_uc001wts.2_Intron|NKX2-1_uc001wtt.2_Missense_Mutation_p.A39V|NKX2-1_uc001wtv.2_Missense_Mutation_p.A39V	NM_001079668	NP_001073136	P43699	NKX21_HUMAN	thyroid transcription factor 1 isoform 1	39					epithelial tube branching involved in lung morphogenesis|globus pallidus development|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to hormone stimulus|thyroid gland development		promoter binding|protein binding|transcription activator activity			skin(1)	1	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)						15				0.257143	18.176824	20.051626	9	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36988447	36988447	10851	14	G	A	A	A	494	38	NKX2-1	1	1
C14orf37	145407	broad.mit.edu	37	14	58599890	58599890	+	Silent	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:58599890C>A	uc010tro.1	-	c.1653G>T	c.(1651-1653)CTG>CTT	p.L551L	C14orf37_uc001xdc.2_Silent_p.L513L|C14orf37_uc001xdd.2_Silent_p.L513L|C14orf37_uc001xde.2_Silent_p.L513L	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	513	Extracellular (Potential).					integral to membrane	binding				0														0.285714	58.421142	61.592941	22	55	KEEP	---	---	---	---	capture		Silent	SNP	58599890	58599890	1820	14	C	A	A	A	210	17	C14orf37	2	2
ATP6V1D	51382	broad.mit.edu	37	14	67807182	67807182	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:67807182C>T	uc001xjf.2	-	c.577G>A	c.(577-579)GAG>AAG	p.E193K	ATP6V1D_uc001xje.2_Non-coding_Transcript	NM_015994	NP_057078	Q9Y5K8	VATD_HUMAN	H(+)-transporting two-sector ATPase	193					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting two-sector ATPase complex, catalytic domain|vacuolar proton-transporting V-type ATPase complex	protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)										0.345455	53.805537	54.966784	19	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67807182	67807182	1201	14	C	T	T	T	377	29	ATP6V1D	2	2
SIPA1L1	26037	broad.mit.edu	37	14	72139160	72139160	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:72139160G>A	uc001xms.2	+	c.2925G>A	c.(2923-2925)GCG>GCA	p.A975A	SIPA1L1_uc001xmt.2_Silent_p.A975A|SIPA1L1_uc001xmu.2_Silent_p.A975A|SIPA1L1_uc001xmv.2_Silent_p.A975A|SIPA1L1_uc010ttm.1_Silent_p.A450A	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	975	PDZ.				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)										0.403509	74.614119	75.077897	23	34	KEEP	---	---	---	---	capture		Silent	SNP	72139160	72139160	14824	14	G	A	A	A	496	39	SIPA1L1	1	1
SETD3	84193	broad.mit.edu	37	14	99927677	99927677	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:99927677C>A	uc001ygc.2	-	c.197G>T	c.(196-198)GGT>GTT	p.G66V	SETD3_uc001ygd.2_Missense_Mutation_p.G66V|SETD3_uc001ygf.2_Missense_Mutation_p.G66V	NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a	66					peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)												0.218182	27.128699	31.113902	12	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99927677	99927677	14621	14	C	A	A	A	234	18	SETD3	2	2
C15orf2	23742	broad.mit.edu	37	15	24924444	24924444	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24924444G>C	uc001ywo.2	+	c.3430G>C	c.(3430-3432)GAA>CAA	p.E1144Q		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	1144					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)						443				0.304878	79.743932	82.528984	25	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24924444	24924444	1834	15	G	C	C	C	429	33	C15orf2	3	3
ATP10A	57194	broad.mit.edu	37	15	25958906	25958906	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:25958906G>A	uc010ayu.2	-	c.2259C>T	c.(2257-2259)ATC>ATT	p.I753I		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	753	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)						877				0.217391	23.633634	27.014969	10	36	KEEP	---	---	---	---	capture		Silent	SNP	25958906	25958906	1135	15	G	A	A	A	525	41	ATP10A	2	2
GABRA5	2558	broad.mit.edu	37	15	27182355	27182355	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:27182355G>A	uc001zbd.1	+	c.604G>A	c.(604-606)GTT>ATT	p.V202I	GABRB3_uc001zbb.2_Intron	NM_000810	NP_000801	P31644	GBRA5_HUMAN	gamma-aminobutyric acid A receptor, alpha 5	202	Extracellular (Potential).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.306122	41.114763	42.7528	15	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27182355	27182355	6415	15	G	A	A	A	520	40	GABRA5	1	1
MGA	23269	broad.mit.edu	37	15	41961679	41961679	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:41961679C>G	uc010ucy.1	+	c.587C>G	c.(586-588)TCT>TGT	p.S196C	MGA_uc001zog.1_Missense_Mutation_p.S196C|MGA_uc010ucz.1_Missense_Mutation_p.S196C	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	196	T-box.				regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)						606				0.349315	159.99106	162.911731	51	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41961679	41961679	9930	15	C	G	G	G	416	32	MGA	3	3
MGA	23269	broad.mit.edu	37	15	42040834	42040834	+	Splice_Site_SNP	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42040834G>A	uc010ucy.1	+	c.5213_splice	c.e16-1	p.E1738_splice	MGA_uc010ucz.1_Splice_Site_SNP_p.E1529_splice|MGA_uc010uda.1_Splice_Site_SNP_p.E354_splice|MGA_uc001zoi.2_5'Flank	NM_001164273	NP_001157745			MAX-interacting protein isoform 1						regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)						606				0.307692	12.399755	12.825743	4	9	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	42040834	42040834	9930	15	G	A	A	A	429	33	MGA	5	2
FAM63B	54629	broad.mit.edu	37	15	59064389	59064389	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:59064389C>T	uc002afj.2	+	c.795C>T	c.(793-795)CCC>CCT	p.P265P	FAM63B_uc002afi.2_Silent_p.P265P|FAM63B_uc002afk.2_Non-coding_Transcript|FAM63B_uc002afl.2_Non-coding_Transcript	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a	265										central_nervous_system(1)	1														0.333333	43.267422	44.285145	14	28	KEEP	---	---	---	---	capture		Silent	SNP	59064389	59064389	5820	15	C	T	T	T	301	24	FAM63B	2	2
RNF111	54778	broad.mit.edu	37	15	59323235	59323235	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:59323235C>G	uc002afw.2	+	c.214C>G	c.(214-216)CAA>GAA	p.Q72E	RNF111_uc002afs.2_Missense_Mutation_p.Q72E|RNF111_uc002aft.2_Missense_Mutation_p.Q72E|RNF111_uc002afu.2_Missense_Mutation_p.Q72E|RNF111_uc002afv.2_Missense_Mutation_p.Q72E	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	72					multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		NSCLC(72;983 1365 10746 34387 47081)								0.4	32.04272	32.261799	10	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59323235	59323235	13902	15	C	G	G	G	377	29	RNF111	3	3
CES7	221223	broad.mit.edu	37	16	55905608	55905608	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55905608C>T	uc002eip.2	-	c.346G>A	c.(346-348)GGA>AGA	p.G116R	CES7_uc002eio.2_Missense_Mutation_p.G116R|CES7_uc002eiq.2_5'UTR|CES7_uc002eir.2_Missense_Mutation_p.G10R	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	116					regulation of synaptic transmission	extracellular region	methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)										0.324324	33.072929	34.094456	12	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55905608	55905608	3405	16	C	T	T	T	299	23	CES7	1	1
AMFR	267	broad.mit.edu	37	16	56436943	56436943	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56436943G>A	uc002eiy.2	-	c.928C>T	c.(928-930)CGT>TGT	p.R310C	AMFR_uc002eix.2_Silent_p.F7F	NM_001144	NP_001135	Q9UKV5	AMFR2_HUMAN	autocrine motility factor receptor	310					endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein oligomerization|protein polyubiquitination	integral to endoplasmic reticulum membrane|integral to membrane of membrane fraction	protein binding|protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			breast(2)	2						Pancreas(2;144 323 39528)								0.3125	70.545232	73.049548	25	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56436943	56436943	574	16	G	A	A	A	481	37	AMFR	1	1
