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
C10orf93	255352	broad.mit.edu	37	10	134755107	134755107	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:134755107C>T	uc001llt.1	-	c.294G>A	c.(292-294)TCG>TCA	p.S98S	C10orf93_uc001llu.2_Silent_p.S98S	NM_173572	NP_775843	Q5SR76	CJ093_HUMAN	hypothetical protein LOC255352	98	TPR 1.						binding			pancreas(1)	1		all_cancers(35;1.8e-07)|all_epithelial(44;6.22e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Colorectal(31;0.119)|Glioma(114;0.172)|Melanoma(40;0.175)		Epithelial(32;4.28e-05)|OV - Ovarian serous cystadenocarcinoma(35;4.31e-05)|all cancers(32;5.02e-05)										0.176471	30.293231	38.663026	15	70	KEEP	---	---	---	---	capture		Silent	SNP	134755107	134755107	1662	10	C	T	T	T	288	23	C10orf93	1	1
CUBN	8029	broad.mit.edu	37	10	16996511	16996511	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:16996511C>A	uc001ioo.2	-	c.4732G>T	c.(4732-4734)GCC>TCC	p.A1578S		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1578	CUB 10.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)	18					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)					2704				0.168142	34.382214	46.151079	19	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16996511	16996511	4211	10	C	A	A	A	325	25	CUBN	2	2
PCDH15	65217	broad.mit.edu	37	10	55912864	55912864	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55912864G>T	uc010qhy.1	-	c.1795C>A	c.(1795-1797)CGA>AGA	p.R599R	PCDH15_uc010qhq.1_Silent_p.R599R|PCDH15_uc010qhr.1_Silent_p.R594R|PCDH15_uc010qhs.1_Silent_p.R606R|PCDH15_uc010qht.1_Silent_p.R601R|PCDH15_uc010qhu.1_Silent_p.R594R|PCDH15_uc001jjv.1_Silent_p.R572R|PCDH15_uc010qhv.1_Silent_p.R594R|PCDH15_uc010qhw.1_Silent_p.R557R|PCDH15_uc010qhx.1_Silent_p.R594R|PCDH15_uc010qhz.1_Silent_p.R594R|PCDH15_uc010qia.1_Silent_p.R572R|PCDH15_uc001jju.1_Silent_p.R594R|PCDH15_uc010qib.1_Silent_p.R572R|PCDH15_uc001jjw.2_Silent_p.R594R	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	594	Cadherin 5.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.105263	3.972382	9.857135	4	34	KEEP	---	---	---	---	capture		Silent	SNP	55912864	55912864	11931	10	G	T	T	T	493	38	PCDH15	1	1
MYPN	84665	broad.mit.edu	37	10	69881674	69881674	+	Missense_Mutation	SNP	A	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:69881674A>C	uc001jnm.3	+	c.479A>C	c.(478-480)GAG>GCG	p.E160A	MYPN_uc001jnl.1_Missense_Mutation_p.E160A|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Missense_Mutation_p.E160A|MYPN_uc001jnp.1_Missense_Mutation_p.E160A|MYPN_uc009xps.2_Missense_Mutation_p.E160A|MYPN_uc009xpt.2_Missense_Mutation_p.E160A|MYPN_uc010qit.1_5'UTR|MYPN_uc010qiu.1_Non-coding_Transcript	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	160	Interaction with CARP.					nucleus|sarcomere	actin binding			ovary(3)	3														0.130841	23.177357	37.355368	14	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69881674	69881674	10493	10	A	C	C	C	143	11	MYPN	4	4
PUS3	83480	broad.mit.edu	37	11	125765210	125765210	+	Missense_Mutation	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:125765210T>C	uc001qcy.2	-	c.853A>G	c.(853-855)ATC>GTC	p.I285V	HYLS1_uc009zbv.2_Intron|HYLS1_uc001qcx.3_Intron	NM_031307	NP_112597	Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	285						nucleus	RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)										0.103093	11.084634	26.305808	10	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125765210	125765210	13290	11	T	C	C	C	637	49	PUS3	4	4
RRM1	6240	broad.mit.edu	37	11	4142838	4142838	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4142838C>T	uc001lyw.3	+	c.881C>T	c.(880-882)CCT>CTT	p.P294L	RRM1_uc009yej.2_Non-coding_Transcript|RRM1_uc009yei.2_Missense_Mutation_p.P254L|RRM1_uc010qyc.1_Missense_Mutation_p.P197L|RRM1_uc010qyd.1_5'UTR	NM_001033	NP_001024	P23921	RIR1_HUMAN	ribonucleoside-diphosphate reductase M1 chain	294					deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion|oxidation-reduction process	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)								0.118182	19.216646	34.954025	13	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4142838	4142838	14161	11	C	T	T	T	312	24	RRM1	2	2
OR4A5	81318	broad.mit.edu	37	11	51412143	51412143	+	Missense_Mutation	SNP	A	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:51412143A>T	uc001nhi.1	-	c.253T>A	c.(253-255)TGT>AGT	p.C85S		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	85	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		all_lung(304;0.236)												0.081967	0.825717	11.676849	5	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51412143	51412143	11449	11	A	T	T	T	91	7	OR4A5	3	3
OR5M8	219484	broad.mit.edu	37	11	56258676	56258676	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56258676G>T	uc001nix.1	-	c.171C>A	c.(169-171)CCC>CCA	p.P57P		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	57	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)													0.129771	23.577192	41.059744	17	114	KEEP	---	---	---	---	capture		Silent	SNP	56258676	56258676	11586	11	G	T	T	T	600	47	OR5M8	2	2
TNKS1BP1	85456	broad.mit.edu	37	11	57089342	57089342	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57089342G>A	uc001njr.2	-	c.18C>T	c.(16-18)CTC>CTT	p.L6L	TNKS1BP1_uc001njs.2_Silent_p.L6L|TNKS1BP1_uc009ymd.1_5'UTR	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	6	Arg/Glu/Lys/Pro-rich (charged).				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)												0.121951	5.543325	11.286736	5	36	KEEP	---	---	---	---	capture		Silent	SNP	57089342	57089342	16861	11	G	A	A	A	574	45	TNKS1BP1	2	2
OSBP	5007	broad.mit.edu	37	11	59361700	59361700	+	Missense_Mutation	SNP	A	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59361700A>C	uc001noc.1	-	c.1340T>G	c.(1339-1341)CTT>CGT	p.L447R	OSBP_uc009ymr.1_Non-coding_Transcript	NM_002556	NP_002547	P22059	OSBP1_HUMAN	oxysterol binding protein	447	Sterol binding (By similarity).				lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)										0.174312	43.0562	53.967106	19	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59361700	59361700	11684	11	A	C	C	C	39	3	OSBP	4	4
MRPL16	54948	broad.mit.edu	37	11	59575233	59575233	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59575233C>T	uc001noh.2	-	c.211G>A	c.(211-213)GAC>AAC	p.D71N		NM_017840	NP_060310	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16 precursor	71							rRNA binding			central_nervous_system(1)	1														0.150142	75.456333	116.8866	53	300	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59575233	59575233	10174	11	C	T	T	T	377	29	MRPL16	2	2
TMEM151A	256472	broad.mit.edu	37	11	66062484	66062484	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66062484G>A	uc001ohl.2	+	c.767G>A	c.(766-768)CGC>CAC	p.R256H		NM_153266	NP_694998	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	256						integral to membrane				central_nervous_system(1)	1														0.210526	8.391192	9.863227	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66062484	66062484	16602	11	G	A	A	A	494	38	TMEM151A	1	1
TPP1	1200	broad.mit.edu	37	11	6636182	6636182	+	Missense_Mutation	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6636182T>C	uc001mel.1	-	c.1466A>G	c.(1465-1467)AAT>AGT	p.N489S	TAF10_uc001mej.1_5'Flank|TPP1_uc001mek.1_Missense_Mutation_p.N246S	NM_000391	NP_000382	O14773	TPP1_HUMAN	tripeptidyl-peptidase I preproprotein	489					bone resorption|cell death|lipid metabolic process|lysosome organization|nervous system development|neuromuscular process controlling balance|peptide catabolic process|protein catabolic process|proteolysis	lysosome|melanosome|soluble fraction	metal ion binding|peptide binding|protein binding|serine-type endopeptidase activity|tripeptidyl-peptidase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)										0.181818	120.485948	143.473157	44	198	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6636182	6636182	16955	11	T	C	C	C	676	52	TPP1	4	4
NLRP14	338323	broad.mit.edu	37	11	7079078	7079078	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7079078C>A	uc001mfb.1	+	c.2462C>A	c.(2461-2463)TCC>TAC	p.S821Y		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	821	LRR 4.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|lung(1)|pancreas(1)	7				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)										0.075862	0.612564	27.343401	11	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7079078	7079078	10879	11	C	A	A	A	403	31	NLRP14	1	1
FAT3	120114	broad.mit.edu	37	11	92533924	92533924	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92533924C>G	uc001pdj.3	+	c.7745C>G	c.(7744-7746)ACT>AGT	p.T2582S		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2582	Cadherin 23.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.090909	6.101067	17.233569	6	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92533924	92533924	5927	11	C	G	G	G	260	20	FAT3	3	3
CWC15	51503	broad.mit.edu	37	11	94705238	94705238	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94705238G>C	uc001pfd.3	-	c.112C>G	c.(112-114)CAT>GAT	p.H38D	CWC15_uc009ywl.1_Missense_Mutation_p.H38D|KDM4D_uc001pfe.2_5'Flank	NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog	38					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												0.187192	105.422976	124.02746	38	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94705238	94705238	4227	11	G	C	C	C	585	45	CWC15	3	3
PXN	5829	broad.mit.edu	37	12	120651681	120651681	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120651681G>A	uc001txt.2	-	c.1473C>T	c.(1471-1473)CTC>CTT	p.L491L	PXN_uc001txu.2_Silent_p.L303L|PXN_uc001txv.2_Silent_p.L372L|PXN_uc001txx.2_Silent_p.L324L|PXN_uc001txy.2_Silent_p.L457L|PXN_uc001txz.2_Non-coding_Transcript	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	491	LIM zinc-binding 3.				cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)									115				0.1875	6.019343	7.479701	3	13	KEEP	---	---	---	---	capture		Silent	SNP	120651681	120651681	13310	12	G	A	A	A	574	45	PXN	2	2
MPHOSPH9	10198	broad.mit.edu	37	12	123706321	123706321	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:123706321G>C	uc001uel.2	-	c.14C>G	c.(13-15)TCT>TGT	p.S5C	MPHOSPH9_uc010tal.1_5'UTR|MPHOSPH9_uc010tam.1_Non-coding_Transcript|MPHOSPH9_uc001uem.2_5'UTR	NM_022782	NP_073619	Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	5					M phase of mitotic cell cycle	Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)										0.129252	41.017522	60.690615	19	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123706321	123706321	10120	12	G	C	C	C	429	33	MPHOSPH9	3	3
AACS	65985	broad.mit.edu	37	12	125561082	125561082	+	Missense_Mutation	SNP	A	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:125561082A>G	uc001uhc.2	+	c.283A>G	c.(283-285)AAA>GAA	p.K95E	AACS_uc009zyg.2_Non-coding_Transcript|AACS_uc001uhd.2_Missense_Mutation_p.K95E|AACS_uc009zyh.2_Non-coding_Transcript	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	95					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)										0.08284	5.721444	35.62263	14	155	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125561082	125561082	10	12	A	G	G	G	65	5	AACS	4	4
EP400	57634	broad.mit.edu	37	12	132547093	132547093	+	Silent	SNP	A	G	G	rs71838933		TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:132547093A>G	uc001ujn.2	+	c.8181A>G	c.(8179-8181)CAA>CAG	p.Q2727Q	EP400_uc001ujl.2_Silent_p.Q2726Q|EP400_uc001ujm.2_Silent_p.Q2646Q|EP400_uc001ujp.2_5'UTR	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	2763	Poly-Gln.|Interaction with ZNF42 (By similarity).				histone H2A acetylation|histone H4 acetylation	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)										0.5	7.050058	7.050058	2	2	KEEP	---	---	---	---	capture		Silent	SNP	132547093	132547093	5342	12	A	G	G	G	24	2	EP400	4	4
LRRK2	120892	broad.mit.edu	37	12	40702915	40702915	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:40702915G>T	uc001rmg.3	+	c.4197G>T	c.(4195-4197)GAG>GAT	p.E1399D	LRRK2_uc009zjw.2_Missense_Mutation_p.E237D|LRRK2_uc001rmi.2_Missense_Mutation_p.E232D	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1399	Roc.				activation of MAPKK activity|determination of adult lifespan|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(11)|lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)|stomach(1)|urinary_tract(1)|pancreas(1)	18	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)								1771				0.0875	1.158161	14.936908	7	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40702915	40702915	9409	12	G	T	T	T	451	35	LRRK2	2	2
CDK4	1019	broad.mit.edu	37	12	58145430	58145430	+	Missense_Mutation	SNP	C	A	A	rs104894340		TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:58145430C>A	uc001spv.2	-	c.71G>T	c.(70-72)CGT>CTT	p.R24L	CDK4_uc010ssb.1_5'UTR|CDK4_uc001spw.2_Non-coding_Transcript	NM_000075	NP_000066	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	24	Protein kinase.		R -> H (in CMM3).		cell division|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|positive regulation of fibroblast proliferation|protein phosphorylation|regulation of gene expression|response to drug|S phase of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol|membrane	ATP binding|cyclin-dependent protein kinase activity|protein binding			central_nervous_system(1)	1	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)							59				0.157895	27.587964	38.172815	15	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58145430	58145430	3270	12	C	A	A	A	247	19	CDK4	1	1
LRRIQ1	84125	broad.mit.edu	37	12	85449619	85449619	+	Missense_Mutation	SNP	A	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85449619A>C	uc001tac.2	+	c.1048A>C	c.(1048-1050)AAA>CAA	p.K350Q	LRRIQ1_uc001tab.1_Missense_Mutation_p.K350Q|LRRIQ1_uc001taa.1_Missense_Mutation_p.K325Q	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	350	Glu-rich.									ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(134;0.212)										0.210526	11.789587	13.262053	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85449619	85449619	9405	12	A	C	C	C	13	1	LRRIQ1	4	4
ALX1	8092	broad.mit.edu	37	12	85680674	85680674	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85680674G>T	uc001tae.3	+	c.575G>T	c.(574-576)CGT>CTT	p.R192L		NM_006982	NP_008913	Q15699	ALX1_HUMAN	cartilage paired-class homeoprotein 1	192					brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription corepressor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(134;0.134)										0.211538	28.697983	32.697084	11	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85680674	85680674	559	12	G	T	T	T	520	40	ALX1	1	1