HAGHL	84264	broad.mit.edu	37	16	777579	777579	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:777579G>A	uc002cjl.1	+	c.70G>A	c.(70-72)GAG>AAG	p.E24K	CCDC78_uc002cjf.2_5'Flank|CCDC78_uc002cji.3_5'Flank|CCDC78_uc002cjg.2_5'Flank|CCDC78_uc002cjj.3_5'Flank|CCDC78_uc002cjh.2_5'Flank|CCDC78_uc010uuo.1_5'Flank|CCDC78_uc002cjk.2_5'Flank|HAGHL_uc002cjm.1_Missense_Mutation_p.E24K|HAGHL_uc002cjn.1_Missense_Mutation_p.E24K|HAGHL_uc002cjo.1_Missense_Mutation_p.E24K|HAGHL_uc010uup.1_Missense_Mutation_p.E24K	NM_207112	NP_996995	Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like isoform 1	24							hydrolase activity|metal ion binding				0		Hepatocellular(780;0.00335)				Pancreas(46;538 1326 12403 32360)								0.210526	8.536232	9.975772	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	777579	777579	7228	16	G	A	A	A	481	37	HAGHL	1	1
CDT1	81620	broad.mit.edu	37	16	88872241	88872241	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:88872241G>C	uc002flu.2	+	c.796G>C	c.(796-798)GAT>CAT	p.D266H		NM_030928	NP_112190	Q9H211	CDT1_HUMAN	chromatin licensing and DNA replication factor	266					DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		Melanoma(159;511 3380 30971)								0.375	26.867979	27.197588	9	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88872241	88872241	3309	16	G	C	C	C	429	33	CDT1	3	3
NF1	4763	broad.mit.edu	37	17	29664477	29664477	+	Silent	SNP	T	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:29664477T>G	uc002hgg.2	+	c.6519T>G	c.(6517-6519)GCT>GCG	p.A2173A	NF1_uc002hgh.2_Silent_p.A2152A|NF1_uc010cso.2_Silent_p.A361A|NF1_uc010wbt.1_5'Flank|NF1_uc010wbu.1_5'Flank	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2173					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.E2143_S2180del(2)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.19403	26.229443	32.090904	13	54	KEEP	---	---	---	---	capture		Silent	SNP	29664477	29664477	10756	17	T	G	G	G	704	55	NF1	4	4
PSMD11	5717	broad.mit.edu	37	17	30781559	30781559	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:30781559C>G	uc010cta.1	+	c.240C>G	c.(238-240)ATC>ATG	p.I80M	PSMD11_uc010wbz.1_Missense_Mutation_p.I80M|PSMD11_uc002hhm.2_Missense_Mutation_p.I80M	NM_002815	NP_002806	O00231	PSD11_HUMAN	proteasome 26S non-ATPase subunit 11	80					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			Ovarian(130;1038 1716 9294 11987 19279)								0.26087	70.064491	74.821941	24	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30781559	30781559	13147	17	C	G	G	G	369	29	PSMD11	3	3
GPR179	440435	broad.mit.edu	37	17	36486375	36486375	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:36486375C>T	uc002hpz.2	-	c.3077G>A	c.(3076-3078)CGA>CAA	p.R1026Q		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	1026	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)												0.215385	34.526916	39.377405	14	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36486375	36486375	6949	17	C	T	T	T	403	31	GPR179	1	1
PSMC3IP	29893	broad.mit.edu	37	17	40729545	40729545	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40729545C>G	uc002iai.2	-	c.69G>C	c.(67-69)CAG>CAC	p.Q23H	PSMC3IP_uc002iaj.2_5'UTR|PSMC3IP_uc002iak.2_Missense_Mutation_p.Q23H|PSMC3IP_uc010wgn.1_5'UTR|PSMC3IP_uc010wgo.1_Non-coding_Transcript|PSMC3IP_uc010wgp.1_Non-coding_Transcript	NM_016556	NP_057640	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein isoform 2	23					DNA recombination|meiosis	nucleus	DNA binding				0		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)										0.32	44.673298	46.1178	16	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40729545	40729545	13141	17	C	G	G	G	415	32	PSMC3IP	3	3
TLK2	11011	broad.mit.edu	37	17	60655841	60655841	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60655841G>A	uc010ddp.2	+	c.1258G>A	c.(1258-1260)GAA>AAA	p.E420K	TLK2_uc002izx.3_Missense_Mutation_p.E246K|TLK2_uc002izz.3_Missense_Mutation_p.E398K|TLK2_uc002jaa.3_Missense_Mutation_p.E366K|TLK2_uc010wpd.1_Missense_Mutation_p.E366K	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	420	Potential.				cell cycle|chromatin modification|intracellular signal transduction|protein phosphorylation|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2										505				0.2	17.374987	20.725823	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60655841	60655841	16474	17	G	A	A	A	533	41	TLK2	2	2
SMAD4	4089	broad.mit.edu	37	18	48584552	48584552	+	Nonsense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:48584552C>G	uc010xdp.1	+	c.725C>G	c.(724-726)TCA>TGA	p.S242*	SMAD4_uc010xdo.1_Non-coding_Transcript|SMAD4_uc002lfb.3_Nonsense_Mutation_p.S87*	NM_005359	NP_005350	Q13485	SMAD4_HUMAN	mothers against decapentaplegic homolog 4	242					BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|promoter binding|protein homodimerization activity|R-SMAD binding|transcription activator activity|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	p.0?(35)		pancreas(169)|large_intestine(108)|thyroid(19)|lung(10)|small_intestine(9)|biliary_tract(8)|upper_aerodigestive_tract(7)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	364		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)						233				0.636364	48.650388	49.009083	14	8	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	48584552	48584552	15258	18	C	G	G	G	377	29	SMAD4	5	3
LAMA1	284217	broad.mit.edu	37	18	6966263	6966263	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:6966263G>A	uc002knm.2	-	c.6933C>T	c.(6931-6933)GAC>GAT	p.D2311D	LAMA1_uc002knl.2_5'Flank|LAMA1_uc010wzj.1_Silent_p.D1787D	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2311	Laminin G-like 2.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.428571	9.124112	9.155208	3	4	KEEP	---	---	---	---	capture		Silent	SNP	6966263	6966263	8928	18	G	A	A	A	516	40	LAMA1	1	1
ATP8B3	148229	broad.mit.edu	37	19	1785556	1785556	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1785556C>T	uc002ltw.2	-	c.3305G>A	c.(3304-3306)CGC>CAC	p.R1102H	ATP8B3_uc002ltv.2_Missense_Mutation_p.R1065H|ATP8B3_uc002ltx.2_Non-coding_Transcript	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3	1102	Extracellular (Potential).				ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.4	31.347949	31.565636	10	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1785556	1785556	1215	19	C	T	T	T	351	27	ATP8B3	1	1
NFIC	4782	broad.mit.edu	37	19	3381997	3381997	+	Silent	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:3381997C>G	uc010xhi.1	+	c.318C>G	c.(316-318)CTC>CTG	p.L106L	NFIC_uc002lxo.2_Silent_p.L97L|NFIC_uc010xhh.1_Silent_p.L97L|NFIC_uc002lxp.2_Silent_p.L106L|NFIC_uc010xhj.1_Silent_p.L106L|NFIC_uc002lxq.1_Silent_p.L58L	NM_205843	NP_995315	P08651	NFIC_HUMAN	nuclear factor I/C isoform 2	106	CTF/NF-I.				DNA replication|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)										0.442105	130.603138	130.884957	42	53	KEEP	---	---	---	---	capture		Silent	SNP	3381997	3381997	10772	19	C	G	G	G	405	32	NFIC	3	3
ZNF180	7733	broad.mit.edu	37	19	44980651	44980651	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44980651G>C	uc002ozf.3	-	c.2047C>G	c.(2047-2049)CAT>GAT	p.H683D	ZNF180_uc002ozh.3_Missense_Mutation_p.H340D|ZNF180_uc002ozi.3_Missense_Mutation_p.H656D|ZNF180_uc002ozg.3_Missense_Mutation_p.H682D|ZNF180_uc010ejm.2_Missense_Mutation_p.H658D	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	683	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				Esophageal Squamous(180;1353 2003 32862 46574 49854)								0.27957	80.335782	84.383396	26	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44980651	44980651	18339	19	G	C	C	C	585	45	ZNF180	3	3
BAX	581	broad.mit.edu	37	19	49464213	49464213	+	Silent	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49464213C>G	uc002plf.1	+	c.516C>G	c.(514-516)CTC>CTG	p.L172L	BAX_uc002plg.1_Silent_p.L135L|BAX_uc002plh.1_Silent_p.L94L|BAX_uc010xzx.1_Intron|BAX_uc002plj.2_Intron|BAX_uc002plk.2_Intron|BAX_uc002pll.2_Intron|BAX_uc002plm.2_Intron	NM_004324	NP_004315	Q07812	BAX_HUMAN	BCL2-associated X protein isoform beta	Error:Variant_position_missing_in_Q07812_after_alignment					activation of caspase activity by cytochrome c|activation of pro-apoptotic gene products|B cell apoptosis|cleavage of lamin|DNA fragmentation involved in apoptotic nuclear change|establishment or maintenance of transmembrane electrochemical gradient|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|induction of retinal programmed cell death|mitochondrial fragmentation involved in apoptosis|mitochondrial fusion|negative regulation of protein binding|negative regulation of survival gene product expression|nuclear fragmentation involved in apoptotic nuclear change|positive regulation of neuron apoptosis|protein homooligomerization|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|release of cytochrome c from mitochondria|release of matrix enzymes from mitochondria|response to toxin|transformed cell apoptosis	cytosol|endoplasmic reticulum membrane|mitochondrial outer membrane|mitochondrial permeability transition pore complex|nucleus	BH3 domain binding|channel activity|lipid binding|protein heterodimerization activity|protein homodimerization activity			lung(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)						57				0.44	35.622387	35.70063	11	14	KEEP	---	---	---	---	capture		Silent	SNP	49464213	49464213	1349	19	C	G	G	G	366	29	BAX	3	3
FTL	2512	broad.mit.edu	37	19	49469553	49469553	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49469553G>C	uc002plo.2	+	c.265G>C	c.(265-267)GAG>CAG	p.E89Q	FTL_uc002pln.1_3'UTR	NM_000146	NP_000137	P02792	FRIL_HUMAN	ferritin, light polypeptide	89	Ferritin-like diiron.			E -> W (in Ref. 12; AA sequence).	cellular iron ion homeostasis|cellular membrane organization|iron ion transport|oxidation-reduction process|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|identical protein binding|oxidoreductase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)									0.326087	48.413689	49.64562	15	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49469553	49469553	6335	19	G	C	C	C	585	45	FTL	3	3
FTL	2512	broad.mit.edu	37	19	49469609	49469609	+	Silent	SNP	G	T	T	rs11553263		TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49469609G>T	uc002plo.2	+	c.321G>T	c.(319-321)CTG>CTT	p.L107L	FTL_uc002pln.1_3'UTR	NM_000146	NP_000137	P02792	FRIL_HUMAN	ferritin, light polypeptide	107	Ferritin-like diiron.				cellular iron ion homeostasis|cellular membrane organization|iron ion transport|oxidation-reduction process|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|identical protein binding|oxidoreductase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)									0.377778	50.564373	51.154153	17	28	KEEP	---	---	---	---	capture		Silent	SNP	49469609	49469609	6335	19	G	T	T	T	574	45	FTL	2	2
SPIB	6689	broad.mit.edu	37	19	50926966	50926966	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50926966G>A	uc002psd.2	+	c.444G>A	c.(442-444)TCG>TCA	p.S148S	SPIB_uc002pse.2_Silent_p.S148S|SPIB_uc010ycc.1_Silent_p.S57S	NM_003121	NP_003112	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	148					regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding			kidney(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)										0.235294	11.291438	12.38063	4	13	KEEP	---	---	---	---	capture		Silent	SNP	50926966	50926966	15562	19	G	A	A	A	496	39	SPIB	1	1
ZNF836	162962	broad.mit.edu	37	19	52658555	52658555	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52658555G>A	uc010ydi.1	-	c.2381C>T	c.(2380-2382)GCA>GTA	p.A794V	ZNF836_uc010ydj.1_Missense_Mutation_p.A794V	NM_001102657	NP_001096127	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	794	C2H2-type 21.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.368932	104.748815	106.293005	38	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52658555	52658555	18786	19	G	A	A	A	598	46	ZNF836	2	2
C3	718	broad.mit.edu	37	19	6707234	6707234	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6707234C>G	uc002mfm.2	-	c.2098G>C	c.(2098-2100)GAG>CAG	p.E700Q		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	700	Anaphylatoxin-like.			E -> Q (in Ref. 5; AA sequence).	complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)										0.4	22.049623	22.236458	8	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6707234	6707234	2296	19	C	G	G	G	390	30	C3	3	3
AKNAD1	254268	broad.mit.edu	37	1	109358811	109358811	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109358811C>G	uc001dwa.2	-	c.2493G>C	c.(2491-2493)AGG>AGC	p.R831S	AKNAD1_uc001dwb.2_Non-coding_Transcript	NM_152763	NP_689976	Q5T1N1	AKND1_HUMAN	hypothetical protein LOC254268	831										ovary(3)	3														0.4	98.242712	98.896062	30	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109358811	109358811	467	1	C	G	G	G	389	30	AKNAD1	3	3
C1orf127	148345	broad.mit.edu	37	1	11008388	11008388	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11008388C>T	uc010oao.1	-	c.1357G>A	c.(1357-1359)GAG>AAG	p.E453K	C1orf127_uc001arr.1_Missense_Mutation_p.E435K|C1orf127_uc001ars.1_Missense_Mutation_p.E427K	NM_173507	NP_775778	B7ZLG7	B7ZLG7_HUMAN	hypothetical protein LOC148345	453										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)										0.326923	47.957401	49.338928	17	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11008388	11008388	2061	1	C	T	T	T	416	32	C1orf127	2	2
FLG	2312	broad.mit.edu	37	1	152285020	152285020	+	Missense_Mutation	SNP	T	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152285020T>C	uc001ezu.1	-	c.2342A>G	c.(2341-2343)GAC>GGC	p.D781G		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	781	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.217204	251.164123	285.410175	101	364	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152285020	152285020	6160	1	T	C	C	C	754	58	FLG	4	4
CHRNB2	1141	broad.mit.edu	37	1	154543728	154543728	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154543728C>T	uc001ffg.2	+	c.429C>T	c.(427-429)ATC>ATT	p.I143I		NM_000748	NP_000739	P17787	ACHB2_HUMAN	neuronal nicotinic acetylcholine receptor beta 2	143	Extracellular (Potential).				B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)									0.206667	71.660448	83.612146	31	119	KEEP	---	---	---	---	capture		Silent	SNP	154543728	154543728	3525	1	C	T	T	T	408	32	CHRNB2	2	2
KIFAP3	22920	broad.mit.edu	37	1	170003513	170003513	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:170003513C>G	uc001ggv.2	-	c.742G>C	c.(742-744)GTT>CTT	p.V248L	KIFAP3_uc010ply.1_3'UTR|KIFAP3_uc001ggw.1_3'UTR	NM_014970	NP_055785	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	248					blood coagulation|plus-end-directed vesicle transport along microtubule|protein complex assembly|signal transduction	centrosome|condensed nuclear chromosome|cytosol|endoplasmic reticulum|kinesin II complex|spindle microtubule	kinesin binding				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.208333	25.623836	29.404896	10	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170003513	170003513	8622	1	C	G	G	G	377	29	KIFAP3	3	3
ASTN1	460	broad.mit.edu	37	1	177133601	177133601	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:177133601C>A	uc001glc.2	-	c.212G>T	c.(211-213)CGC>CTC	p.R71L	ASTN1_uc001glb.1_Missense_Mutation_p.R71L|ASTN1_uc001gld.1_Missense_Mutation_p.R71L|ASTN1_uc009wwx.1_Missense_Mutation_p.R71L	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	71					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	11										849				0.419355	34.518222	34.704404	13	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177133601	177133601	1083	1	C	A	A	A	351	27	ASTN1	1	1
ZNF648	127665	broad.mit.edu	37	1	182026921	182026921	+	Silent	SNP	G	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:182026921G>T	uc001goz.2	-	c.225C>A	c.(223-225)GGC>GGA	p.G75G		NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	75					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						NSCLC(71;908 1374 5429 20458 35642)								0.301587	49.57112	51.807795	19	44	KEEP	---	---	---	---	capture		Silent	SNP	182026921	182026921	18658	1	G	T	T	T	587	46	ZNF648	2	2