KCTD4	386618	broad.mit.edu	37	13	45768147	45768147	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:45768147C>T	uc001uzx.3	-	c.556G>A	c.(556-558)GAG>AAG	p.E186K	GTF2F2_uc001uzv.2_Intron|GTF2F2_uc001uzw.2_Intron	NM_198404	NP_940686	Q8WVF5	KCTD4_HUMAN	potassium channel tetramerisation domain	186						voltage-gated potassium channel complex	voltage-gated potassium channel activity				0		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)										0.081633	0.283606	26.48525	12	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45768147	45768147	8417	13	C	T	T	T	390	30	KCTD4	2	2
UGGT2	55757	broad.mit.edu	37	13	96624892	96624892	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:96624892C>T	uc001vmt.2	-	c.1126G>A	c.(1126-1128)GAT>AAT	p.D376N		NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	376					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3														0.088235	2.098237	19.58282	9	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96624892	96624892	17500	13	C	T	T	T	403	31	UGGT2	1	1
TRAPPC6B	122553	broad.mit.edu	37	14	39628703	39628703	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:39628703G>C	uc001wut.1	-	c.133C>G	c.(133-135)CAA>GAA	p.Q45E	TRAPPC6B_uc001wuu.1_Missense_Mutation_p.Q45E|TRAPPC6B_uc001wuv.1_Non-coding_Transcript|TRAPPC6B_uc010tqd.1_Intron	NM_001079537	NP_001073005	Q86SZ2	TPC6B_HUMAN	trafficking protein particle complex 6B isoform	45					vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)										0.1	13.669278	32.983055	12	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39628703	39628703	17008	14	G	C	C	C	624	48	TRAPPC6B	3	3
NIN	51199	broad.mit.edu	37	14	51288719	51288719	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:51288719C>A	uc001wyi.2	-	c.56G>T	c.(55-57)AGT>ATT	p.S19I	NIN_uc001wyj.2_Non-coding_Transcript|NIN_uc001wyk.2_Missense_Mutation_p.S19I|NIN_uc010tqp.1_Intron|NIN_uc001wym.2_Missense_Mutation_p.S19I|NIN_uc001wyo.2_Missense_Mutation_p.S19I|NIN_uc001wyp.1_Splice_Site_SNP	NM_020921	NP_065972	Q8N4C6	NIN_HUMAN	ninein isoform 2	19	EF-hand 1.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	all_epithelial(31;0.00244)|Breast(41;0.127)									745				0.09611	23.791903	95.327096	42	395	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51288719	51288719	10818	14	C	A	A	A	260	20	NIN	2	2
SQRDL	58472	broad.mit.edu	37	15	45981368	45981368	+	Silent	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45981368C>G	uc001zvt.2	+	c.1248C>G	c.(1246-1248)CTC>CTG	p.L416L	SQRDL_uc001zvu.2_Silent_p.L416L|SQRDL_uc001zvv.2_Silent_p.L416L	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor	416					oxidation-reduction process		oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)										0.113636	31.591312	57.487304	20	156	KEEP	---	---	---	---	capture		Silent	SNP	45981368	45981368	15643	15	C	G	G	G	366	29	SQRDL	3	3
C15orf26	161502	broad.mit.edu	37	15	81440802	81440802	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:81440802G>T	uc002bgb.2	+	c.834G>T	c.(832-834)ATG>ATT	p.M278I		NM_173528	NP_775799	Q6P656	CO026_HUMAN	hypothetical protein LOC161502	278											0														0.089552	5.392334	28.186705	12	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81440802	81440802	1837	15	G	T	T	T	624	48	C15orf26	2	2
SH3GL3	6457	broad.mit.edu	37	15	84245390	84245390	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:84245390G>T	uc002bju.2	+	c.545G>T	c.(544-546)CGA>CTA	p.R182L	SH3GL3_uc010uot.1_Missense_Mutation_p.R174L|SH3GL3_uc002bjw.2_Missense_Mutation_p.R174L|SH3GL3_uc002bjx.2_Missense_Mutation_p.R105L|SH3GL3_uc002bjv.2_Non-coding_Transcript	NM_003027	NP_003018	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	174	BAR.				central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			central_nervous_system(1)|pancreas(1)	2														0.097826	7.221206	22.103852	9	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84245390	84245390	14744	15	G	T	T	T	481	37	SH3GL3	1	1
BAIAP3	8938	broad.mit.edu	37	16	1392790	1392790	+	Missense_Mutation	SNP	T	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1392790T>A	uc002clk.1	+	c.1241T>A	c.(1240-1242)CTG>CAG	p.L414Q	BAIAP3_uc002clj.2_Missense_Mutation_p.L396Q|BAIAP3_uc010uuz.1_Missense_Mutation_p.L379Q|BAIAP3_uc010uva.1_Missense_Mutation_p.L351Q|BAIAP3_uc010uvc.1_Missense_Mutation_p.L343Q	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	414					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)												0.142857	7.081181	10.522493	4	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1392790	1392790	1325	16	T	A	A	A	715	55	BAIAP3	3	3
BAIAP3	8938	broad.mit.edu	37	16	1392793	1392793	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1392793G>T	uc002clk.1	+	c.1244G>T	c.(1243-1245)CGG>CTG	p.R415L	BAIAP3_uc002clj.2_Missense_Mutation_p.R397L|BAIAP3_uc010uuz.1_Missense_Mutation_p.R380L|BAIAP3_uc010uva.1_Missense_Mutation_p.R352L|BAIAP3_uc010uvc.1_Missense_Mutation_p.R344L	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	415					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)												0.129032	5.695069	9.835364	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1392793	1392793	1325	16	G	T	T	T	507	39	BAIAP3	1	1
ITGAL	3683	broad.mit.edu	37	16	30495497	30495497	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30495497G>A	uc002dyi.3	+	c.919G>A	c.(919-921)GCG>ACG	p.A307T	ITGAL_uc010veu.1_Non-coding_Transcript|ITGAL_uc002dyj.3_Missense_Mutation_p.A224T|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	307	VWFA.|Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(1)	7					Efalizumab(DB00095)	NSCLC(110;1462 1641 3311 33990 49495)								0.141447	61.614098	99.328746	43	261	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30495497	30495497	8190	16	G	A	A	A	494	38	ITGAL	1	1
PHKG2	5261	broad.mit.edu	37	16	30768316	30768316	+	Silent	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30768316C>A	uc002dzi.1	+	c.1131C>A	c.(1129-1131)CTC>CTA	p.L377L	PHKG2_uc002dzj.1_Silent_p.L271L|PHKG2_uc002dzk.1_Silent_p.L373L	NM_000294	NP_000285	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	373					glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process|protein phosphorylation	cytosol	ATP binding|calmodulin binding|phosphorylase kinase activity			ovary(1)	1			Colorectal(24;0.198)							76				0.13089	23.874782	49.338303	25	166	KEEP	---	---	---	---	capture		Silent	SNP	30768316	30768316	12271	16	C	A	A	A	405	32	PHKG2	2	2
SETD1A	9739	broad.mit.edu	37	16	30972797	30972797	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30972797C>T	uc002ead.1	+	c.456C>T	c.(454-456)GTC>GTT	p.V152V	SETD1A_uc002eae.1_Silent_p.V152V	NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	152	RRM.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)	2														0.122807	7.081142	15.024297	7	50	KEEP	---	---	---	---	capture		Silent	SNP	30972797	30972797	14618	16	C	T	T	T	366	29	SETD1A	2	2
ITGAM	3684	broad.mit.edu	37	16	31341648	31341648	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31341648G>T	uc002ebr.2	+	c.3083G>T	c.(3082-3084)TGC>TTC	p.C1028F	ITGAM_uc002ebq.2_Missense_Mutation_p.C1027F|ITGAM_uc010can.2_Missense_Mutation_p.C433F	NM_001145808	NP_001139280	P11215	ITAM_HUMAN	integrin alpha M isoform 1 precursor	1027	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1														0.173469	33.608021	43.479702	17	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31341648	31341648	8191	16	G	T	T	T	598	46	ITGAM	2	2
NLRC5	84166	broad.mit.edu	37	16	57063703	57063703	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57063703C>T	uc002ekk.1	+	c.2262C>T	c.(2260-2262)CTC>CTT	p.L754L	NLRC5_uc010ccq.1_Non-coding_Transcript|NLRC5_uc002ekn.2_Intron|NLRC5_uc002ekl.2_Silent_p.L559L|NLRC5_uc002ekm.2_Silent_p.L559L|NLRC5_uc010ccr.1_Non-coding_Transcript	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	754	LRR 3.				defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|breast(1)|skin(1)	6		all_neural(199;0.225)												0.134615	9.885803	16.620545	7	45	KEEP	---	---	---	---	capture		Silent	SNP	57063703	57063703	10873	16	C	T	T	T	366	29	NLRC5	2	2
NIP7	51388	broad.mit.edu	37	16	69373735	69373735	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:69373735G>A	uc002exa.2	+	c.3G>A	c.(1-3)ATG>ATA	p.M1I	COG8_uc002ewy.2_5'Flank|COG8_uc002ewz.3_5'Flank|NIP7_uc002exb.2_Missense_Mutation_p.M1I	NM_016101	NP_057185	Q9Y221	NIP7_HUMAN	nuclear import 7	1					ribosome assembly	nucleolus	protein binding|RNA binding			breast(1)	1		Ovarian(137;0.101)										OREG0023907	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.093079	6.058587	75.834634	39	380	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69373735	69373735	10822	16	G	A	A	A	598	46	NIP7	2	2
TAT	6898	broad.mit.edu	37	16	71604652	71604652	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71604652C>A	uc002fap.2	-	c.842G>T	c.(841-843)CGC>CTC	p.R281L		NM_000353	NP_000344	P17735	ATTY_HUMAN	tyrosine aminotransferase	281					2-oxoglutarate metabolic process|glutamate metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-tyrosine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(2)	2		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Glutamic Acid(DB00142)|L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Pyridoxal Phosphate(DB00114)	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)								0.108696	5.644093	12.620001	5	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71604652	71604652	16112	16	C	A	A	A	351	27	TAT	1	1
GLG1	2734	broad.mit.edu	37	16	74524978	74524978	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74524978C>A	uc002fcx.2	-	c.1370G>T	c.(1369-1371)CGA>CTA	p.R457L	GLG1_uc002fcy.3_Missense_Mutation_p.R457L|GLG1_uc002fcw.3_Missense_Mutation_p.R446L|GLG1_uc002fcz.3_Intron	NM_012201	NP_036333	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 1	457	Extracellular (Potential).|Cys-rich GLG1 6.					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2										1034				0.163636	49.71414	67.45578	27	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74524978	74524978	6704	16	C	A	A	A	403	31	GLG1	1	1
WDR59	79726	broad.mit.edu	37	16	74920199	74920199	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74920199G>A	uc002fdh.1	-	c.2515C>T	c.(2515-2517)CGA>TGA	p.R839*	WDR59_uc002fdf.1_Nonsense_Mutation_p.R284*|WDR59_uc002fdg.1_Nonsense_Mutation_p.R431*	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	839										ovary(1)|breast(1)	2														0.111111	16.802896	42.377043	19	152	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	74920199	74920199	17881	16	G	A	A	A	493	38	WDR59	5	1
C17orf48	56985	broad.mit.edu	37	17	10614344	10614344	+	Silent	SNP	A	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10614344A>T	uc002gmt.2	+	c.912A>T	c.(910-912)CCA>CCT	p.P304P	C17orf48_uc002gmu.2_Non-coding_Transcript|C17orf48_uc002gmv.2_Non-coding_Transcript	NM_020233	NP_064618	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol pyrophosphatase	304							ADP-ribose diphosphatase activity|CDP-glycerol diphosphatase activity|metal ion binding				0														0.125	13.460893	25.56338	11	77	KEEP	---	---	---	---	capture		Silent	SNP	10614344	10614344	1915	17	A	T	T	T	80	7	C17orf48	3	3
NLE1	54475	broad.mit.edu	37	17	33460195	33460195	+	Silent	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33460195G>C	uc002hiy.1	-	c.1440C>G	c.(1438-1440)CTC>CTG	p.L480L	NLE1_uc010ctn.1_Intron|NLE1_uc002hiz.1_Silent_p.L188L	NM_018096	NP_060566	Q9NVX2	NLE1_HUMAN	Notchless gene homolog isoform a	480	WD 8.					nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)												0.090164	11.237489	31.901639	11	111	KEEP	---	---	---	---	capture		Silent	SNP	33460195	33460195	10863	17	G	C	C	C	522	41	NLE1	3	3
ITGAE	3682	broad.mit.edu	37	17	3649126	3649126	+	Missense_Mutation	SNP	A	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:3649126A>C	uc002fwo.3	-	c.2251T>G	c.(2251-2253)TGC>GGC	p.C751G		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	751	Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		NSCLC(182;635 2928 8995 38788)				37				0.122137	25.914598	44.222826	16	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3649126	3649126	8189	17	A	C	C	C	91	7	ITGAE	4	4
MED1	5469	broad.mit.edu	37	17	37566052	37566052	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37566052G>A	uc002hrv.3	-	c.2422C>T	c.(2422-2424)CGA>TGA	p.R808*	MED1_uc010wee.1_Nonsense_Mutation_p.R636*|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1	808	Interaction with ESR1.				androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|kidney(1)	2		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		Pancreas(21;279 768 2492 4877 24026)								0.224044	96.476711	109.287767	41	142	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	37566052	37566052	9814	17	G	A	A	A	480	37	MED1	5	1
TTC25	83538	broad.mit.edu	37	17	40093098	40093098	+	Silent	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40093098C>G	uc002hyj.3	+	c.543C>G	c.(541-543)CTC>CTG	p.L181L	TTC25_uc010cxt.2_Non-coding_Transcript|TTC25_uc010cxs.1_Silent_p.L181L	NM_031421	NP_113609	Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25	181						cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)												0.130208	48.972131	74.487285	25	167	KEEP	---	---	---	---	capture		Silent	SNP	40093098	40093098	17247	17	C	G	G	G	366	29	TTC25	3	3
DGKE	8526	broad.mit.edu	37	17	54912529	54912529	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:54912529C>T	uc002iur.2	+	c.373C>T	c.(373-375)CAC>TAC	p.H125Y	DGKE_uc002ius.1_Missense_Mutation_p.H125Y|C17orf67_uc002iuq.2_5'Flank	NM_003647	NP_003638	P52429	DGKE_HUMAN	diacylglycerol kinase epsilon	125	Phorbol-ester/DAG-type 2.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|phospholipid biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding|protein binding			breast(2)	2	Breast(9;3.59e-07)													0.103774	6.637717	23.224211	11	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54912529	54912529	4647	17	C	T	T	T	273	21	DGKE	2	2
PPM1D	8493	broad.mit.edu	37	17	58725387	58725387	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58725387C>G	uc002iyt.1	+	c.961C>G	c.(961-963)CCA>GCA	p.P321A	PPM1D_uc010ddm.1_Non-coding_Transcript	NM_003620	NP_003611	O15297	PPM1D_HUMAN	protein phosphatase 1D	321	PP2C-like.				negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)											0.169591	77.68086	95.334151	29	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58725387	58725387	12772	17	C	G	G	G	390	30	PPM1D	3	3