RNASEL	6041	broad.mit.edu	37	1	182555637	182555637	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:182555637G>A	uc001gpj.1	-	c.305C>T	c.(304-306)GCG>GTG	p.A102V	RNASEL_uc009wxz.1_Missense_Mutation_p.A102V|RNASEL_uc001gpk.2_Missense_Mutation_p.A102V|RNASEL_uc009wya.1_Missense_Mutation_p.A102V	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	102	ANK 3.				mRNA processing|protein phosphorylation|response to virus|type I interferon-mediated signaling pathway	mitochondrion	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding			ovary(4)	4										183				0.2	19.073625	22.822799	9	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	182555637	182555637	13893	1	G	A	A	A	494	38	RNASEL	1	1
RGS16	6004	broad.mit.edu	37	1	182571203	182571203	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:182571203C>T	uc001gpl.3	-	c.285G>A	c.(283-285)TGG>TGA	p.W95*	RGS16_uc010pnv.1_Nonsense_Mutation_p.W95*	NM_002928	NP_002919	O15492	RGS16_HUMAN	regulator of G-protein signalling 16	95	RGS.				negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(1)	1												OREG0014036	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.278846	76.737074	81.308273	29	75	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	182571203	182571203	13772	1	C	T	T	T	338	26	RGS16	5	2
HMCN1	83872	broad.mit.edu	37	1	186023068	186023068	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186023068C>T	uc001grq.1	+	c.6812C>T	c.(6811-6813)GCG>GTG	p.A2271V		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	2271	Ig-like C2-type 20.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.17284	27.072246	35.206507	14	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186023068	186023068	7511	1	C	T	T	T	351	27	HMCN1	1	1
F13B	2165	broad.mit.edu	37	1	197036345	197036345	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197036345C>T	uc001gtt.1	-	c.9G>A	c.(7-9)TTG>TTA	p.L3L		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	3					blood coagulation	extracellular region				central_nervous_system(1)	1														0.155172	17.367543	23.930947	9	49	KEEP	---	---	---	---	capture		Silent	SNP	197036345	197036345	5535	1	C	T	T	T	376	29	F13B	2	2
CRB1	23418	broad.mit.edu	37	1	197411420	197411420	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197411420G>A	uc001gtz.2	+	c.4003G>A	c.(4003-4005)GAC>AAC	p.D1335N	CRB1_uc010poz.1_Missense_Mutation_p.D1311N|CRB1_uc010ppa.1_Non-coding_Transcript|CRB1_uc009wza.2_Missense_Mutation_p.D1223N|CRB1_uc010ppb.1_Missense_Mutation_p.D799N|CRB1_uc010ppd.1_Missense_Mutation_p.D816N|CRB1_uc001gub.1_3'UTR	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1335	Extracellular (Potential).				cell-cell signaling|establishment or maintenance of cell polarity|response to stimulus|visual perception	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|large_intestine(1)	6														0.454545	349.811796	350.262277	115	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197411420	197411420	3987	1	G	A	A	A	533	41	CRB1	2	2
LMOD1	25802	broad.mit.edu	37	1	201868453	201868453	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201868453C>G	uc001gxb.2	-	c.1688G>C	c.(1687-1689)GGA>GCA	p.G563A	LMOD1_uc010ppu.1_Missense_Mutation_p.G512A	NM_012134	NP_036266	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	563					muscle contraction	cytoskeleton|cytosol|membrane fraction	tropomyosin binding			ovary(1)|pancreas(1)|skin(1)	3														0.545455	21.151068	21.170837	6	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	201868453	201868453	9185	1	C	G	G	G	390	30	LMOD1	3	3
CENPF	1063	broad.mit.edu	37	1	214788288	214788288	+	Silent	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:214788288C>G	uc001hkm.2	+	c.276C>G	c.(274-276)GTC>GTG	p.V92V		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	92	Interaction with SNAP25 and required for localization to the cytoplasm (By similarity).|Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)	12				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		Colon(80;575 1284 11000 14801 43496)								0.226415	32.871295	36.514812	12	41	KEEP	---	---	---	---	capture		Silent	SNP	214788288	214788288	3364	1	C	G	G	G	366	29	CENPF	3	3
HSPG2	3339	broad.mit.edu	37	1	22166366	22166366	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:22166366C>T	uc009vqd.2	-	c.9661G>A	c.(9661-9663)GAG>AAG	p.E3221K	HSPG2_uc001bfj.2_Missense_Mutation_p.E3220K	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	3220	Ig-like C2-type 18.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)	8		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)									0.314607	75.876347	78.593895	28	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22166366	22166366	7730	1	C	T	T	T	377	29	HSPG2	2	2
OPN3	23596	broad.mit.edu	37	1	241767856	241767856	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241767856G>A	uc001hza.2	-	c.399C>T	c.(397-399)ACC>ACT	p.T133T	OPN3_uc001hzb.2_Non-coding_Transcript|OPN3_uc001hzc.2_Intron	NM_014322	NP_055137	Q9H1Y3	OPN3_HUMAN	opsin 3	133	Helical; Name=3; (Potential).				phototransduction|protein-chromophore linkage|regulation of circadian rhythm|visual perception	integral to plasma membrane	G-protein coupled photoreceptor activity				0	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)											0.193548	15.233	17.948839	6	25	KEEP	---	---	---	---	capture		Silent	SNP	241767856	241767856	11287	1	G	A	A	A	496	39	OPN3	1	1
CDC20	991	broad.mit.edu	37	1	43826219	43826219	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43826219C>T	uc001cix.2	+	c.803C>T	c.(802-804)TCT>TTT	p.S268F	CDC20_uc001ciy.2_Missense_Mutation_p.S268F	NM_001255	NP_001246	Q12834	CDC20_HUMAN	cell division cycle 20	268	WD 3.				activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	cytosol|nucleoplasm|spindle	enzyme binding|protein C-terminus binding				0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				Esophageal Squamous(137;1154 1759 10362 10401 46925)								0.380531	130.888573	132.306324	43	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43826219	43826219	3187	1	C	T	T	T	416	32	CDC20	2	2
PYGB	5834	broad.mit.edu	37	20	25263896	25263896	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:25263896G>A	uc002wup.2	+	c.1603G>A	c.(1603-1605)GTG>ATG	p.V535M		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	535					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)	1					Pyridoxal Phosphate(DB00114)									0.490196	77.372081	77.37636	25	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25263896	25263896	13318	20	G	A	A	A	520	40	PYGB	1	1
HNF4A	3172	broad.mit.edu	37	20	42984468	42984468	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42984468C>T	uc002xlv.2	+	c.24C>T	c.(22-24)CTC>CTT	p.L8L	HNF4A_uc010zwo.1_5'UTR|HNF4A_uc002xlt.2_Silent_p.L8L|HNF4A_uc002xlu.2_Silent_p.L8L	NM_175914	NP_787110	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform d	156					blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|promoter binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			Colon(79;2 1269 8820 14841 52347)								0.689655	68.911343	69.84124	20	9	KEEP	---	---	---	---	capture		Silent	SNP	42984468	42984468	7545	20	C	T	T	T	392	31	HNF4A	1	1
SLC17A9	63910	broad.mit.edu	37	20	61596969	61596969	+	Missense_Mutation	SNP	G	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61596969G>T	uc002yea.3	+	c.953G>T	c.(952-954)GGC>GTC	p.G318V	SLC17A9_uc002ydz.3_Missense_Mutation_p.G312V|SLC17A9_uc011aap.1_Missense_Mutation_p.G338V	NM_022082	NP_071365	Q9BYT1	S17A9_HUMAN	vesicular nucleotide transporter SLC17A9	318	Helical; (Potential).				exocytosis|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1														0.275556	157.765027	167.96708	62	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61596969	61596969	14920	20	G	T	T	T	546	42	SLC17A9	2	2
PTK6	5753	broad.mit.edu	37	20	62168655	62168655	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62168655C>A	uc002yfg.2	-	c.13G>T	c.(13-15)GAC>TAC	p.D5Y	PTK6_uc011aay.1_5'UTR|PTK6_uc011aba.1_Missense_Mutation_p.D5Y	NM_005975	NP_005966	Q13882	PTK6_HUMAN	PTK6 protein tyrosine kinase 6	5					protein phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			kidney(1)	1	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)							575				0.692308	24.768434	25.1938	9	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62168655	62168655	13219	20	C	A	A	A	390	30	PTK6	2	2