TANC2	26115	broad.mit.edu	37	17	61498475	61498475	+	Missense_Mutation	SNP	A	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61498475A>G	uc002jal.3	+	c.5132A>G	c.(5131-5133)TAC>TGC	p.Y1711C	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Missense_Mutation_p.Y822C	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1711							binding			ovary(2)	2														0.088123	19.457311	64.18922	23	238	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61498475	61498475	16066	17	A	G	G	G	182	14	TANC2	4	4
POLG2	11232	broad.mit.edu	37	17	62492601	62492601	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62492601C>T	uc002jei.2	-	c.486G>A	c.(484-486)CTG>CTA	p.L162L	POLG2_uc010deg.1_Silent_p.L162L	NM_007215	NP_009146	Q9UHN1	DPOG2_HUMAN	DNA polymerase subunit gamma-2, mitochondrial	162					DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			Colon(3;18 21 435 17652 48887)								0.155102	60.07161	87.938238	38	207	KEEP	---	---	---	---	capture		Silent	SNP	62492601	62492601	12629	17	C	T	T	T	366	29	POLG2	2	2
SLC39A11	201266	broad.mit.edu	37	17	70732859	70732859	+	Splice_Site_SNP	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:70732859C>G	uc002jjb.2	-	c.623_splice	c.e7-1	p.E208_splice	SLC39A11_uc002jja.2_Splice_Site_SNP_p.E201_splice	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						NSCLC(95;736 1527 12296 39625 41839)								0.088608	12.620251	39.644591	14	144	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	70732859	70732859	15111	17	C	G	G	G	416	32	SLC39A11	5	3
COG1	9382	broad.mit.edu	37	17	71197584	71197584	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:71197584G>A	uc002jjg.2	+	c.1618G>A	c.(1618-1620)GAC>AAC	p.D540N	COG1_uc002jjh.2_Missense_Mutation_p.D540N|COG1_uc002jjf.1_Missense_Mutation_p.D540N	NM_018714	NP_061184	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	540					Golgi organization|intra-Golgi vesicle-mediated transport|protein transport	Golgi membrane|Golgi transport complex	protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.197)											0.092715	10.453514	60.883268	28	274	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71197584	71197584	3795	17	G	A	A	A	585	45	COG1	2	2
CD300LB	124599	broad.mit.edu	37	17	72527484	72527484	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:72527484C>A	uc002jkx.2	-	c.117G>T	c.(115-117)TGG>TGT	p.W39C	CD300LB_uc010wqz.1_Missense_Mutation_p.W39C	NM_174892	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	2						integral to membrane|plasma membrane	receptor activity			ovary(1)	1														0.13	16.29948	29.644526	13	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72527484	72527484	3127	17	C	A	A	A	338	26	CD300LB	2	2
POLR2A	5430	broad.mit.edu	37	17	7405004	7405004	+	Missense_Mutation	SNP	A	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7405004A>G	uc002ghf.3	+	c.2305A>G	c.(2305-2307)ATG>GTG	p.M769V		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	769					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)												0.091954	5.084937	19.630799	8	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7405004	7405004	12642	17	A	G	G	G	208	16	POLR2A	4	4
TP53	7157	broad.mit.edu	37	17	7577081	7577081	+	Missense_Mutation	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577081T>C	uc002gim.2	-	c.857A>G	c.(856-858)GAA>GGA	p.E286G	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.E286G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.E154G|TP53_uc010cng.1_Missense_Mutation_p.E154G|TP53_uc002gii.1_Missense_Mutation_p.E154G|TP53_uc010cnh.1_Missense_Mutation_p.E286G|TP53_uc010cni.1_Missense_Mutation_p.E286G|TP53_uc002gij.2_Missense_Mutation_p.E286G	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	286	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		E -> V (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> G (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).|E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.E286G(14)|p.0?(6)|p.E286V(6)|p.?(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.E286A(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.EE286del(CAL78-Tumor)|p.TEE284del(HCC1833-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.171875	26.388378	32.897775	11	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577081	7577081	16923	17	T	C	C	C	806	62	TP53	4	4
GALNT1	2589	broad.mit.edu	37	18	33282891	33282891	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:33282891G>C	uc010dmu.2	+	c.1330G>C	c.(1330-1332)GAT>CAT	p.D444H	GALNT1_uc002kyz.3_Missense_Mutation_p.D384H|GALNT1_uc002kzb.2_Missense_Mutation_p.D444H	NM_020474	NP_065207	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	444	Lumenal (Potential).|Ricin B-type lectin.				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2														0.134831	25.356556	36.844255	12	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33282891	33282891	6471	18	G	C	C	C	429	33	GALNT1	3	3
PIK3C3	5289	broad.mit.edu	37	18	39647380	39647380	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:39647380C>T	uc002lap.2	+	c.2552C>T	c.(2551-2553)TCG>TTG	p.S851L	PIK3C3_uc010xcl.1_Missense_Mutation_p.S788L|PIK3C3_uc002laq.2_Missense_Mutation_p.S336L	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3	851	PI3K/PI4K.				cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(7)|ovary(1)	8						NSCLC(37;552 1060 2683 16430 37914)				441	TSP Lung(28;0.18)			0.2	26.364299	31.388121	12	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39647380	39647380	12336	18	C	T	T	T	403	31	PIK3C3	1	1
ATP5A1	498	broad.mit.edu	37	18	43671709	43671709	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43671709C>T	uc002lbr.1	-	c.248G>A	c.(247-249)CGC>CAC	p.R83H	ATP5A1_uc010dnl.1_Missense_Mutation_p.R33H|ATP5A1_uc002lbs.1_Missense_Mutation_p.R33H|ATP5A1_uc002lbt.1_Missense_Mutation_p.R83H|ATP5A1_uc010xct.1_Missense_Mutation_p.R33H|ATP5A1_uc010dnm.1_Non-coding_Transcript	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	83					ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|mitochondrial ATP synthesis coupled proton transport|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0														0.124224	23.188295	45.415934	20	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43671709	43671709	1166	18	C	T	T	T	351	27	ATP5A1	1	1
ALPK2	115701	broad.mit.edu	37	18	56203560	56203560	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:56203560C>G	uc002lhj.3	-	c.3859G>C	c.(3859-3861)GAA>CAA	p.E1287Q	ALPK2_uc002lhk.1_Missense_Mutation_p.E618Q	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1287					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11										343				0.056034	-14.820106	33.254394	13	219	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56203560	56203560	548	18	C	G	G	G	377	29	ALPK2	3	3
TNFRSF11A	8792	broad.mit.edu	37	18	60028991	60028991	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:60028991G>T	uc002lin.2	+	c.695G>T	c.(694-696)GGC>GTC	p.G232V	TNFRSF11A_uc010dpv.2_Intron	NM_003839	NP_003830	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily,	232	Helical; (Potential).				adaptive immune response|cell-cell signaling|circadian temperature homeostasis|monocyte chemotaxis|osteoclast differentiation|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|response to interleukin-1|response to lipopolysaccharide	external side of plasma membrane|integral to membrane	metal ion binding|tumor necrosis factor receptor activity				0		Colorectal(73;0.188)												0.146392	116.533426	174.799924	71	414	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60028991	60028991	16825	18	G	T	T	T	546	42	TNFRSF11A	2	2
CLUL1	27098	broad.mit.edu	37	18	645015	645015	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:645015G>A	uc010wys.1	+	c.1471G>A	c.(1471-1473)GAA>AAA	p.E491K	CLUL1_uc002kkp.2_Missense_Mutation_p.E439K|CLUL1_uc002kkq.2_Missense_Mutation_p.E439K	NM_199167	NP_954636	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal) precursor	439					cell death	extracellular region				ovary(2)	2														0.201681	46.877563	56.795059	24	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	645015	645015	3708	18	G	A	A	A	585	45	CLUL1	2	2
TWSG1	57045	broad.mit.edu	37	18	9396447	9396447	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:9396447G>A	uc002knz.2	+	c.393G>A	c.(391-393)GAG>GAA	p.E131E	TWSG1_uc002koa.2_Silent_p.E56E	NM_020648	NP_065699	Q9GZX9	TWSG1_HUMAN	twisted gastrulation precursor	131										ovary(1)|pancreas(1)	2														0.062069	-8.448124	20.552229	9	136	KEEP	---	---	---	---	capture		Silent	SNP	9396447	9396447	17341	18	G	A	A	A	425	33	TWSG1	2	2
QTRT1	81890	broad.mit.edu	37	19	10823252	10823252	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10823252G>C	uc002mpr.2	+	c.809G>C	c.(808-810)TGC>TCC	p.C270S	DNM2_uc010dxk.2_5'Flank	NM_031209	NP_112486	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	270					queuosine biosynthetic process	mitochondrion|nucleus|ribosome	metal ion binding|queuine tRNA-ribosyltransferase activity				0			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)											0.114286	49.305396	90.36359	32	248	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10823252	10823252	13343	19	G	C	C	C	598	46	QTRT1	3	3
ZNF763	284390	broad.mit.edu	37	19	12087895	12087895	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12087895G>T	uc010xmf.1	+	c.106G>T	c.(106-108)GAG>TAG	p.E36*	ZNF763_uc002msv.2_Nonsense_Mutation_p.E19*|ZNF763_uc002msw.2_Nonsense_Mutation_p.E16*|ZNF763_uc010xmg.1_Intron	NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763	16	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1														0.124324	24.38532	49.923661	23	162	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	12087895	12087895	18735	19	G	T	T	T	533	41	ZNF763	5	2
FARSA	2193	broad.mit.edu	37	19	13035487	13035487	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13035487G>A	uc002mvs.2	-	c.1161C>T	c.(1159-1161)CTC>CTT	p.L387L	FARSA_uc002mvt.2_Non-coding_Transcript|FARSA_uc010xmv.1_Silent_p.L356L|FARSA_uc010dyy.1_Silent_p.L308L	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	387					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)									0.093333	0.861628	13.346712	7	68	KEEP	---	---	---	---	capture		Silent	SNP	13035487	13035487	5915	19	G	A	A	A	574	45	FARSA	2	2
SLC1A6	6511	broad.mit.edu	37	19	15079239	15079239	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15079239C>A	uc002naa.1	-	c.424G>T	c.(424-426)GCG>TCG	p.A142S	SLC1A6_uc010dzu.1_Missense_Mutation_p.A142S|SLC1A6_uc010xod.1_Intron|SLC1A6_uc002nab.2_Missense_Mutation_p.A142S|SLC1A6_uc002nac.2_Missense_Mutation_p.A142S|SLC1A6_uc002nad.1_Missense_Mutation_p.A142S	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity	142	Helical; (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)	5					L-Glutamic Acid(DB00142)									0.129032	5.679555	9.83322	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15079239	15079239	14932	19	C	A	A	A	351	27	SLC1A6	1	1
FAM129C	199786	broad.mit.edu	37	19	17653042	17653042	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17653042C>T	uc010xpr.1	+	c.1361C>T	c.(1360-1362)GCA>GTA	p.A454V	FAM129C_uc010xpq.1_Missense_Mutation_p.A454V|FAM129C_uc002ngy.3_Missense_Mutation_p.A180V|FAM129C_uc010xpu.1_Missense_Mutation_p.A180V|FAM129C_uc002ngz.3_Non-coding_Transcript|FAM129C_uc010eaw.2_Missense_Mutation_p.A180V|FAM129C_uc002nhb.2_Missense_Mutation_p.A53V	NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a	454											0														0.118971	33.401697	77.711034	37	274	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17653042	17653042	5635	19	C	T	T	T	325	25	FAM129C	2	2
ZNF257	113835	broad.mit.edu	37	19	22272062	22272062	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22272062C>G	uc010ecx.2	+	c.1510C>G	c.(1510-1512)CAA>GAA	p.Q504E	ZNF257_uc010ecy.2_Missense_Mutation_p.Q472E	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	504	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.15625	26.106917	33.325614	10	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22272062	22272062	18391	19	C	G	G	G	377	29	ZNF257	3	3
NPHS1	4868	broad.mit.edu	37	19	36322010	36322010	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36322010C>T	uc002oby.2	-	c.3426G>A	c.(3424-3426)CTG>CTA	p.L1142L	NPHS1_uc010eem.1_Non-coding_Transcript	NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	1142	Cytoplasmic (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.162921	47.788291	66.994632	29	149	KEEP	---	---	---	---	capture		Silent	SNP	36322010	36322010	10986	19	C	T	T	T	366	29	NPHS1	2	2
SFRS16	11129	broad.mit.edu	37	19	45559743	45559743	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45559743G>A	uc002pak.2	+	c.415G>A	c.(415-417)GAT>AAT	p.D139N	SFRS16_uc002pal.2_Non-coding_Transcript|SFRS16_uc010xxh.1_Missense_Mutation_p.D77N|SFRS16_uc002pam.2_Missense_Mutation_p.D139N|SFRS16_uc002pan.1_Non-coding_Transcript	NM_007056	NP_008987	Q8N2M8	CLASR_HUMAN	splicing factor, arginine/serine-rich 16	139					mRNA processing|RNA splicing	nucleus					0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)										0.064286	-8.948676	18.697	9	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45559743	45559743	14662	19	G	A	A	A	585	45	SFRS16	2	2
ZC3H4	23211	broad.mit.edu	37	19	47569697	47569697	+	Silent	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:47569697C>A	uc002pga.3	-	c.3828G>T	c.(3826-3828)CCG>CCT	p.P1276P	ZC3H4_uc002pgb.1_Non-coding_Transcript	NM_015168	NP_055983	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1276							nucleic acid binding|zinc ion binding			ovary(2)	2		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)										0.214286	7.118077	8.172865	3	11	KEEP	---	---	---	---	capture		Silent	SNP	47569697	47569697	18158	19	C	A	A	A	288	23	ZC3H4	1	1
CRX	1406	broad.mit.edu	37	19	48342693	48342693	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48342693G>A	uc002phq.3	+	c.369G>A	c.(367-369)ACG>ACA	p.T123T		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	123					organ morphogenesis|response to stimulus|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		Pancreas(57;461 1196 22201 40716 47188)								0.125	17.600585	36.290331	17	119	KEEP	---	---	---	---	capture		Silent	SNP	48342693	48342693	4041	19	G	A	A	A	509	40	CRX	1	1