IL10RB	3588	broad.mit.edu	37	21	34649001	34649001	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:34649001G>A	uc002yrl.1	+	c.280G>A	c.(280-282)GAA>AAA	p.E94K	IL10RB_uc002yrh.1_Missense_Mutation_p.E162K|IL10RB_uc002yri.1_Missense_Mutation_p.E45K|IL10RB_uc002yrk.1_Missense_Mutation_p.E92K	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor	92	Extracellular (Potential).				immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						Melanoma(67;315 1275 21667 21943 44564)								0.368852	130.95838	132.795936	45	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34649001	34649001	7922	21	G	A	A	A	585	45	IL10RB	2	2
EWSR1	2130	broad.mit.edu	37	22	29668239	29668239	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:29668239G>A	uc003aev.2	+	c.48G>A	c.(46-48)CAG>CAA	p.Q16Q	EWSR1_uc003aes.3_Silent_p.Q16Q|EWSR1_uc003aet.2_Silent_p.Q16Q|EWSR1_uc003aew.2_Silent_p.Q16Q|EWSR1_uc003aex.2_Silent_p.Q16Q	NM_013986	NP_053733	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 1	16	31 X approximate tandem repeats.|EAD (Gln/Pro/Thr-rich).|1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2262)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2524)|soft_tissue(700)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|ovary(1)	3249										161				0.369565	52.858307	53.547601	17	29	KEEP	---	---	---	---	capture		Silent	SNP	29668239	29668239	5489	22	G	A	A	A	451	35	EWSR1	2	2
EIF3L	51386	broad.mit.edu	37	22	38274173	38274173	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:38274173G>A	uc003auf.2	+	c.1570G>A	c.(1570-1572)GAT>AAT	p.D524N	EIF3L_uc003aue.1_Missense_Mutation_p.D524N|EIF3L_uc011ann.1_Missense_Mutation_p.D476N|EIF3L_uc003aug.2_Missense_Mutation_p.D416N|EIF3L_uc003auh.2_Missense_Mutation_p.D257N	NM_016091	NP_057175	Q9Y262	EIF3L_HUMAN	eukaryotic translation initiation factor 3	524						eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1														0.354167	50.263745	51.16239	17	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38274173	38274173	5213	22	G	A	A	A	585	45	EIF3L	2	2
GPR45	11250	broad.mit.edu	37	2	105859054	105859054	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:105859054C>T	uc002tco.1	+	c.739C>T	c.(739-741)CGG>TGG	p.R247W		NM_007227	NP_009158	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	247	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)	2														0.350427	106.779035	109.069795	41	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105859054	105859054	6971	2	C	T	T	T	347	27	GPR45	1	1
ZEB2	9839	broad.mit.edu	37	2	145161555	145161555	+	Silent	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:145161555G>C	uc002tvu.2	-	c.735C>G	c.(733-735)CTC>CTG	p.L245L	ZEB2_uc002tvv.2_Silent_p.L239L|ZEB2_uc010zbm.1_Silent_p.L216L|ZEB2_uc010fnp.2_Silent_p.L153L|ZEB2_uc010fnq.1_Silent_p.L274L	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	245	C2H2-type 2.				negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|large_intestine(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.112)		Melanoma(33;1235 1264 5755 16332)								0.326087	94.119023	96.58722	30	62	KEEP	---	---	---	---	capture		Silent	SNP	145161555	145161555	18212	2	G	C	C	C	418	33	ZEB2	3	3
IFIH1	64135	broad.mit.edu	37	2	163134108	163134108	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:163134108C>G	uc002uce.2	-	c.1861G>C	c.(1861-1863)GAT>CAT	p.D621H		NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	621					innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|regulation of apoptosis|response to virus	cytosol|nucleus	ATP binding|DNA binding|helicase activity|protein binding|ribonucleoprotein binding|RNA binding|zinc ion binding			ovary(1)	1														0.352941	78.581263	79.877389	24	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	163134108	163134108	7821	2	C	G	G	G	416	32	IFIH1	3	3
COBLL1	22837	broad.mit.edu	37	2	165584560	165584560	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165584560G>A	uc010zcw.1	-	c.739C>T	c.(739-741)CAA>TAA	p.Q247*	COBLL1_uc002ucp.2_Nonsense_Mutation_p.Q194*|COBLL1_uc002ucq.2_Nonsense_Mutation_p.Q194*|COBLL1_uc010zcx.1_Nonsense_Mutation_p.Q240*|COBLL1_uc002ucs.1_Non-coding_Transcript	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	232										ovary(2)|pancreas(1)	3														0.404762	94.412581	95.109158	34	50	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	165584560	165584560	3792	2	G	A	A	A	585	45	COBLL1	5	2
SESTD1	91404	broad.mit.edu	37	2	180014079	180014079	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:180014079C>T	uc002uni.3	-	c.526G>A	c.(526-528)GAA>AAA	p.E176K		NM_178123	NP_835224	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	176					regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)											0.333333	16.743814	17.186718	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	180014079	180014079	14615	2	C	T	T	T	377	29	SESTD1	2	2
XRCC5	7520	broad.mit.edu	37	2	217012854	217012854	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:217012854C>T	uc002vfy.2	+	c.1525C>T	c.(1525-1527)CAG>TAG	p.Q509*	XRCC5_uc002vfz.2_Nonsense_Mutation_p.Q395*	NM_021141	NP_066964	P13010	XRCC5_HUMAN	ATP-dependent DNA helicase II	509	Pro-rich.				double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|telomeric DNA binding			kidney(1)	1		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)										0.358333	122.573251	124.701248	43	77	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	217012854	217012854	18039	2	C	T	T	T	377	29	XRCC5	5	2
SP140	11262	broad.mit.edu	37	2	231135347	231135347	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231135347G>A	uc002vql.2	+	c.1491G>A	c.(1489-1491)AGG>AGA	p.R497R	SP140_uc010zma.1_Non-coding_Transcript|SP140_uc002vqn.2_Silent_p.R383R|SP140_uc002vqm.2_Silent_p.R437R|SP140_uc010fxl.2_Silent_p.R470R	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1	497	Nuclear localization signal (Potential).				defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)					p.R497R(BT474-Tumor)	802				0.16129	9.953831	13.338404	5	26	KEEP	---	---	---	---	capture		Silent	SNP	231135347	231135347	15462	2	G	A	A	A	529	41	SP140	2	2
C2orf63	130162	broad.mit.edu	37	2	55439826	55439826	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:55439826G>C	uc002ryi.2	-	c.482C>G	c.(481-483)CCT>CGT	p.P161R	C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Missense_Mutation_p.P39R	NM_152385	NP_689598	Q8NHS4	CB063_HUMAN	hypothetical protein LOC130162 isoform 1	161							binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)											0.27907	29.064242	30.965697	12	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55439826	55439826	2270	2	G	C	C	C	455	35	C2orf63	3	3
OTX1	5013	broad.mit.edu	37	2	63280140	63280140	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63280140C>T	uc002scd.2	+	c.15C>T	c.(13-15)CTC>CTT	p.L5L	OTX1_uc010ypt.1_5'UTR	NM_014562	NP_055377	P32242	OTX1_HUMAN	orthodenticle homeobox 1	5						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(2)	2	Lung NSC(7;0.121)|all_lung(7;0.211)													0.163636	35.133875	46.91581	18	92	KEEP	---	---	---	---	capture		Silent	SNP	63280140	63280140	11733	2	C	T	T	T	366	29	OTX1	2	2
DYSF	8291	broad.mit.edu	37	2	71901354	71901354	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71901354G>A	uc010fen.2	+	c.5812G>A	c.(5812-5814)GAG>AAG	p.E1938K	DYSF_uc010feg.2_Missense_Mutation_p.E1930K|DYSF_uc010feh.2_Missense_Mutation_p.E1906K|DYSF_uc002sig.3_Missense_Mutation_p.E1885K|DYSF_uc010yqx.1_Non-coding_Transcript|DYSF_uc010fee.2_Missense_Mutation_p.E1920K|DYSF_uc010fef.2_Missense_Mutation_p.E1937K|DYSF_uc002sie.2_Missense_Mutation_p.E1899K|DYSF_uc010fei.2_Missense_Mutation_p.E1916K|DYSF_uc010fek.2_Missense_Mutation_p.E1917K|DYSF_uc010fej.2_Missense_Mutation_p.E1907K|DYSF_uc010fel.2_Missense_Mutation_p.E1886K|DYSF_uc010feo.2_Missense_Mutation_p.E1931K|DYSF_uc010fem.2_Missense_Mutation_p.E1921K|DYSF_uc002sif.2_Missense_Mutation_p.E1900K|DYSF_uc010yqy.1_Missense_Mutation_p.E780K|DYSF_uc010yqz.1_Missense_Mutation_p.E660K	NM_001130987	NP_001124459	O75923	DYSF_HUMAN	dysferlin isoform 1	1899	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.4	46.502213	46.84854	16	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71901354	71901354	5045	2	G	A	A	A	585	45	DYSF	2	2