SIGLEC14	100049587	broad.mit.edu	37	19	52149116	52149116	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52149116G>T	uc002pxf.3	-	c.619C>A	c.(619-621)CAT>AAT	p.H207N		NM_001098612	NP_001092082	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14 precursor	207	Ig-like C2-type 1.|Extracellular (Potential).				cell adhesion	integral to membrane|plasma membrane	protein binding|sugar binding			ovary(1)	1		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)										0.0875	2.161551	15.935519	7	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52149116	52149116	14804	19	G	T	T	T	611	47	SIGLEC14	2	2
ZNF616	90317	broad.mit.edu	37	19	52618739	52618739	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52618739G>A	uc002pym.2	-	c.1678C>T	c.(1678-1680)CAA>TAA	p.Q560*	ZNF616_uc002pyn.2_Non-coding_Transcript	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616	560	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)										0.096154	3.068073	20.087288	10	94	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52618739	52618739	18636	19	G	A	A	A	585	45	ZNF616	5	2
TSEN34	79042	broad.mit.edu	37	19	54696204	54696204	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54696204G>C	uc010yeo.1	+	c.725G>C	c.(724-726)GGT>GCT	p.G242A	MBOAT7_uc002qdq.2_5'Flank|MBOAT7_uc002qdr.2_5'Flank|MBOAT7_uc002qds.2_5'Flank|MBOAT7_uc010yen.1_5'Flank|MBOAT7_uc002qdt.3_5'Flank|TSEN34_uc002qdu.2_Missense_Mutation_p.G242A|TSEN34_uc002qdv.2_Missense_Mutation_p.G242A|TSEN34_uc002qdw.2_Missense_Mutation_p.G242A	NM_024075	NP_076980	Q9BSV6	SEN34_HUMAN	tRNA-intron endonuclease 34	242					mRNA processing|tRNA-type intron splice site recognition and cleavage	nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity				0	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					Esophageal Squamous(37;841 964 4869 42824)								0.077586	1.405155	22.558038	9	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54696204	54696204	17164	19	G	C	C	C	572	44	TSEN34	3	3
FUT3	2525	broad.mit.edu	37	19	5844225	5844225	+	Missense_Mutation	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:5844225T>C	uc002mdk.2	-	c.626A>G	c.(625-627)TAC>TGC	p.Y209C	FUT3_uc002mdm.2_Missense_Mutation_p.Y209C|FUT3_uc002mdj.2_Missense_Mutation_p.Y209C|FUT3_uc002mdl.2_Missense_Mutation_p.Y209C	NM_001097641	NP_001091110	P21217	FUT3_HUMAN	fucosyltransferase 3	209	Lumenal (Potential).				protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity				0						Esophageal Squamous(82;745 1728 24593 44831)								0.186441	58.041813	68.862958	22	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5844225	5844225	6356	19	T	C	C	C	741	57	FUT3	4	4
PPM1J	333926	broad.mit.edu	37	1	113253122	113253122	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:113253122C>G	uc001ect.1	-	c.1330G>C	c.(1330-1332)GAC>CAC	p.D444H	PPM1J_uc009wgl.1_Non-coding_Transcript|PPM1J_uc001ecs.1_Missense_Mutation_p.D238H	NM_005167	NP_005158	Q5JR12	PPM1J_HUMAN	protein phosphatase 1J (PP2C domain containing)	444	PP2C-like.									central_nervous_system(1)	1	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.15	25.241483	34.645282	12	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113253122	113253122	12777	1	C	G	G	G	390	30	PPM1J	3	3
MAD2L2	10459	broad.mit.edu	37	1	11740467	11740467	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11740467G>T	uc001asp.2	-	c.102C>A	c.(100-102)CGC>CGA	p.R34R	MAD2L2_uc009vnc.2_Silent_p.R34R|MAD2L2_uc001asq.3_Silent_p.R34R	NM_006341	NP_006332	Q9UI95	MD2L2_HUMAN	MAD2 homolog	34	Mediates interaction with REV1 and REV3L and homodimerization.|HORMA.				cell division|DNA damage response, signal transduction resulting in transcription|double-strand break repair|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of gene-specific transcription|positive regulation of peptidyl-serine phosphorylation|regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleoplasm|spindle|zeta DNA polymerase complex	JUN kinase binding				0	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)										0.075377	-2.281762	34.468229	15	184	KEEP	---	---	---	---	capture		Silent	SNP	11740467	11740467	9527	1	G	T	T	T	483	38	MAD2L2	1	1
SCNN1D	6339	broad.mit.edu	37	1	1222560	1222560	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1222560C>A	uc001adt.1	+	c.1191C>A	c.(1189-1191)TAC>TAA	p.Y397*	SCNN1D_uc001adu.1_Nonsense_Mutation_p.Y233*|SCNN1D_uc001adw.2_Nonsense_Mutation_p.Y299*|SCNN1D_uc001adx.2_5'UTR|SCNN1D_uc001adv.2_Nonsense_Mutation_p.Y233*	NM_001130413	NP_001123885	P51172	SCNND_HUMAN	sodium channel, nonvoltage-gated 1, delta	233	Extracellular (By similarity).				response to stimulus|sensory perception of taste	integral to membrane	ligand-gated sodium channel activity|protein binding				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)									0.194444	14.602413	17.739498	7	29	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	1222560	1222560	14411	1	C	A	A	A	233	18	SCNN1D	5	2
HRNR	388697	broad.mit.edu	37	1	152191367	152191367	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152191367G>T	uc001ezt.1	-	c.2738C>A	c.(2737-2739)TCC>TAC	p.S913Y		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	913	10.				keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.099526	7.70718	41.554705	21	190	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152191367	152191367	7653	1	G	T	T	T	533	41	HRNR	2	2
SHC1	6464	broad.mit.edu	37	1	154940731	154940731	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154940731G>A	uc001ffw.2	-	c.753C>T	c.(751-753)ATC>ATT	p.I251I	SHC1_uc001ffu.2_5'Flank|SHC1_uc001ffz.1_Silent_p.I22I|SHC1_uc001ffv.2_Silent_p.I251I|SHC1_uc001ffx.2_Silent_p.I141I|SHC1_uc001ffy.2_Silent_p.I141I	NM_001130040	NP_001123512	P29353	SHC1_HUMAN	SHC-transforming protein 1 isoform 3	251	PID.				activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth	cytosol|mitochondrial matrix|Shc-EGFR complex	epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			NSCLC(4;32 234 1864 2492 3259 13747 17376)				160				0.069597	-13.209735	39.041692	19	254	KEEP	---	---	---	---	capture		Silent	SNP	154940731	154940731	14762	1	G	A	A	A	577	45	SHC1	2	2
RCC2	55920	broad.mit.edu	37	1	17755624	17755624	+	Silent	SNP	T	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17755624T>A	uc001bal.2	-	c.357A>T	c.(355-357)CGA>CGT	p.R119R	RCC2_uc001bam.2_Silent_p.R119R	NM_001136204	NP_001129676	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	119	RCC1 1.				cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)										0.113821	9.853211	27.974266	14	109	KEEP	---	---	---	---	capture		Silent	SNP	17755624	17755624	13643	1	T	A	A	A	795	62	RCC2	3	3
FAM129A	116496	broad.mit.edu	37	1	184863220	184863220	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:184863220C>T	uc001gra.2	-	c.307G>A	c.(307-309)GAG>AAG	p.E103K	FAM129A_uc009wyh.1_Missense_Mutation_p.E103K|FAM129A_uc009wyi.1_Intron	NM_052966	NP_443198	Q9BZQ8	NIBAN_HUMAN	niban protein isoform 2	103					negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)	3														0.073171	-5.535631	17.541945	9	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	184863220	184863220	5633	1	C	T	T	T	377	29	FAM129A	2	2
ASPM	259266	broad.mit.edu	37	1	197112595	197112595	+	Missense_Mutation	SNP	T	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197112595T>G	uc001gtu.2	-	c.787A>C	c.(787-789)AGT>CGT	p.S263R	ASPM_uc001gtv.2_Missense_Mutation_p.S263R|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	263					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.104762	9.84545	26.159118	11	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197112595	197112595	1075	1	T	G	G	G	715	55	ASPM	4	4
PPP1R15B	84919	broad.mit.edu	37	1	204379201	204379201	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204379201C>G	uc001hav.3	-	c.1339G>C	c.(1339-1341)GAT>CAT	p.D447H		NM_032833	NP_116222	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	447					regulation of translation					ovary(1)|pancreas(1)	2	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)											0.062874	-8.007807	58.469442	21	313	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204379201	204379201	12799	1	C	G	G	G	390	30	PPP1R15B	3	3
SLC26A9	115019	broad.mit.edu	37	1	205890767	205890767	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:205890767G>C	uc001hdp.2	-	c.1982C>G	c.(1981-1983)ACC>AGC	p.T661S	SLC26A9_uc001hdo.2_Missense_Mutation_p.T329S|SLC26A9_uc001hdq.2_Missense_Mutation_p.T661S	NM_134325	NP_599152	Q7LBE3	S26A9_HUMAN	solute carrier family 26, member 9 isoform b	661	STAS.					integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)	1	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)											0.142857	9.581912	13.021951	4	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	205890767	205890767	15021	1	G	C	C	C	572	44	SLC26A9	3	3
KIF17	57576	broad.mit.edu	37	1	21014237	21014237	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:21014237C>T	uc001bdr.3	-	c.1582G>A	c.(1582-1584)GAA>AAA	p.E528K	KIF17_uc001bdp.3_5'Flank|KIF17_uc001bdq.3_5'Flank|KIF17_uc009vpx.2_Intron|KIF17_uc001bds.3_Missense_Mutation_p.E528K	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a	528					microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)	3		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)										0.162393	34.677213	47.3356	19	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21014237	21014237	8590	1	C	T	T	T	390	30	KIF17	2	2
USP48	84196	broad.mit.edu	37	1	22030794	22030794	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:22030794C>G	uc010odq.1	-	c.2512G>C	c.(2512-2514)GAT>CAT	p.D838H	USP48_uc001bfa.2_Missense_Mutation_p.D364H|USP48_uc001bfb.2_Missense_Mutation_p.D826H|USP48_uc009vqc.2_Missense_Mutation_p.D760H|USP48_uc001bfc.2_Missense_Mutation_p.D826H|USP48_uc001bfd.1_5'UTR	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	826					ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)										0.112903	20.150426	38.506146	14	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22030794	22030794	17643	1	C	G	G	G	416	32	USP48	3	3
OR2C3	81472	broad.mit.edu	37	1	247694892	247694892	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247694892C>T	uc009xgy.2	-	c.922G>A	c.(922-924)GAG>AAG	p.E308K	C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron|LOC148824_uc001idd.2_5'Flank	NM_198074	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C,	308	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)											0.101449	6.369954	17.306263	7	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247694892	247694892	11399	1	C	T	T	T	416	32	OR2C3	2	2
DHDDS	79947	broad.mit.edu	37	1	26774059	26774059	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26774059G>T	uc001bmk.2	+	c.450G>T	c.(448-450)CTG>CTT	p.L150L	DHDDS_uc001bml.2_Silent_p.L150L|DHDDS_uc001bmm.2_Silent_p.L57L|DHDDS_uc001bmn.2_Silent_p.L111L|DHDDS_uc010ofd.1_Intron	NM_024887	NP_079163	Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase isoform a	150							protein binding|transferase activity, transferring alkyl or aryl (other than methyl) groups			breast(3)	3		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)										0.083333	-0.211136	12.500106	6	66	KEEP	---	---	---	---	capture		Silent	SNP	26774059	26774059	4657	1	G	T	T	T	574	45	DHDDS	2	2
C1orf173	127254	broad.mit.edu	37	1	75038823	75038823	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75038823G>T	uc001dgg.2	-	c.2571C>A	c.(2569-2571)GAC>GAA	p.D857E		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	857	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.107759	21.546044	57.207333	25	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75038823	75038823	2081	1	G	T	T	T	568	44	C1orf173	2	2
ST6GALNAC3	256435	broad.mit.edu	37	1	76779523	76779523	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:76779523G>A	uc001dhh.2	+	c.52G>A	c.(52-54)GCG>ACG	p.A18T	ST6GALNAC3_uc001dhg.3_Missense_Mutation_p.A18T|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1	18	Helical; Signal-anchor for type II membrane protein; (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)	3														0.114504	17.739865	36.923246	15	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76779523	76779523	15743	1	G	A	A	A	442	34	ST6GALNAC3	2	2
GBP6	163351	broad.mit.edu	37	1	89846103	89846103	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:89846103C>T	uc001dnf.2	+	c.784C>T	c.(784-786)CAG>TAG	p.Q262*	GBP6_uc010ost.1_Nonsense_Mutation_p.Q132*	NM_198460	NP_940862	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	262							GTP binding|GTPase activity			ovary(2)	2		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)										0.145455	13.459753	20.112685	8	47	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	89846103	89846103	6544	1	C	T	T	T	273	21	GBP6	5	2
PDYN	5173	broad.mit.edu	37	20	1961296	1961296	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:1961296C>T	uc010gaj.2	-	c.438G>A	c.(436-438)ATG>ATA	p.M146I	PDYN_uc002wfv.2_Missense_Mutation_p.M146I|PDYN_uc010zpt.1_5'UTR	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	146					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			ovary(1)	1														0.067485	-8.818279	22.770885	11	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1961296	1961296	12120	20	C	T	T	T	377	29	PDYN	2	2
TOP1	7150	broad.mit.edu	37	20	39728776	39728776	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:39728776C>G	uc002xjl.2	+	c.1056C>G	c.(1054-1056)AAC>AAG	p.N352K		NM_003286	NP_003277	P11387	TOP1_HUMAN	DNA topoisomerase I	352					DNA topological change|DNA unwinding involved in replication|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)					252				0.126761	13.126568	22.777315	9	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39728776	39728776	16905	20	C	G	G	G	259	20	TOP1	3	3
EYA2	2139	broad.mit.edu	37	20	45725774	45725774	+	Missense_Mutation	SNP	A	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:45725774A>T	uc002xsn.2	+	c.870A>T	c.(868-870)TTA>TTT	p.L290F	EYA2_uc002xsm.2_Missense_Mutation_p.L285F|EYA2_uc010ghp.2_Missense_Mutation_p.L285F|EYA2_uc002xso.2_Missense_Mutation_p.L285F|EYA2_uc002xsp.2_Missense_Mutation_p.L285F|EYA2_uc002xsq.2_Missense_Mutation_p.L285F	NM_172113	NP_742111	O00167	EYA2_HUMAN	RecName: Full=Eyes absent homolog 2;          EC=3.1.3.48;	285					DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				Pancreas(120;56 1725 18501 25218 43520)								0.127596	59.018993	104.563141	43	294	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45725774	45725774	5523	20	A	T	T	T	180	14	EYA2	3	3
TAF4	6874	broad.mit.edu	37	20	60584215	60584215	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:60584215C>T	uc002ybs.2	-	c.1777G>A	c.(1777-1779)GTG>ATG	p.V593M		NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4	593	TAFH.				interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|general RNA polymerase II transcription factor activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription coactivator activity|transcription initiation factor activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)											0.12	11.023939	21.647048	9	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60584215	60584215	16047	20	C	T	T	T	247	19	TAF4	1	1
SRMS	6725	broad.mit.edu	37	20	62178813	62178813	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62178813C>T	uc002yfi.1	-	c.4G>A	c.(4-6)GAG>AAG	p.E2K		NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory	2					protein phosphorylation		ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(1)	1	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)							557				0.132075	9.335894	16.266968	7	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62178813	62178813	15666	20	C	T	T	T	390	30	SRMS	2	2
HAO1	54363	broad.mit.edu	37	20	7915177	7915177	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:7915177G>T	uc002wmw.1	-	c.243C>A	c.(241-243)GCC>GCA	p.A81A	HAO1_uc010gbu.2_Silent_p.A81A	NM_017545	NP_060015	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase 1	81	FMN hydroxy acid dehydrogenase.				cellular nitrogen compound metabolic process|fatty acid alpha-oxidation|glycolate catabolic process|glyoxylate metabolic process	peroxisomal matrix	FMN binding|glycolate oxidase activity|glyoxylate oxidase activity			ovary(3)	3														0.081633	-0.515869	25.686578	12	135	KEEP	---	---	---	---	capture		Silent	SNP	7915177	7915177	7233	20	G	T	T	T	600	47	HAO1	2	2
MYO18B	84700	broad.mit.edu	37	22	26422991	26422991	+	Missense_Mutation	SNP	T	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26422991T>A	uc003abz.1	+	c.7051T>A	c.(7051-7053)TGC>AGC	p.C2351S	MYO18B_uc003aca.1_Missense_Mutation_p.C2232S|MYO18B_uc010guy.1_Missense_Mutation_p.C2233S|MYO18B_uc010guz.1_Missense_Mutation_p.C2231S|MYO18B_uc011aka.1_Missense_Mutation_p.C1505S|MYO18B_uc011akb.1_Missense_Mutation_p.C1864S|MYO18B_uc010gva.1_Missense_Mutation_p.C334S|MYO18B_uc010gvb.1_Non-coding_Transcript	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2351						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12										968				0.072222	-5.97301	27.94628	13	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26422991	26422991	10461	22	T	A	A	A	715	55	MYO18B	3	3
SFI1	9814	broad.mit.edu	37	22	31924785	31924785	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:31924785C>T	uc003ale.2	+	c.202C>T	c.(202-204)CTA>TTA	p.L68L	SFI1_uc003ald.1_Silent_p.L68L|SFI1_uc003alf.2_Silent_p.L68L|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Silent_p.L68L|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	68					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1														0.095808	12.46336	39.838067	16	151	KEEP	---	---	---	---	capture		Silent	SNP	31924785	31924785	14645	22	C	T	T	T	415	32	SFI1	2	2
TNRC6B	23112	broad.mit.edu	37	22	40697001	40697001	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40697001G>A	uc011aor.1	+	c.3928G>A	c.(3928-3930)GAG>AAG	p.E1310K	TNRC6B_uc003aym.2_Missense_Mutation_p.E506K|TNRC6B_uc003ayn.3_Missense_Mutation_p.E1200K|TNRC6B_uc003ayo.2_Missense_Mutation_p.E1057K	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	1310					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0										794				0.166667	7.786109	10.313606	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40697001	40697001	16882	22	G	A	A	A	429	33	TNRC6B	2	2
C2orf40	84417	broad.mit.edu	37	2	106694260	106694260	+	Silent	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:106694260C>A	uc010fjf.2	+	c.325C>A	c.(325-327)CGA>AGA	p.R109R		NM_032411	NP_115787	Q9H1Z8	AUGN_HUMAN	esophageal cancer related gene 4 protein	109						extracellular region|transport vesicle					0														0.114754	18.761439	36.604535	14	108	KEEP	---	---	---	---	capture		Silent	SNP	106694260	106694260	2253	2	C	A	A	A	399	31	C2orf40	1	1
IL1F6	27179	broad.mit.edu	37	2	113763598	113763598	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:113763598C>T	uc010yxr.1	+	c.58C>T	c.(58-60)CAT>TAT	p.H20Y		NM_014440	NP_055255	Q9UHA7	IL1F6_HUMAN	interleukin 1 family, member 6 (epsilon)	20					immune response|inflammatory response	extracellular space	cytokine activity|interleukin-1 receptor binding			ovary(2)	2														0.090278	2.455612	26.858049	13	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113763598	113763598	7955	2	C	T	T	T	377	29	IL1F6	2	2
MKI67IP	84365	broad.mit.edu	37	2	122488554	122488554	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:122488554C>T	uc002tnk.2	-	c.479G>A	c.(478-480)CGG>CAG	p.R160Q	MKI67IP_uc010fls.2_Missense_Mutation_p.R160Q	NM_032390	NP_115766	Q9BYG3	MK67I_HUMAN	MKI67 interacting nucleolar phosphoprotein	160					protein complex assembly|rRNA metabolic process|rRNA transcription	condensed nuclear chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding				0														0.106667	14.493034	37.531161	16	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122488554	122488554	9989	2	C	T	T	T	299	23	MKI67IP	1	1
ACMSD	130013	broad.mit.edu	37	2	135621051	135621051	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:135621051G>A	uc002ttz.2	+	c.336G>A	c.(334-336)GTG>GTA	p.V112V	ACMSD_uc002tua.2_Silent_p.V54V	NM_138326	NP_612199	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	112					quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(221;0.115)										0.134328	28.955753	46.335934	18	116	KEEP	---	---	---	---	capture		Silent	SNP	135621051	135621051	145	2	G	A	A	A	600	47	ACMSD	2	2
THSD7B	80731	broad.mit.edu	37	2	138373849	138373849	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:138373849G>A	uc002tva.1	+	c.3441G>A	c.(3439-3441)CTG>CTA	p.L1147L	THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)										0.122699	17.436527	40.270963	20	143	KEEP	---	---	---	---	capture		Silent	SNP	138373849	138373849	16408	2	G	A	A	A	574	45	THSD7B	2	2
PLA2R1	22925	broad.mit.edu	37	2	160836348	160836348	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:160836348C>G	uc002ube.1	-	c.2261G>C	c.(2260-2262)AGA>ACA	p.R754T	PLA2R1_uc010zcp.1_Missense_Mutation_p.R754T|PLA2R1_uc002ubf.2_Missense_Mutation_p.R754T	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	754	Extracellular (Potential).|C-type lectin 4.				endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)	1														0.137931	8.979151	12.656028	4	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160836348	160836348	12436	2	C	G	G	G	416	32	PLA2R1	3	3
TTN	7273	broad.mit.edu	37	2	179479392	179479392	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179479392G>T	uc010zfg.1	-	c.41145C>A	c.(41143-41145)ACC>ACA	p.T13715T	TTN_uc010zfh.1_Silent_p.T7410T|TTN_uc010zfi.1_Silent_p.T7343T|TTN_uc010zfj.1_Silent_p.T7218T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1580										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.137255	10.789999	17.284034	7	44	KEEP	---	---	---	---	capture		Silent	SNP	179479392	179479392	17290	2	G	T	T	T	496	39	TTN	1	1
DNAH7	56171	broad.mit.edu	37	2	196664163	196664163	+	Missense_Mutation	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:196664163T>C	uc002utj.3	-	c.10210A>G	c.(10210-10212)AGA>GGA	p.R3404G		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3404	AAA 6 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(2)	2														0.084034	1.764499	22.672579	10	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196664163	196664163	4789	2	T	C	C	C	713	55	DNAH7	4	4
SPAG16	79582	broad.mit.edu	37	2	215274887	215274887	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:215274887G>T	uc002veq.2	+	c.1744G>T	c.(1744-1746)GGC>TGC	p.G582C	SPAG16_uc002ver.2_Missense_Mutation_p.G528C|SPAG16_uc010zjk.1_Missense_Mutation_p.G488C|VWC2L_uc002vet.2_5'Flank|VWC2L_uc010zjl.1_5'Flank	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	582	WD 6.				cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)	1		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)										0.095652	5.231929	24.104217	11	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215274887	215274887	15481	2	G	T	T	T	611	47	SPAG16	2	2
SERPINE2	5270	broad.mit.edu	37	2	224847476	224847476	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:224847476C>G	uc010zlr.1	-	c.943G>C	c.(943-945)GAT>CAT	p.D315H	SERPINE2_uc002vnt.2_Missense_Mutation_p.D303H|SERPINE2_uc002vnu.2_Missense_Mutation_p.D303H|SERPINE2_uc002vnv.2_Missense_Mutation_p.D303H	NM_001136530	NP_001130002	P07093	GDN_HUMAN	plasminogen activator inhibitor type 1, member 2	303					negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)										0.115385	8.736407	16.291617	6	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	224847476	224847476	14600	2	C	G	G	G	416	32	SERPINE2	3	3
COL4A4	1286	broad.mit.edu	37	2	227924124	227924124	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:227924124C>T	uc010zlt.1	-	c.2380G>A	c.(2380-2382)GAA>AAA	p.E794K		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	794	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|breast(1)|pancreas(1)	10		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)										0.122222	36.259874	74.029967	33	237	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	227924124	227924124	3831	2	C	T	T	T	377	29	COL4A4	2	2
DGKD	8527	broad.mit.edu	37	2	234358641	234358641	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234358641G>C	uc002vui.1	+	c.1902G>C	c.(1900-1902)CAG>CAC	p.Q634H	DGKD_uc002vuj.1_Missense_Mutation_p.Q590H|DGKD_uc010fyh.1_Missense_Mutation_p.Q501H|DGKD_uc010fyi.1_Non-coding_Transcript	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	634					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)									0.078947	3.586893	17.347825	6	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234358641	234358641	4646	2	G	C	C	C	425	33	DGKD	3	3
C2orf86	51057	broad.mit.edu	37	2	63666936	63666936	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63666936C>A	uc002sch.2	-	c.454G>T	c.(454-456)GAC>TAC	p.D152Y	C2orf86_uc002scf.2_5'Flank|C2orf86_uc010ypu.1_5'Flank|C2orf86_uc002scg.2_5'UTR|C2orf86_uc002sci.1_Missense_Mutation_p.D128Y|C2orf86_uc010fcr.1_Missense_Mutation_p.D42Y	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	152					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0														0.166667	41.429765	55.976627	23	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63666936	63666936	2293	2	C	A	A	A	377	29	C2orf86	2	2
MOGS	7841	broad.mit.edu	37	2	74690085	74690085	+	Silent	SNP	T	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74690085T>G	uc010ffj.2	-	c.831A>C	c.(829-831)GTA>GTC	p.V277V	MOGS_uc010ffh.2_Silent_p.V2V|MOGS_uc010yrt.1_Silent_p.V158V|MOGS_uc010ffi.2_Silent_p.V171V|MOGS_uc010yru.1_3'UTR	NM_006302	NP_006293	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase isoform 1	277	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|membrane fraction	mannosyl-oligosaccharide glucosidase activity				0														0.123967	80.691803	130.813573	45	318	KEEP	---	---	---	---	capture		Silent	SNP	74690085	74690085	10088	2	T	G	G	G	782	61	MOGS	4	4
RETSAT	54884	broad.mit.edu	37	2	85576586	85576586	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85576586C>T	uc002spd.2	-	c.918G>A	c.(916-918)GTG>GTA	p.V306V	RETSAT_uc010fge.2_Non-coding_Transcript|RETSAT_uc010ysm.1_Silent_p.V245V|RETSAT_uc010fgf.2_Silent_p.V97V	NM_017750	NP_060220	Q6NUM9	RETST_HUMAN	all-trans-13,14-dihydroretinol saturase	306					oxidation-reduction process|retinol metabolic process	endoplasmic reticulum membrane|nuclear outer membrane	all-trans-retinol 13,14-reductase activity|electron carrier activity			ovary(1)	1					Vitamin A(DB00162)									0.105263	5.774616	20.498451	10	85	KEEP	---	---	---	---	capture		Silent	SNP	85576586	85576586	13708	2	C	T	T	T	366	29	RETSAT	2	2
KIAA2018	205717	broad.mit.edu	37	3	113375010	113375010	+	Nonsense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113375010G>C	uc003eam.2	-	c.5519C>G	c.(5518-5520)TCA>TGA	p.S1840*	KIAA2018_uc003eal.2_Nonsense_Mutation_p.S1784*	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	1840						membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|transcription regulator activity			ovary(1)	1														0.140244	47.912453	68.404929	23	141	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	113375010	113375010	8579	3	G	C	C	C	585	45	KIAA2018	5	3
CPNE4	131034	broad.mit.edu	37	3	131261579	131261579	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:131261579C>T	uc011blq.1	-	c.1415G>A	c.(1414-1416)CGG>CAG	p.R472Q	CPNE4_uc003eok.2_Missense_Mutation_p.R454Q|CPNE4_uc003eol.2_Missense_Mutation_p.R472Q|CPNE4_uc003eom.2_Missense_Mutation_p.R454Q|CPNE4_uc003eoj.2_Missense_Mutation_p.R5Q	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV	454	VWFA.									central_nervous_system(1)	1														0.079208	-4.380898	13.960553	8	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131261579	131261579	3952	3	C	T	T	T	299	23	CPNE4	1	1
MED12L	116931	broad.mit.edu	37	3	150883660	150883660	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:150883660C>T	uc003eyp.2	+	c.1385C>T	c.(1384-1386)ACG>ATG	p.T462M	MED12L_uc011bnz.1_Missense_Mutation_p.T322M|MED12L_uc003eyn.2_Missense_Mutation_p.T462M|MED12L_uc003eyo.2_Missense_Mutation_p.T462M	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	462					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	RNA polymerase II transcription mediator activity			ovary(4)|large_intestine(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)							59				0.094059	9.569967	43.02233	19	183	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150883660	150883660	9818	3	C	T	T	T	247	19	MED12L	1	1
MAP3K13	9175	broad.mit.edu	37	3	185167766	185167766	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185167766G>T	uc010hyf.2	+	c.1089G>T	c.(1087-1089)TGG>TGT	p.W363C	MAP3K13_uc011brt.1_Missense_Mutation_p.W156C|MAP3K13_uc003fph.3_Missense_Mutation_p.W131C|MAP3K13_uc011bru.1_Missense_Mutation_p.W219C|MAP3K13_uc003fpi.2_Missense_Mutation_p.W363C|MAP3K13_uc010hyg.2_Missense_Mutation_p.W53C	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase	363	Protein kinase.				activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)							296				0.149123	24.889266	38.371057	17	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185167766	185167766	9630	3	G	T	T	T	559	43	MAP3K13	2	2