CTNNA2	1496	broad.mit.edu	37	2	80101245	80101245	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:80101245G>A	uc010ysh.1	+	c.629G>A	c.(628-630)CGA>CAA	p.R210Q	CTNNA2_uc010yse.1_Missense_Mutation_p.R210Q|CTNNA2_uc010ysf.1_Missense_Mutation_p.R210Q|CTNNA2_uc010ysg.1_Missense_Mutation_p.R210Q	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	210					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)	8										489				0.254902	35.258203	38.032804	13	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80101245	80101245	4172	2	G	A	A	A	481	37	CTNNA2	1	1
SLC7A14	57709	broad.mit.edu	37	3	170216672	170216672	+	Silent	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:170216672C>A	uc003fgz.2	-	c.543G>T	c.(541-543)GGG>GGT	p.G181G	CLDN11_uc011bpt.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	181						integral to membrane	amino acid transmembrane transporter activity			ovary(2)|liver(1)|central_nervous_system(1)	4	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)											0.52	37.965864	37.974285	13	12	KEEP	---	---	---	---	capture		Silent	SNP	170216672	170216672	15193	3	C	A	A	A	379	30	SLC7A14	2	2
RNF168	165918	broad.mit.edu	37	3	196199040	196199040	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:196199040C>G	uc003fwq.2	-	c.1366G>C	c.(1366-1368)GAG>CAG	p.E456Q	RNF168_uc010iah.2_Missense_Mutation_p.E289Q	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	456	MIU motif 2.				double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)										0.565217	225.285004	225.714047	65	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196199040	196199040	13936	3	C	G	G	G	390	30	RNF168	3	3
EFHB	151651	broad.mit.edu	37	3	19940970	19940970	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:19940970C>A	uc003cbl.3	-	c.1456G>T	c.(1456-1458)GAT>TAT	p.D486Y	EFHB_uc003cbm.2_Missense_Mutation_p.D356Y	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	486					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0														0.636364	66.782076	67.321949	21	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19940970	19940970	5133	3	C	A	A	A	377	29	EFHB	2	2
SCN11A	11280	broad.mit.edu	37	3	38938482	38938482	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38938482C>A	uc011ays.1	-	c.2257G>T	c.(2257-2259)GAT>TAT	p.D753Y	SCN11A_uc010hhn.1_5'Flank	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	753	II.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)									0.521739	29.943402	29.950432	12	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38938482	38938482	14395	3	C	A	A	A	390	30	SCN11A	2	2
TTC21A	199223	broad.mit.edu	37	3	39159580	39159580	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39159580G>A	uc003cje.2	+	c.737G>A	c.(736-738)AGC>AAC	p.S246N	TTC21A_uc003cja.2_Missense_Mutation_p.S246N|TTC21A_uc010hho.1_Missense_Mutation_p.S168N|TTC21A_uc003cjb.2_3'UTR|TTC21A_uc003cjc.2_Missense_Mutation_p.S246N|TTC21A_uc003cjd.2_Non-coding_Transcript|TTC21A_uc011ayx.1_Missense_Mutation_p.S205N	NM_001105513	NP_001098983	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 1	246	TPR 5.						binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)										0.592593	106.806985	107.211308	32	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39159580	39159580	17241	3	G	A	A	A	442	34	TTC21A	2	2
CX3CR1	1524	broad.mit.edu	37	3	39307728	39307728	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39307728C>T	uc003cjl.2	-	c.273G>A	c.(271-273)TTG>TTA	p.L91L		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	91	Extracellular (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)										0.386364	47.057621	47.557722	17	27	KEEP	---	---	---	---	capture		Silent	SNP	39307728	39307728	4235	3	C	T	T	T	376	29	CX3CR1	2	2
COL25A1	84570	broad.mit.edu	37	4	109784503	109784503	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109784503C>T	uc003hze.1	-	c.1124G>A	c.(1123-1125)CGA>CAA	p.R375Q	COL25A1_uc003hzg.2_Missense_Mutation_p.R375Q|COL25A1_uc003hzd.2_Non-coding_Transcript|COL25A1_uc003hzf.2_Missense_Mutation_p.R156Q	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	375	Extracellular (Potential).|Collagen-like 5.					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)										0.333333	22.695025	23.283929	8	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109784503	109784503	3822	4	C	T	T	T	403	31	COL25A1	1	1
CRIPAK	285464	broad.mit.edu	37	4	1389587	1389587	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:1389587C>T	uc003gdf.2	+	c.1288C>T	c.(1288-1290)CGT>TGT	p.R430C		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	430	Interaction with PAK1.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)											0.147541	16.764193	24.016791	9	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1389587	1389587	4016	4	C	T	T	T	247	19	CRIPAK	1	1
TBC1D19	55296	broad.mit.edu	37	4	26675489	26675489	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:26675489G>C	uc003gsf.3	+	c.795G>C	c.(793-795)TTG>TTC	p.L265F	TBC1D19_uc010iew.2_Missense_Mutation_p.L265F|TBC1D19_uc011bxu.1_Missense_Mutation_p.L200F	NM_018317	NP_060787	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	265	Rab-GAP TBC.					intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)												0.227273	14.665594	16.165714	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26675489	26675489	16129	4	G	C	C	C	581	45	TBC1D19	3	3
HTT	3064	broad.mit.edu	37	4	3156082	3156082	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:3156082G>A	uc011bvq.1	+	c.3567G>A	c.(3565-3567)GAG>GAA	p.E1189E		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	1187					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			ovary(1)|lung(1)	2		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)										0.307692	10.993102	11.422934	4	9	KEEP	---	---	---	---	capture		Silent	SNP	3156082	3156082	7757	4	G	A	A	A	425	33	HTT	2	2
MAN2B2	23324	broad.mit.edu	37	4	6580191	6580191	+	Silent	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:6580191G>C	uc003gjf.1	+	c.357G>C	c.(355-357)GTG>GTC	p.V119V	MAN2B2_uc003gje.1_Silent_p.V119V|MAN2B2_uc011bwf.1_Silent_p.V119V	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	119					mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2														0.285714	11.393615	11.970916	4	10	KEEP	---	---	---	---	capture		Silent	SNP	6580191	6580191	9600	4	G	C	C	C	574	45	MAN2B2	3	3
GRM1	2911	broad.mit.edu	37	6	146351273	146351273	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146351273C>G	uc010khw.1	+	c.620C>G	c.(619-621)TCT>TGT	p.S207C	GRM1_uc010khu.1_Missense_Mutation_p.S207C|GRM1_uc010khv.1_Missense_Mutation_p.S207C|GRM1_uc003qll.2_Missense_Mutation_p.S207C|GRM1_uc011edz.1_Missense_Mutation_p.S207C|GRM1_uc011eea.1_Missense_Mutation_p.S207C	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	207	Extracellular (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.25	59.264698	63.80691	20	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146351273	146351273	7075	6	C	G	G	G	416	32	GRM1	3	3
PLEKHG1	57480	broad.mit.edu	37	6	151089832	151089832	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:151089832C>T	uc011eem.1	+	c.647C>T	c.(646-648)TCA>TTA	p.S216L	PLEKHG1_uc011eel.1_Missense_Mutation_p.S197L|PLEKHG1_uc003qny.1_Missense_Mutation_p.S157L|PLEKHG1_uc003qnz.2_Missense_Mutation_p.S157L	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	157	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)										0.130435	3.921285	6.966969	3	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151089832	151089832	12494	6	C	T	T	T	377	29	PLEKHG1	2	2
HIST1H2BC	8347	broad.mit.edu	37	6	26123793	26123793	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26123793C>G	uc003ngk.3	-	c.340G>C	c.(340-342)GAG>CAG	p.E114Q	HIST1H2BC_uc003ngl.2_Missense_Mutation_p.E114Q|HIST1H2AC_uc003ngm.2_5'Flank|HIST1H2AC_uc003ngn.2_5'Flank|HIST1H2AC_uc003ngo.2_5'Flank|HIST1H2AC_uc003ngp.2_5'Flank	NM_003526	NP_003517	P62807	H2B1C_HUMAN	histone cluster 1, H2bc	114					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding|protein binding			ovary(1)	1														0.3	61.135603	63.646052	21	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26123793	26123793	7427	6	C	G	G	G	390	30	HIST1H2BC	3	3