LPP	4026	broad.mit.edu	37	3	188426068	188426068	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:188426068G>T	uc003frs.1	+	c.1127G>T	c.(1126-1128)GGG>GTG	p.G376V	LPP_uc011bsg.1_Missense_Mutation_p.G229V|LPP_uc011bsi.1_Missense_Mutation_p.G376V|LPP_uc003frt.2_Missense_Mutation_p.G376V|LPP_uc011bsj.1_Missense_Mutation_p.G213V	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation	376					cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|ovary(1)	162	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)						184				0.116505	12.16614	27.041131	12	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	188426068	188426068	9296	3	G	T	T	T	559	43	LPP	2	2
CCDC13	152206	broad.mit.edu	37	3	42777198	42777198	+	Splice_Site_SNP	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:42777198C>T	uc003cly.3	-	c.1371_splice	c.e10+1	p.H457_splice		NM_144719	NP_653320			coiled-coil domain containing 13											ovary(1)	1														0.140426	48.331911	77.657474	33	202	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	42777198	42777198	2885	3	C	T	T	T	247	19	CCDC13	5	1
CCR2	729230	broad.mit.edu	37	3	46399605	46399605	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:46399605G>A	uc003cpn.3	+	c.587G>A	c.(586-588)CGA>CAA	p.R196Q	CCR2_uc003cpm.3_Missense_Mutation_p.R196Q	NM_001123041	NP_001116513	P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2 isoform A	196	Extracellular (Potential).				astrocyte cell migration|blood vessel remodeling|cellular defense response|chemokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response|interspecies interaction between organisms|JAK-STAT cascade|monocyte extravasation|negative regulation of adenylate cyclase activity|negative regulation of angiogenesis|negative regulation of eosinophil degranulation|negative regulation of type 2 immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of immune complex clearance by monocytes and macrophages|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-2 production|positive regulation of monocyte chemotaxis|positive regulation of T cell chemotaxis|positive regulation of T cell extravasation|positive regulation of T-helper 1 type immune response|positive regulation of tumor necrosis factor biosynthetic process|regulation of vascular endothelial growth factor production|T-helper 17 cell chemotaxis	cytosol|dendrite|integral to plasma membrane|perikaryon|perinuclear region of cytoplasm|soluble fraction	C-C chemokine receptor activity|CCR2 chemokine receptor binding|protein homodimerization activity			lung(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)										0.107759	46.518804	117.30773	50	414	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46399605	46399605	3068	3	G	A	A	A	481	37	CCR2	1	1
SCAP	22937	broad.mit.edu	37	3	47456482	47456482	+	Silent	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47456482C>A	uc003crh.1	-	c.3141G>T	c.(3139-3141)GGG>GGT	p.G1047G	SCAP_uc011baz.1_Silent_p.G791G|SCAP_uc003crg.2_Silent_p.G654G	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein	1047	Interaction with SREBF2 (By similarity).|Cytoplasmic (By similarity).				cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		Pancreas(149;978 1908 29304 37806 46700)								0.117647	3.175806	8.064787	4	30	KEEP	---	---	---	---	capture		Silent	SNP	47456482	47456482	14358	3	C	A	A	A	379	30	SCAP	2	2
SCAP	22937	broad.mit.edu	37	3	47456639	47456639	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47456639C>G	uc003crh.1	-	c.3088G>C	c.(3088-3090)GAT>CAT	p.D1030H	SCAP_uc011baz.1_Missense_Mutation_p.D774H|SCAP_uc003crg.2_Missense_Mutation_p.D637H	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein	1030	Interaction with SREBF2 (By similarity).|Cytoplasmic (By similarity).|WD 3.				cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		Pancreas(149;978 1908 29304 37806 46700)								0.090909	2.930586	12.211858	5	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47456639	47456639	14358	3	C	G	G	G	377	29	SCAP	3	3
CELSR3	1951	broad.mit.edu	37	3	48677227	48677227	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48677227G>A	uc003cuf.1	-	c.10085C>T	c.(10084-10086)TCA>TTA	p.S3362L	CELSR3_uc010hkf.2_Missense_Mutation_p.S554L|CELSR3_uc010hkg.2_Missense_Mutation_p.S1247L|CELSR3_uc003cul.2_Missense_Mutation_p.S3264L	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	3264	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)										0.156398	55.326421	79.120019	33	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48677227	48677227	3356	3	G	A	A	A	585	45	CELSR3	2	2
P4HTM	54681	broad.mit.edu	37	3	49042348	49042348	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49042348G>T	uc003cvh.2	+	c.942G>T	c.(940-942)CTG>CTT	p.L314L	P4HTM_uc003cvg.2_Silent_p.L314L|WDR6_uc011bbx.1_5'Flank|WDR6_uc003cvj.2_5'Flank|WDR6_uc011bby.1_5'Flank|WDR6_uc010hkn.2_5'Flank|WDR6_uc011bbz.1_5'Flank	NM_177938	NP_808807	Q9NXG6	P4HTM_HUMAN	hypoxia-inducible factor prolyl 4-hydroxylase	314	Lumenal (Potential).|Fe2OG dioxygenase.				oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)									0.117647	11.691413	23.905819	10	75	KEEP	---	---	---	---	capture		Silent	SNP	49042348	49042348	11773	3	G	T	T	T	587	46	P4HTM	2	2
P4HTM	54681	broad.mit.edu	37	3	49042350	49042350	+	Missense_Mutation	SNP	A	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49042350A>C	uc003cvh.2	+	c.944A>C	c.(943-945)CAG>CCG	p.Q315P	P4HTM_uc003cvg.2_Missense_Mutation_p.Q315P|WDR6_uc011bbx.1_5'Flank|WDR6_uc003cvj.2_5'Flank|WDR6_uc011bby.1_5'Flank|WDR6_uc010hkn.2_5'Flank|WDR6_uc011bbz.1_5'Flank	NM_177938	NP_808807	Q9NXG6	P4HTM_HUMAN	hypoxia-inducible factor prolyl 4-hydroxylase	315	Lumenal (Potential).|Fe2OG dioxygenase.				oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)									0.127907	13.77827	25.377174	11	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49042350	49042350	11773	3	A	C	C	C	91	7	P4HTM	4	4
LAMB2	3913	broad.mit.edu	37	3	49161339	49161339	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49161339G>A	uc003cwe.2	-	c.3619C>T	c.(3619-3621)CGT>TGT	p.R1207C		NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	1207	Domain II.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.098361	3.103132	12.952036	6	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49161339	49161339	8934	3	G	A	A	A	507	39	LAMB2	1	1
MST1	4485	broad.mit.edu	37	3	49724892	49724892	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49724892G>A	uc003cxg.2	-	c.375C>T	c.(373-375)ATC>ATT	p.I125I	MST1_uc011bcs.1_Silent_p.I125I|MST1_uc010hkx.2_Silent_p.I46I|MST1_uc011bct.1_Silent_p.I125I|MST1_uc011bcu.1_Intron|RNF123_uc003cxh.2_5'Flank	NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth	111	Kringle 1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GBM(110;181 1524 8005 22865 46297)								0.179245	36.766925	47.026829	19	87	KEEP	---	---	---	---	capture		Silent	SNP	49724892	49724892	10283	3	G	A	A	A	577	45	MST1	2	2
FLNB	2317	broad.mit.edu	37	3	58080588	58080588	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:58080588G>T	uc010hne.2	+	c.813G>T	c.(811-813)GTG>GTT	p.V271V	FLNB_uc003djj.2_Silent_p.V271V|FLNB_uc003djk.2_Silent_p.V271V|FLNB_uc010hnf.2_Silent_p.V271V|FLNB_uc003djl.2_Silent_p.V102V|FLNB_uc003djm.2_Silent_p.V102V	NM_001164317	NP_001157789	O75369	FLNB_HUMAN	filamin B isoform 1	271	Filamin 1.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(6)|ovary(3)	9				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)						676				0.127451	24.810986	52.44127	26	178	KEEP	---	---	---	---	capture		Silent	SNP	58080588	58080588	6176	3	G	T	T	T	574	45	FLNB	2	2
LEF1	51176	broad.mit.edu	37	4	109088908	109088908	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109088908C>T	uc003hyt.1	-	c.16G>A	c.(16-18)GGA>AGA	p.G6R	LEF1_uc011cfj.1_5'Flank|LEF1_uc011cfk.1_5'Flank|LEF1_uc003hyu.1_Missense_Mutation_p.G6R|LEF1_uc003hyv.1_Missense_Mutation_p.G6R|LEF1_uc010imb.1_Non-coding_Transcript	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	6	Poly-Gly.|CTNNB1-binding (By similarity).				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of caspase activity|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of gene-specific transcription|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|promoter binding|transcription activator activity|transcription repressor activity			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)										0.082707	1.433084	24.976437	11	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109088908	109088908	9038	4	C	T	T	T	299	23	LEF1	1	1
SPATA5	166378	broad.mit.edu	37	4	124235149	124235149	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:124235149C>G	uc003iez.3	+	c.2612C>G	c.(2611-2613)CCT>CGT	p.P871R		NM_145207	NP_660208	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	871					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0														0.117647	16.122469	30.791503	12	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124235149	124235149	15521	4	C	G	G	G	312	24	SPATA5	3	3
FHDC1	85462	broad.mit.edu	37	4	153874673	153874673	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:153874673G>A	uc003inf.2	+	c.521G>A	c.(520-522)CGG>CAG	p.R174Q		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	174	FH2.				actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)													0.142857	26.724249	40.492982	16	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153874673	153874673	6114	4	G	A	A	A	507	39	FHDC1	1	1
JAKMIP1	152789	broad.mit.edu	37	4	6055780	6055780	+	Silent	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:6055780G>C	uc010idb.1	-	c.1803C>G	c.(1801-1803)CTC>CTG	p.L601L	JAKMIP1_uc010idc.1_Silent_p.L416L|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc003giu.3_Silent_p.L601L|JAKMIP1_uc011bwc.1_Silent_p.L436L|JAKMIP1_uc003giv.3_Silent_p.L601L|JAKMIP1_uc010ide.2_3'UTR	NM_001099433	NP_001092903	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	601	Mediates interaction with TYK2 and GABBR1.|Potential.				protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|ovary(1)|pancreas(1)	3														0.106762	45.384438	88.470682	30	251	KEEP	---	---	---	---	capture		Silent	SNP	6055780	6055780	8244	4	G	C	C	C	470	37	JAKMIP1	3	3
UGT2B10	7365	broad.mit.edu	37	4	69682206	69682206	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:69682206G>T	uc003hee.2	+	c.469G>T	c.(469-471)GAG>TAG	p.E157*	UGT2B10_uc011cam.1_Intron	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1	157					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(2)	2						Melanoma(133;755 1763 25578 26334 46021)								0.077586	-3.028176	18.176002	9	107	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	69682206	69682206	17514	4	G	T	T	T	585	45	UGT2B10	5	2
TADA2B	93624	broad.mit.edu	37	4	7056332	7056332	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:7056332G>C	uc003gjw.3	+	c.814G>C	c.(814-816)GAT>CAT	p.D272H	TADA2B_uc010idi.2_Missense_Mutation_p.D197H	NM_152293	NP_689506	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2 (ADA2 homolog,	272					regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|zinc ion binding				0														0.105882	13.208902	26.325014	9	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7056332	7056332	16032	4	G	C	C	C	585	45	TADA2B	3	3
COPS4	51138	broad.mit.edu	37	4	83984321	83984321	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:83984321G>C	uc010ijw.2	+	c.808G>C	c.(808-810)GAT>CAT	p.D270H	COPS4_uc003hoa.2_Missense_Mutation_p.D270H|COPS4_uc003hob.2_Missense_Mutation_p.D270H|COPS4_uc010ijx.2_Missense_Mutation_p.D270H	NM_016129	NP_057213	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	270	PCI.					cytoplasm|signalosome	protein binding			kidney(1)	1		Hepatocellular(203;0.114)												0.111111	17.280146	30.737651	10	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83984321	83984321	3873	4	G	C	C	C	429	33	COPS4	3	3
TIGD2	166815	broad.mit.edu	37	4	90034222	90034222	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:90034222G>A	uc003hsk.2	+	c.97G>A	c.(97-99)GTG>ATG	p.V33M	FAM13A_uc003hsh.1_5'Flank	NM_145715	NP_663761	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	33	H-T-H motif (By similarity).|HTH psq-type.					chromosome, centromeric region|nucleus	DNA binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)										0.120879	24.82378	50.469304	22	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90034222	90034222	16425	4	G	A	A	A	520	40	TIGD2	1	1
PCDHB11	56125	broad.mit.edu	37	5	140580730	140580730	+	Silent	SNP	C	T	T	rs114264306	by1000genomes	TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140580730C>T	uc003liy.2	+	c.1383C>T	c.(1381-1383)CGC>CGT	p.R461R	PCDHB11_uc011daj.1_Silent_p.R96R	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	461	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.090047	5.00388	40.754616	19	192	KEEP	---	---	---	---	capture		Silent	SNP	140580730	140580730	11956	5	C	T	T	T	340	27	PCDHB11	1	1
PCDHGC4	56098	broad.mit.edu	37	5	140865098	140865098	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140865098G>C	uc003lky.1	+	c.358G>C	c.(358-360)GAG>CAG	p.E120Q	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc011dbb.1_Missense_Mutation_p.E120Q	NM_018928	NP_061751	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4 isoform 1	120	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.075862	3.108844	29.841226	11	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140865098	140865098	11990	5	G	C	C	C	429	33	PCDHGC4	3	3
ZNF354C	30832	broad.mit.edu	37	5	178506452	178506452	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178506452G>A	uc003mju.2	+	c.1019G>A	c.(1018-1020)AGA>AAA	p.R340K		NM_014594	NP_055409	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	340	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)										0.052288	-29.369323	35.479063	16	290	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178506452	178506452	18458	5	G	A	A	A	429	33	ZNF354C	2	2
ADAMTS2	9509	broad.mit.edu	37	5	178581848	178581848	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178581848G>A	uc003mjw.2	-	c.1205C>T	c.(1204-1206)TCA>TTA	p.S402L	ADAMTS2_uc011dgm.1_Missense_Mutation_p.S402L	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	402	Peptidase M12B.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)						1974				0.210526	7.687329	9.162507	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178581848	178581848	266	5	G	A	A	A	585	45	ADAMTS2	2	2
RNASEN	29102	broad.mit.edu	37	5	31515172	31515172	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31515172C>T	uc003jhg.2	-	c.1213G>A	c.(1213-1215)GAA>AAA	p.E405K	RNASEN_uc003jhh.2_Missense_Mutation_p.E368K|RNASEN_uc003jhi.2_Missense_Mutation_p.E368K|RNASEN_uc010iui.1_Missense_Mutation_p.E328K	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	405					gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0														0.142857	45.086412	68.330029	27	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31515172	31515172	13894	5	C	T	T	T	416	32	RNASEN	2	2
NIPBL	25836	broad.mit.edu	37	5	36985803	36985803	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:36985803C>T	uc003jkl.3	+	c.2521C>T	c.(2521-2523)CGA>TGA	p.R841*	NIPBL_uc003jkk.3_Nonsense_Mutation_p.R841*|NIPBL_uc003jkm.1_Nonsense_Mutation_p.R720*	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	841					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding|transcription repressor activity			ovary(3)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	8	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)						p.R841*(JHUEM1-Tumor)	934				0.12	9.328897	19.951086	9	66	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	36985803	36985803	10829	5	C	T	T	T	399	31	NIPBL	5	1
ARL15	54622	broad.mit.edu	37	5	53467697	53467697	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:53467697C>G	uc003jpg.1	-	c.110G>C	c.(109-111)TGC>TCC	p.C37S	ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	37							GTP binding			ovary(1)	1		Lung NSC(810;0.000779)												0.155556	14.093573	19.194803	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53467697	53467697	946	5	C	G	G	G	325	25	ARL15	3	3
RNF180	285671	broad.mit.edu	37	5	63509899	63509899	+	Missense_Mutation	SNP	A	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:63509899A>T	uc003jti.2	+	c.746A>T	c.(745-747)CAT>CTT	p.H249L	RNF180_uc003jth.3_Missense_Mutation_p.H249L|RNF180_uc010iws.2_Intron	NM_001113561	NP_001107033	Q86T96	RN180_HUMAN	ring finger protein 180 isoform 1	249	Cytoplasmic (Potential).					integral to membrane|nuclear envelope	zinc ion binding				0		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)										0.104895	15.02363	37.217898	15	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63509899	63509899	13941	5	A	T	T	T	104	8	RNF180	3	3
C5orf44	80006	broad.mit.edu	37	5	64956651	64956651	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:64956651G>C	uc003jua.3	+	c.824G>C	c.(823-825)GGA>GCA	p.G275A	C5orf44_uc003jtz.3_Missense_Mutation_p.G275A|C5orf44_uc003juc.3_Missense_Mutation_p.G269A|C5orf44_uc010iwv.2_Missense_Mutation_p.G269A	NM_001093755	NP_001087224	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 1	275										ovary(1)	1														0.222222	25.180403	27.735496	8	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64956651	64956651	2401	5	G	C	C	C	533	41	C5orf44	3	3
RGNEF	64283	broad.mit.edu	37	5	73048996	73048996	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:73048996G>A	uc010izf.2	+	c.444G>A	c.(442-444)GAG>GAA	p.E148E	RGNEF_uc003kcx.2_Silent_p.E148E|RGNEF_uc003kcy.1_Silent_p.E148E|RGNEF_uc011csq.1_Silent_p.E148E	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor	148					cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)										0.166667	10.154816	13.316205	5	25	KEEP	---	---	---	---	capture		Silent	SNP	73048996	73048996	13756	5	G	A	A	A	464	36	RGNEF	2	2
ASCC3	10973	broad.mit.edu	37	6	100957385	100957385	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:100957385C>G	uc003pqk.2	-	c.6486G>C	c.(6484-6486)ATG>ATC	p.M2162I		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	2162	SEC63 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)	5		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)										0.082645	4.947527	26.390969	10	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100957385	100957385	1051	6	C	G	G	G	377	29	ASCC3	3	3
C6orf170	221322	broad.mit.edu	37	6	121624836	121624836	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:121624836G>A	uc003pyo.1	-	c.1007C>T	c.(1006-1008)TCA>TTA	p.S336L	C6orf170_uc003pyq.1_Non-coding_Transcript	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322	336					multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)										0.173913	14.668311	19.288645	8	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121624836	121624836	2449	6	G	A	A	A	585	45	C6orf170	2	2
HIVEP2	3097	broad.mit.edu	37	6	143095798	143095798	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:143095798C>G	uc003qjd.2	-	c.78G>C	c.(76-78)TGG>TGC	p.W26C		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	26					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		Esophageal Squamous(107;843 1510 13293 16805 42198)								0.079755	14.502968	73.231203	26	300	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143095798	143095798	7478	6	C	G	G	G	390	30	HIVEP2	3	3
MAP3K4	4216	broad.mit.edu	37	6	161470184	161470184	+	Missense_Mutation	SNP	A	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161470184A>T	uc003qtn.2	+	c.880A>T	c.(880-882)ATT>TTT	p.I294F	MAP3K4_uc010kkc.1_Missense_Mutation_p.I294F|MAP3K4_uc003qto.2_Missense_Mutation_p.I294F|MAP3K4_uc011efz.1_Non-coding_Transcript|MAP3K4_uc011ega.1_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	294					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)						511				0.133929	24.352038	38.908573	15	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161470184	161470184	9635	6	A	T	T	T	208	16	MAP3K4	3	3
FAM65B	9750	broad.mit.edu	37	6	24843425	24843425	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:24843425C>G	uc003neo.1	-	c.1585G>C	c.(1585-1587)GAG>CAG	p.E529Q	FAM65B_uc011djs.1_Missense_Mutation_p.E508Q|FAM65B_uc011dju.1_Missense_Mutation_p.E513Q|FAM65B_uc003nep.2_Missense_Mutation_p.E479Q|FAM65B_uc011djt.1_Missense_Mutation_p.E479Q	NM_014722	NP_055537	Q9Y4F9	FA65B_HUMAN	hypothetical protein LOC9750 isoform 1	529					cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1														0.095588	12.068034	34.386464	13	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24843425	24843425	5823	6	C	G	G	G	377	29	FAM65B	3	3
DAAM2	23500	broad.mit.edu	37	6	39835326	39835326	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:39835326C>G	uc003oow.2	+	c.469C>G	c.(469-471)CTG>GTG	p.L157V	DAAM2_uc010jxc.2_Missense_Mutation_p.L157V|DAAM2_uc003oox.2_Missense_Mutation_p.L157V	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of	157	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)													0.064286	-3.52244	24.091554	9	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39835326	39835326	4382	6	C	G	G	G	415	32	DAAM2	3	3
C6orf138	442213	broad.mit.edu	37	6	47976380	47976380	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:47976380G>T	uc011dwm.1	-	c.846C>A	c.(844-846)TTC>TTA	p.F282L	C6orf138_uc011dwn.1_Missense_Mutation_p.F46L|C6orf138_uc003ozf.2_Missense_Mutation_p.F299L	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	299	Helical; (Potential).|SSD.					integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1														0.2	14.102639	17.034684	7	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47976380	47976380	2435	6	G	T	T	T	425	33	C6orf138	2	2
DST	667	broad.mit.edu	37	6	56371470	56371470	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56371470C>G	uc003pdf.2	-	c.13000G>C	c.(13000-13002)GAT>CAT	p.D4334H	DST_uc003pcz.3_Missense_Mutation_p.D4156H|DST_uc011dxj.1_Missense_Mutation_p.D4185H|DST_uc011dxk.1_Missense_Mutation_p.D4196H|DST_uc003pcy.3_Missense_Mutation_p.D3830H	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	6242	Spectrin 13.				cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)							2498				0.137931	18.558816	25.912055	8	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56371470	56371470	4967	6	C	G	G	G	416	32	DST	3	3
ELOVL4	6785	broad.mit.edu	37	6	80629227	80629227	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:80629227C>T	uc003pja.3	-	c.579G>A	c.(577-579)GTG>GTA	p.V193V	ELOVL4_uc011dyt.1_Intron	NM_022726	NP_073563	Q9GZR5	ELOV4_HUMAN	elongation of very long chain fatty acids-like	193	Helical; (Potential).				fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process|visual perception	integral to endoplasmic reticulum membrane	G-protein coupled photoreceptor activity|protein binding|transferase activity, transferring acyl groups other than amino-acyl groups			ovary(1)	1		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)									0.197368	30.07531	36.563971	15	61	KEEP	---	---	---	---	capture		Silent	SNP	80629227	80629227	5268	6	C	T	T	T	366	29	ELOVL4	2	2
CNR1	1268	broad.mit.edu	37	6	88854698	88854698	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:88854698C>G	uc011dzq.1	-	c.296G>C	c.(295-297)GGG>GCG	p.G99A	CNR1_uc010kbz.2_Missense_Mutation_p.G99A|CNR1_uc011dzr.1_Missense_Mutation_p.G99A|CNR1_uc011dzs.1_Missense_Mutation_p.G99A|CNR1_uc003pmq.3_Missense_Mutation_p.G99A|CNR1_uc011dzt.1_Missense_Mutation_p.G99A|CNR1_uc010kca.2_Missense_Mutation_p.G66A	NM_001160260	NP_001153732	P21554	CNR1_HUMAN	cannabinoid receptor 1 isoform a	99	Extracellular (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	cannabinoid receptor activity|protein binding				0		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Marinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)									0.085366	2.064331	16.358358	7	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88854698	88854698	3769	6	C	G	G	G	286	22	CNR1	3	3
ANKRD7	56311	broad.mit.edu	37	7	117876197	117876197	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:117876197C>G	uc003vji.2	+	c.571C>G	c.(571-573)CAA>GAA	p.Q191E		NM_019644	NP_062618	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	191	ANK 5.				male gonad development						0														0.256881	84.439621	90.288141	28	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117876197	117876197	694	7	C	G	G	G	377	29	ANKRD7	3	3
LRRC4	64101	broad.mit.edu	37	7	127670635	127670635	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:127670635G>A	uc003vmk.2	-	c.59C>T	c.(58-60)CCG>CTG	p.P20L	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	20						cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)										0.10828	15.199065	39.047488	17	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127670635	127670635	9372	7	G	A	A	A	507	39	LRRC4	1	1
CPA4	51200	broad.mit.edu	37	7	129945750	129945750	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:129945750C>A	uc003vpr.2	+	c.581C>A	c.(580-582)ACG>AAG	p.T194K	CPA4_uc011kpd.1_Missense_Mutation_p.T161K|CPA4_uc011kpe.1_Missense_Mutation_p.T90K	NM_016352	NP_057436	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4 preproprotein	194					histone acetylation|proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)													0.272	95.599775	101.45486	34	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129945750	129945750	3930	7	C	A	A	A	247	19	CPA4	1	1
MLL3	58508	broad.mit.edu	37	7	151884816	151884816	+	Missense_Mutation	SNP	A	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:151884816A>C	uc003wla.2	-	c.4777T>G	c.(4777-4779)TCT>GCT	p.S1593A	MLL3_uc003wkz.2_Missense_Mutation_p.S654A	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	1593					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			pancreas(12)|ovary(7)|large_intestine(6)|central_nervous_system(4)|urinary_tract(1)|skin(1)	31	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		Colon(68;14 1149 1884 27689 34759)				1780				0.106742	18.890298	46.223796	19	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151884816	151884816	10012	7	A	C	C	C	143	11	MLL3	4	4
HOXA6	3203	broad.mit.edu	37	7	27187160	27187160	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27187160G>T	uc003syo.1	-	c.209C>A	c.(208-210)GCG>GAG	p.A70E	HOXA6_uc003syq.1_Intron	NM_024014	NP_076919	P31267	HXA6_HUMAN	homeobox A6	70					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)|central_nervous_system(1)	2														0.25	64.688866	70.611321	26	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27187160	27187160	7588	7	G	T	T	T	494	38	HOXA6	1	1
INHBA	3624	broad.mit.edu	37	7	41729294	41729294	+	Missense_Mutation	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:41729294T>C	uc003thq.2	-	c.1235A>G	c.(1234-1236)AAA>AGA	p.K412R	INHBA_uc003thr.2_Missense_Mutation_p.K412R	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	412					cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway|regulation of gene-specific transcription from RNA polymerase II promoter	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity|transcription activator activity			lung(5)|ovary(1)	6										102	TSP Lung(11;0.080)			0.3	128.394878	133.028685	39	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41729294	41729294	8042	7	T	C	C	C	832	64	INHBA	4	4
AKAP9	10142	broad.mit.edu	37	7	91660865	91660865	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91660865G>A	uc003ulg.2	+	c.4285G>A	c.(4285-4287)GTT>ATT	p.V1429I	AKAP9_uc003ule.2_Missense_Mutation_p.V1441I|AKAP9_uc003ulf.2_Missense_Mutation_p.V1429I|AKAP9_uc003uli.2_Missense_Mutation_p.V1054I	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1441	Potential.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)							807				0.133929	22.946253	37.507672	15	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91660865	91660865	462	7	G	A	A	A	520	40	AKAP9	1	1
AKAP9	10142	broad.mit.edu	37	7	91700233	91700233	+	Silent	SNP	A	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91700233A>G	uc003ulg.2	+	c.6522A>G	c.(6520-6522)AAA>AAG	p.K2174K	AKAP9_uc003ulf.2_Silent_p.K2166K|AKAP9_uc003uli.2_Silent_p.K1797K|AKAP9_uc003ulj.2_5'UTR	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2186	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)							807				0.291667	141.394253	146.990356	42	102	KEEP	---	---	---	---	capture		Silent	SNP	91700233	91700233	462	7	A	G	G	G	24	2	AKAP9	4	4
RGS22	26166	broad.mit.edu	37	8	100990155	100990155	+	Missense_Mutation	SNP	T	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:100990155T>G	uc003yjb.1	-	c.3509A>C	c.(3508-3510)AAA>ACA	p.K1170T	RGS22_uc003yja.1_Missense_Mutation_p.K989T|RGS22_uc003yjc.1_Missense_Mutation_p.K1158T	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	1170	Potential.				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|breast(1)|central_nervous_system(1)	5			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)							790				0.069767	-0.021536	16.415151	6	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100990155	100990155	13779	8	T	G	G	G	832	64	RGS22	4	4