TREML1	340205	broad.mit.edu	37	6	41118012	41118012	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41118012C>G	uc011duc.1	-	c.608G>C	c.(607-609)AGA>ACA	p.R203T	TREML1_uc003opx.2_Intron|TREML1_uc011dud.1_Missense_Mutation_p.R92T	NM_178174	NP_835468	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid	203	Cytoplasmic (Potential).				calcium-mediated signaling|innate immune response|platelet activation	cell surface|integral to membrane|plasma membrane|platelet alpha granule	protein binding|receptor activity			breast(1)	1	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.375	30.71651	31.027394	9	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41118012	41118012	17016	6	C	G	G	G	416	32	TREML1	3	3
DSP	1832	broad.mit.edu	37	6	7581355	7581355	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:7581355G>A	uc003mxp.1	+	c.4932G>A	c.(4930-4932)CTG>CTA	p.L1644L	DSP_uc003mxq.1_Intron	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	1644	Central fibrous rod domain.|Potential.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)										0.677966	120.342851	121.981846	40	19	KEEP	---	---	---	---	capture		Silent	SNP	7581355	7581355	4965	6	G	A	A	A	574	45	DSP	2	2
SLC12A9	56996	broad.mit.edu	37	7	100457570	100457570	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100457570G>C	uc003uwp.2	+	c.1041G>C	c.(1039-1041)TTG>TTC	p.L347F	SLC12A9_uc003uwq.2_Missense_Mutation_p.L258F|SLC12A9_uc011kki.1_5'UTR|SLC12A9_uc003uwr.2_Missense_Mutation_p.L83F|SLC12A9_uc003uws.2_5'UTR|SLC12A9_uc003uwt.2_Missense_Mutation_p.L83F|SLC12A9_uc003uwv.2_5'UTR	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride	347	Helical; (Potential).					integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)													0.320513	79.394092	81.601994	25	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100457570	100457570	14885	7	G	C	C	C	581	45	SLC12A9	3	3
OR2F2	135948	broad.mit.edu	37	7	143633081	143633081	+	Silent	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143633081C>T	uc011ktv.1	+	c.756C>T	c.(754-756)TAC>TAT	p.Y252Y		NM_001004685	NP_001004685	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0903)													0.34375	62.631713	64.011323	22	42	KEEP	---	---	---	---	capture		Silent	SNP	143633081	143633081	11403	7	C	T	T	T	246	19	OR2F2	1	1
HOXA1	3198	broad.mit.edu	37	7	27134880	27134880	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27134880C>A	uc003sye.2	-	c.652G>T	c.(652-654)GGG>TGG	p.G218W	HOXA1_uc003syd.2_3'UTR	NM_005522	NP_005513	P49639	HXA1_HUMAN	homeobox A1 isoform a	218						nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.333333	25.068302	25.73137	9	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27134880	27134880	7580	7	C	A	A	A	312	24	HOXA1	2	2
COBL	23242	broad.mit.edu	37	7	51096213	51096213	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:51096213C>G	uc003tps.2	-	c.2751G>C	c.(2749-2751)CAG>CAC	p.Q917H	COBL_uc003tpr.3_Missense_Mutation_p.Q860H|COBL_uc011kcl.1_Missense_Mutation_p.Q860H|COBL_uc003tpp.3_Missense_Mutation_p.Q646H|COBL_uc003tpq.3_Missense_Mutation_p.Q801H|COBL_uc003tpo.3_Missense_Mutation_p.Q402H	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	860										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.463768	105.112257	105.188601	32	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51096213	51096213	3791	7	C	G	G	G	415	32	COBL	3	3
COBL	23242	broad.mit.edu	37	7	51096593	51096593	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:51096593C>T	uc003tps.2	-	c.2371G>A	c.(2371-2373)GAC>AAC	p.D791N	COBL_uc003tpr.3_Missense_Mutation_p.D734N|COBL_uc011kcl.1_Missense_Mutation_p.D734N|COBL_uc003tpp.3_Missense_Mutation_p.D520N|COBL_uc003tpq.3_Missense_Mutation_p.D675N|COBL_uc003tpo.3_Missense_Mutation_p.D276N	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	734										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.318182	37.332671	38.626688	14	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51096593	51096593	3791	7	C	T	T	T	377	29	COBL	2	2
SAMD9L	219285	broad.mit.edu	37	7	92763767	92763767	+	Silent	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92763767G>A	uc003umh.1	-	c.1518C>T	c.(1516-1518)AGC>AGT	p.S506S	SAMD9L_uc003umj.1_Silent_p.S506S|SAMD9L_uc003umi.1_Silent_p.S506S|SAMD9L_uc010lfb.1_Silent_p.S506S|SAMD9L_uc003umk.1_Silent_p.S506S|SAMD9L_uc010lfc.1_Silent_p.S506S|SAMD9L_uc010lfd.1_Silent_p.S506S|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	506										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)		STAD - Stomach adenocarcinoma(171;0.000302)											0.351852	105.307597	107.402211	38	70	KEEP	---	---	---	---	capture		Silent	SNP	92763767	92763767	14307	7	G	A	A	A	490	38	SAMD9L	1	1
CYP11B1	1584	broad.mit.edu	37	8	143958264	143958264	+	Silent	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:143958264C>G	uc010mey.2	-	c.846G>C	c.(844-846)CTG>CTC	p.L282L	CYP11B1_uc010mex.2_5'Flank|CYP11B1_uc003yxh.2_5'Flank|CYP11B1_uc003yxi.2_Silent_p.L211L|CYP11B1_uc003yxj.2_Silent_p.L211L	NM_000497	NP_000488	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B,	211					aldosterone biosynthetic process|cortisol biosynthetic process|glucose homeostasis|immune response|oxidation-reduction process|regulation of blood pressure|response to stress|xenobiotic metabolic process	mitochondrial inner membrane	electron carrier activity|heme binding|steroid 11-beta-monooxygenase activity			ovary(3)	3	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Mitotane(DB00648)									0.380952	16.446518	16.723004	8	13	KEEP	---	---	---	---	capture		Silent	SNP	143958264	143958264	4310	8	C	G	G	G	262	21	CYP11B1	3	3
NPM2	10361	broad.mit.edu	37	8	21890671	21890671	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:21890671C>T	uc003xab.2	+	c.301C>T	c.(301-303)CCA>TCA	p.P101S	NPM2_uc003xac.2_Missense_Mutation_p.P101S|NPM2_uc003xad.2_Missense_Mutation_p.P101S|NPM2_uc003xae.2_Missense_Mutation_p.P101S|NPM2_uc003xaf.2_Missense_Mutation_p.P101S	NM_182795	NP_877724	Q86SE8	NPM2_HUMAN	nucleoplasmin 2	101					chromatin remodeling|embryo development|oocyte differentiation|positive regulation of meiosis|regulation of exit from mitosis|single fertilization	cytoplasmic chromatin|nuclear chromatin	histone binding|nucleic acid binding				0				Colorectal(74;8.48e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0618)										0.153846	16.566206	22.52299	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21890671	21890671	10993	8	C	T	T	T	286	22	NPM2	2	2
SFTPC	6440	broad.mit.edu	37	8	22019333	22019333	+	Missense_Mutation	SNP	T	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:22019333T>A	uc003xaw.3	+	c.139T>A	c.(139-141)TGC>AGC	p.C47S	SFTPC_uc003xax.3_5'UTR|SFTPC_uc011kza.1_5'UTR|SFTPC_uc003xaz.2_5'UTR|SFTPC_uc003xay.3_5'UTR	NM_003018	NP_003009	P11686	PSPC_HUMAN	surfactant protein C precursor	Error:Variant_position_missing_in_P11686_after_alignment					respiratory gaseous exchange	extracellular space					0				Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)										0.278481	63.215656	66.703015	22	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22019333	22019333	14683	8	T	A	A	A	703	55	SFTPC	3	3
RAD54B	25788	broad.mit.edu	37	8	95406084	95406084	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95406084C>G	uc003ygk.2	-	c.1405G>C	c.(1405-1407)GAA>CAA	p.E469Q	RAD54B_uc010may.1_Missense_Mutation_p.E276Q|RAD54B_uc003ygl.1_Non-coding_Transcript	NM_012415	NP_036547	Q9Y620	RA54B_HUMAN	RAD54 homolog B	469	Helicase ATP-binding.				mitotic recombination|reciprocal meiotic recombination	nucleus	ATP binding|DNA binding|DNA helicase activity|RNA helicase activity			kidney(2)|lung(1)	3	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)											0.337209	90.16374	92.172102	29	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95406084	95406084	13452	8	C	G	G	G	416	32	RAD54B	3	3