KIAA1429	25962	broad.mit.edu	37	8	95508682	95508682	+	Silent	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95508682G>A	uc003ygo.1	-	c.4257C>T	c.(4255-4257)CTC>CTT	p.L1419L	KIAA1429_uc010maz.1_Non-coding_Transcript	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	1419					mRNA processing|RNA splicing	nucleus				ovary(1)	1	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)											0.136691	27.523267	45.291737	19	120	KEEP	---	---	---	---	capture		Silent	SNP	95508682	95508682	8540	8	G	A	A	A	574	45	KIAA1429	2	2
PALM2-AKAP2	445815	broad.mit.edu	37	9	112705636	112705636	+	Missense_Mutation	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:112705636G>C	uc004bei.2	+	c.1167G>C	c.(1165-1167)GAG>GAC	p.E389D	PALM2_uc004bef.2_Missense_Mutation_p.E391D|PALM2_uc004beg.2_Missense_Mutation_p.E357D|PALM2_uc004beh.3_Missense_Mutation_p.E389D|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	Error:Variant_position_missing_in_Q9Y2D5_after_alignment							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.139073	36.668024	55.698698	21	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112705636	112705636	11826	9	G	C	C	C	425	33	PALM2-AKAP2	3	3
ADAMTSL1	92949	broad.mit.edu	37	9	18574179	18574179	+	Missense_Mutation	SNP	T	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:18574179T>A	uc003zne.3	+	c.389T>A	c.(388-390)CTG>CAG	p.L130Q	ADAMTSL1_uc003znb.2_Missense_Mutation_p.L130Q|ADAMTSL1_uc003znc.3_Missense_Mutation_p.L130Q	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	130						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|lung(1)	4				GBM - Glioblastoma multiforme(50;1.29e-17)										0.071823	-4.071696	30.105303	13	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18574179	18574179	275	9	T	A	A	A	715	55	ADAMTSL1	3	3
DNAI1	27019	broad.mit.edu	37	9	34514476	34514476	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:34514476C>G	uc003zum.2	+	c.1654C>G	c.(1654-1656)CAC>GAC	p.H552D		NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	552	WD 3.				cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)										0.084656	9.543523	42.635618	16	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34514476	34514476	4792	9	C	G	G	G	273	21	DNAI1	3	3
MLANA	2315	broad.mit.edu	37	9	5892506	5892506	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:5892506G>T	uc003zjo.1	+	c.32G>T	c.(31-33)GGT>GTT	p.G11V		NM_005511	NP_005502	Q16655	MAR1_HUMAN	melan-A	11						endoplasmic reticulum membrane|integral to plasma membrane|melanosome|trans-Golgi network	protein binding				0		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)										0.096774	3.200512	13.306145	6	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5892506	5892506	10001	9	G	T	T	T	572	44	MLANA	2	2
PTPRD	5789	broad.mit.edu	37	9	8518128	8518128	+	Silent	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8518128C>G	uc003zkk.2	-	c.1263G>C	c.(1261-1263)CCG>CCC	p.P421P	PTPRD_uc003zkp.2_Silent_p.P421P|PTPRD_uc003zkq.2_Silent_p.P421P|PTPRD_uc003zkr.2_Silent_p.P415P|PTPRD_uc003zks.2_Silent_p.P411P|PTPRD_uc003zkl.2_Silent_p.P421P|PTPRD_uc003zkm.2_Silent_p.P408P|PTPRD_uc003zkn.2_Silent_p.P421P|PTPRD_uc003zko.2_Silent_p.P418P	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	421	Fibronectin type-III 2.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.114155	38.317958	70.460628	25	194	KEEP	---	---	---	---	capture		Silent	SNP	8518128	8518128	13256	9	C	G	G	G	392	31	PTPRD	3	3
MCART6	401612	broad.mit.edu	37	X	103349436	103349436	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:103349436G>A	uc004elu.2	-	c.505C>T	c.(505-507)CGG>TGG	p.R169W		NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	169	Solcar 2.				transport	integral to membrane|mitochondrial inner membrane					0														0.169492	65.81821	90.188403	40	196	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103349436	103349436	9760	23	G	A	A	A	493	38	MCART6	1	1
CXorf41	139212	broad.mit.edu	37	X	106466059	106466059	+	Silent	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:106466059C>T	uc004enc.2	+	c.417C>T	c.(415-417)TGC>TGT	p.C139C	CXorf41_uc004end.2_Silent_p.C139C	NM_173494	NP_775765	Q9NQM4	CX041_HUMAN	hypothetical protein LOC139212	139											0														0.142077	31.800972	54.47547	26	157	KEEP	---	---	---	---	capture		Silent	SNP	106466059	106466059	4271	23	C	T	T	T	324	25	CXorf41	2	2
ZCCHC12	170261	broad.mit.edu	37	X	117960105	117960105	+	Missense_Mutation	SNP	A	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:117960105A>G	uc004equ.2	+	c.898A>G	c.(898-900)AGA>GGA	p.R300G		NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	300					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1														0.132075	39.090879	67.142467	28	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117960105	117960105	18169	23	A	G	G	G	88	7	ZCCHC12	4	4
GRIA3	2892	broad.mit.edu	37	X	122537344	122537344	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:122537344C>G	uc004etq.3	+	c.1267C>G	c.(1267-1269)CGG>GGG	p.R423G	GRIA3_uc004etr.3_Missense_Mutation_p.R423G|GRIA3_uc004ets.3_Non-coding_Transcript|GRIA3_uc011muf.1_Missense_Mutation_p.R407G	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	423	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|pancreas(1)	4					L-Glutamic Acid(DB00142)					217				0.102041	29.445528	68.078689	25	220	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122537344	122537344	7047	23	C	G	G	G	399	31	GRIA3	3	3
TLR7	51284	broad.mit.edu	37	X	12904699	12904699	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:12904699G>T	uc004cvc.2	+	c.1072G>T	c.(1072-1074)GCA>TCA	p.A358S		NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN	toll-like receptor 7 precursor	358	Extracellular (Potential).|LRR 12.				cellular response to mechanical stimulus|defense response to virus|I-kappaB phosphorylation|inflammatory response|innate immune response|positive regulation of chemokine production|positive regulation of inflammatory response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus	early phagosome|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosome|plasma membrane	double-stranded RNA binding|single-stranded RNA binding|siRNA binding|transmembrane receptor activity			ovary(1)	1					Imiquimod(DB00724)					69				0.096774	8.147551	33.370512	15	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12904699	12904699	16486	23	G	T	T	T	598	46	TLR7	2	2
CDR1	1038	broad.mit.edu	37	X	139865753	139865753	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:139865753C>T	uc004fbg.1	-	c.779G>A	c.(778-780)TGG>TAG	p.W260*		NM_004065	NP_004056	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1,	260											0	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)												0.111111	26.798184	56.408637	22	176	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	139865753	139865753	3300	23	C	T	T	T	273	21	CDR1	5	2
MTM1	4534	broad.mit.edu	37	X	149839952	149839952	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149839952G>A	uc004fef.3	+	c.1696G>A	c.(1696-1698)GAA>AAA	p.E566K	MTM1_uc011mxx.1_Non-coding_Transcript|MTM1_uc011mxy.1_Missense_Mutation_p.E529K|MTM1_uc011mxz.1_Missense_Mutation_p.E451K|MTM1_uc010nte.2_Missense_Mutation_p.E434K	NM_000252	NP_000243	Q13496	MTM1_HUMAN	myotubularin	566					endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			ovary(1)|kidney(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.102564	4.938883	17.221653	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149839952	149839952	10330	23	G	A	A	A	481	37	MTM1	1	1
GPR50	9248	broad.mit.edu	37	X	150349062	150349063	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150349062_150349063CC>AA	uc010ntg.1	+	c.1007_1008CC>AA	c.(1006-1008)GCC>GAA	p.A336E	GPR50_uc011myc.1_3'UTR	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	336	Cytoplasmic (Potential).|Pro-rich.				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)													0.075472	-9.278924	30.039796	16	196	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	150349062	150349063	6972	23	CC	AA	AA	AA	338	26	GPR50	2	2
SCML1	6322	broad.mit.edu	37	X	17762333	17762333	+	Missense_Mutation	SNP	C	G	G			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:17762333C>G	uc004cyb.2	+	c.27C>G	c.(25-27)ATC>ATG	p.I9M	SCML1_uc004cyc.2_Missense_Mutation_p.I9M|SCML1_uc004cyd.2_Intron|SCML1_uc004cye.2_Intron	NM_001037540	NP_001032629	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 isoform a	9					anatomical structure morphogenesis|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)	3	Hepatocellular(33;0.183)													0.102564	21.588569	46.135103	16	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17762333	17762333	14391	23	C	G	G	G	395	31	SCML1	3	3
MAGEB18	286514	broad.mit.edu	37	X	26157580	26157580	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:26157580C>A	uc004dbq.1	+	c.478C>A	c.(478-480)CTT>ATT	p.L160I		NM_173699	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	160	MAGE.						protein binding			central_nervous_system(1)	1														0.151515	8.051553	11.891733	5	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26157580	26157580	9556	23	C	A	A	A	260	20	MAGEB18	2	2
ZNF41	7592	broad.mit.edu	37	X	47308566	47308566	+	Missense_Mutation	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47308566G>T	uc004dhs.3	-	c.729C>A	c.(727-729)AAC>AAA	p.N243K	ZNF41_uc004dhu.3_Missense_Mutation_p.N235K|ZNF41_uc004dht.3_Missense_Mutation_p.N115K|ZNF41_uc004dhv.3_Missense_Mutation_p.N211K|ZNF41_uc004dhw.3_Missense_Mutation_p.N203K|ZNF41_uc004dhy.3_Missense_Mutation_p.N201K|ZNF41_uc004dhx.3_Missense_Mutation_p.N201K|ZNF41_uc011mlm.1_Missense_Mutation_p.N115K	NM_153380	NP_700359	P51814	ZNF41_HUMAN	zinc finger protein 41	243					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3		all_lung(315;0.000129)												0.153226	68.757373	97.336021	38	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47308566	47308566	18482	23	G	T	T	T	464	36	ZNF41	2	2
ZNF182	7569	broad.mit.edu	37	X	47835779	47835779	+	Silent	SNP	G	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47835779G>T	uc004dir.2	-	c.1707C>A	c.(1705-1707)CCC>CCA	p.P569P	ZNF182_uc004dis.2_Silent_p.P550P|ZNF182_uc004dit.2_Silent_p.P569P|ZNF182_uc011mlu.1_Silent_p.P549P	NM_006962	NP_008893	P17025	ZN182_HUMAN	zinc finger protein 21 isoform 1	569					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3														0.155963	27.796777	40.123986	17	92	KEEP	---	---	---	---	capture		Silent	SNP	47835779	47835779	18341	23	G	T	T	T	444	35	ZNF182	2	2
NUDT11	55190	broad.mit.edu	37	X	51239057	51239057	+	Silent	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:51239057C>A	uc010njt.2	-	c.240G>T	c.(238-240)CTG>CTT	p.L80L		NM_018159	NP_060629	Q96G61	NUD11_HUMAN	nudix-type motif 11	80	Nudix hydrolase.					cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					GBM(38;198 791 1498 11752 13599)				29				0.096386	3.832441	17.393803	8	75	KEEP	---	---	---	---	capture		Silent	SNP	51239057	51239057	11132	23	C	A	A	A	262	21	NUDT11	2	2
PHF8	23133	broad.mit.edu	37	X	54029107	54029107	+	Missense_Mutation	SNP	G	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54029107G>A	uc004dsu.2	-	c.1063C>T	c.(1063-1065)CAT>TAT	p.H355Y	PHF8_uc004dst.2_Missense_Mutation_p.H319Y|PHF8_uc004dsv.2_Missense_Mutation_p.H185Y|PHF8_uc004dsw.2_Missense_Mutation_p.H319Y|PHF8_uc004dsx.2_Missense_Mutation_p.H83Y|PHF8_uc004dsy.2_Missense_Mutation_p.H319Y	NM_015107	NP_055922	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	355	JmjC.	Iron; catalytic.			brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|oxidation-reduction process|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent	nucleolus	chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(3)	3														0.073529	-0.981473	11.735345	5	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54029107	54029107	12263	23	G	A	A	A	611	47	PHF8	2	2
FAM120C	54954	broad.mit.edu	37	X	54161289	54161289	+	Missense_Mutation	SNP	C	T	T			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54161289C>T	uc004dsz.3	-	c.1591G>A	c.(1591-1593)GAT>AAT	p.D531N	FAM120C_uc011moh.1_Missense_Mutation_p.D531N	NM_017848	NP_060318	Q9NX05	F120C_HUMAN	hypothetical protein LOC54954	531										ovary(1)|central_nervous_system(1)	2														0.145455	12.159523	18.813322	8	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54161289	54161289	5615	23	C	T	T	T	377	29	FAM120C	2	2
PGK1	5230	broad.mit.edu	37	X	77373668	77373668	+	Splice_Site_SNP	SNP	G	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77373668G>C	uc004ecz.3	+	c.641_splice	c.e6+1	p.G214_splice	PGK1_uc010nlz.2_Splice_Site_SNP|PGK1_uc011mqq.1_Splice_Site_SNP_p.G186_splice	NM_000291	NP_000282			phosphoglycerate kinase 1						gluconeogenesis|glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1														0.093333	13.729869	38.683452	14	136	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	77373668	77373668	12213	23	G	C	C	C	572	44	PGK1	5	3
ZCCHC5	203430	broad.mit.edu	37	X	77912563	77912563	+	Missense_Mutation	SNP	C	A	A			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77912563C>A	uc004edc.1	-	c.1355G>T	c.(1354-1356)GGT>GTT	p.G452V		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	452	CCHC-type.						nucleic acid binding|zinc ion binding			ovary(1)	1														0.104478	6.082006	16.502541	7	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77912563	77912563	18179	23	C	A	A	A	234	18	ZCCHC5	2	2
ZCCHC5	203430	broad.mit.edu	37	X	77913582	77913582	+	Silent	SNP	T	C	C			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77913582T>C	uc004edc.1	-	c.336A>G	c.(334-336)CCA>CCG	p.P112P		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	112	Pro-rich.						nucleic acid binding|zinc ion binding			ovary(1)	1														0.166667	9.956409	13.116572	5	25	KEEP	---	---	---	---	capture		Silent	SNP	77913582	77913582	18179	23	T	C	C	C	704	55	ZCCHC5	4	4
KIF26A	26153	broad.mit.edu	37	14	104643849	104643849	+	Frame_Shift_Del	DEL	C	-	-			TCGA-44-3396-01	TCGA-44-3396-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:104643849_104643849delC	uc001yos.3	+	c.4724_4724delC	c.(4723-4725)GCCfs	p.A1575fs		NM_015656	NP_056471	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1575					blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity			pancreas(1)	1		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	104643849	104643849	8605	14	C	-	-	-	338	26	KIF26A	5	5