MPDZ	8777	broad.mit.edu	37	9	13126722	13126722	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:13126722C>G	uc010mhy.2	-	c.4514G>C	c.(4513-4515)GGA>GCA	p.G1505A	MPDZ_uc003zky.3_Missense_Mutation_p.G67A|MPDZ_uc010mib.2_Missense_Mutation_p.G210A|MPDZ_uc010mhx.2_Missense_Mutation_p.G327A|MPDZ_uc011lmm.1_Missense_Mutation_p.G364A|MPDZ_uc003zkz.3_Missense_Mutation_p.G198A|MPDZ_uc010mhz.2_Missense_Mutation_p.G1472A|MPDZ_uc011lmn.1_Missense_Mutation_p.G1472A|MPDZ_uc003zlb.3_Missense_Mutation_p.G1505A|MPDZ_uc010mia.1_Missense_Mutation_p.G1505A	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1505	PDZ 9.				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)										0.263158	13.671761	14.633251	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13126722	13126722	10114	9	C	G	G	G	390	30	MPDZ	3	3
NRK	203447	broad.mit.edu	37	X	105167115	105167115	+	Silent	SNP	A	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:105167115A>T	uc004emd.2	+	c.2616A>T	c.(2614-2616)CCA>CCT	p.P872P	NRK_uc010npc.1_Silent_p.P540P	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	872					protein phosphorylation		ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14										430				0.346457	134.664636	137.306599	44	83	KEEP	---	---	---	---	capture		Silent	SNP	105167115	105167115	11060	23	A	T	T	T	80	7	NRK	3	3
DOCK11	139818	broad.mit.edu	37	X	117788871	117788871	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:117788871C>T	uc004eqp.2	+	c.4916C>T	c.(4915-4917)GCG>GTG	p.A1639V	DOCK11_uc004eqq.2_Missense_Mutation_p.A1418V	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1639	DHR-2.				blood coagulation	cytosol	GTP binding			ovary(3)	3														0.361345	121.363936	123.388291	43	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117788871	117788871	4870	23	C	T	T	T	351	27	DOCK11	1	1
SLC9A6	10479	broad.mit.edu	37	X	135115594	135115594	+	Missense_Mutation	SNP	A	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135115594A>G	uc004ezk.2	+	c.1669A>G	c.(1669-1671)AGA>GGA	p.R557G	SLC9A6_uc004ezj.2_Missense_Mutation_p.R525G	NM_001042537	NP_001036002	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen	525					regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.351562	137.216214	139.712417	45	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135115594	135115594	15215	23	A	G	G	G	140	11	SLC9A6	4	4
CD99L2	83692	broad.mit.edu	37	X	149944650	149944650	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149944650G>A	uc004fel.2	-	c.652C>T	c.(652-654)CAG>TAG	p.Q218*	CD99L2_uc004fek.2_Non-coding_Transcript|CD99L2_uc004fem.2_Nonsense_Mutation_p.Q169*|CD99L2_uc004fen.2_Nonsense_Mutation_p.Q146*|CD99L2_uc004feo.2_Non-coding_Transcript|CD99L2_uc011myb.1_Nonsense_Mutation_p.Q145*	NM_031462	NP_113650	Q8TCZ2	C99L2_HUMAN	CD99 antigen-like 2 isoform E3'-E4'-E3-E4	218	Cytoplasmic (Potential).				cell adhesion	cell junction|integral to membrane				large_intestine(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.328125	58.653783	60.329937	21	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	149944650	149944650	3179	23	G	A	A	A	585	45	CD99L2	5	2
DMD	1756	broad.mit.edu	37	X	31279101	31279101	+	Missense_Mutation	SNP	G	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:31279101G>T	uc004dda.1	-	c.9257C>A	c.(9256-9258)CCC>CAC	p.P3086H	DMD_uc004dcq.1_Missense_Mutation_p.P357H|DMD_uc004dcr.1_Missense_Mutation_p.P626H|DMD_uc004dcs.1_Missense_Mutation_p.P626H|DMD_uc004dct.1_Missense_Mutation_p.P626H|DMD_uc004dcu.1_Missense_Mutation_p.P626H|DMD_uc004dcv.1_Missense_Mutation_p.P626H|DMD_uc004dcw.2_Missense_Mutation_p.P1742H|DMD_uc004dcx.2_Missense_Mutation_p.P1745H|DMD_uc004dcz.2_Missense_Mutation_p.P2963H|DMD_uc004dcy.1_Missense_Mutation_p.P3082H|DMD_uc004ddb.1_Missense_Mutation_p.P3078H|DMD_uc004dcm.1_Missense_Mutation_p.P18H|DMD_uc004dcn.1_Missense_Mutation_p.P18H|DMD_uc004dco.1_Missense_Mutation_p.P18H|DMD_uc004dcp.1_Missense_Mutation_p.P18H|DMD_uc011mkb.1_Missense_Mutation_p.P18H|DMD_uc010ngm.2_Missense_Mutation_p.P18H	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	3086	Interaction with SYNM (By similarity).|WW.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.377778	50.662401	51.252871	17	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31279101	31279101	4760	23	G	T	T	T	559	43	DMD	2	2
TRO	7216	broad.mit.edu	37	X	54950106	54950106	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54950106C>G	uc004dtq.2	+	c.1141C>G	c.(1141-1143)CAG>GAG	p.Q381E	TRO_uc011moj.1_Missense_Mutation_p.Q324E|TRO_uc004dts.2_Missense_Mutation_p.Q381E|TRO_uc004dtr.2_Missense_Mutation_p.Q381E|TRO_uc004dtt.2_Non-coding_Transcript|TRO_uc004dtu.2_Intron|TRO_uc004dtv.2_Intron|TRO_uc011mok.1_Intron|TRO_uc004dtw.2_Intron|TRO_uc004dtx.2_5'Flank	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	381					embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1														0.25	16.329715	17.701872	6	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54950106	54950106	17125	23	C	G	G	G	377	29	TRO	3	3
ZXDA	7789	broad.mit.edu	37	X	57935303	57935303	+	Missense_Mutation	SNP	A	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:57935303A>T	uc004dve.2	-	c.1552T>A	c.(1552-1554)TGT>AGT	p.C518S		NM_007156	NP_009087	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	518	Required for interaction with ZXDC.|C2H2-type 9.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.44186	58.000186	58.128711	19	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57935303	57935303	18855	23	A	T	T	T	91	7	ZXDA	3	3
MLL	4297	broad.mit.edu	37	11	118363894	118363894	+	Frame_Shift_Del	DEL	A	-	-			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118363894_118363894delA	uc001ptb.2	+	c.5127_5127delA	c.(5125-5127)TTAfs	p.L1709fs	MLL_uc001pta.2_Frame_Shift_Del_p.L1706fs	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1706	Bromo; divergent.				apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|unmethylated CpG binding|zinc ion binding			ovary(5)|kidney(5)|lung(3)|pancreas(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)	18	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)						723				0.36			33	58		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	118363894	118363894	10010	11	A	-	-	-	193	15	MLL	5	5
SLC5A12	159963	broad.mit.edu	37	11	26725075	26725076	+	Splice_Site_Ins	INS	-	A	A			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:26725075_26725076insA	uc001mra.2	-	c.821_splice	c.e6+1	p.L274_splice	SLC5A12_uc001mrb.2_Splice_Site_Ins|SLC5A12_uc001mrc.3_Splice_Site_Ins_p.L274_splice	NM_178498	NP_848593			solute carrier family 5 (sodium/glucose						sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(1)	1														0.38			39	63		---	---	---	---	capture_indel		Splice_Site_Ins	INS	26725075	26725076	15161	11	-	A	A	A	781	61	SLC5A12	5	5
NFKBIZ	64332	broad.mit.edu	37	3	101571949	101571950	+	Frame_Shift_Ins	INS	-	C	C			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:101571949_101571950insC	uc003dvp.2	+	c.579_580insC	c.(577-582)ACACCAfs	p.T193fs	NFKBIZ_uc003dvo.2_Frame_Shift_Ins_p.T93fs|NFKBIZ_uc010hpo.2_Frame_Shift_Ins_p.T93fs|NFKBIZ_uc003dvq.2_Frame_Shift_Ins_p.T193fs	NM_031419	NP_113607	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene	193_194					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2														0.59			23	16		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	101571949	101571950	10783	3	-	C	C	C	67	6	NFKBIZ	5	5
UBQLN1	29979	broad.mit.edu	37	9	86279969	86279970	+	Frame_Shift_Ins	INS	-	T	T			TCGA-05-5715-01	TCGA-05-5715-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:86279969_86279970insT	uc004amv.2	-	c.1423_1424insA	c.(1423-1425)ACGfs	p.T475fs	UBQLN1_uc004amw.2_Frame_Shift_Ins_p.T447fs	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1	475					apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						Melanoma(186;1284 2073 12755 14558 18426)								0.46			13	15		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	86279969	86279970	17454	9	-	T	T	T	520	40	UBQLN1	5	5
