Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
WAPAL	23063	broad.mit.edu	36	10	88250235	88250235	+	Nonsense_Mutation	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:88250235C>A	uc001kdn.1	-	c.874G>T	c.(874-876)GAA>TAA	p.E292*	WAPAL_uc001kdo.1_Nonsense_Mutation_p.E249*|WAPAL_uc009xsw.1_Nonsense_Mutation_p.E249*	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog	249	Mediates interaction with the cohesin complex.				cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1														0.204545	54.450045	65.151828	27	105	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	88250235	88250235	17820	10	C	A	A	32	32	WAPAL	A	5	3
PTEN	5728	broad.mit.edu	36	10	89710856	89710856	+	Splice_Site_SNP	SNP	G	C	C			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710856G>C	uc001kfb.1	+	c.e9_splice_site				NM_000314	NP_000305			phosphatase and tensin homolog						apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.?(5)|p.D326_K342del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31	(U138MG-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.465116	64.296378	64.341857	20	23	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	89710856	89710856	13192	10	G	C	C	44	44	PTEN	C	5	3
AMPD3	272	broad.mit.edu	36	11	10456849	10456849	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:10456849C>T	uc001min.1	+	c.449C>T	c.(448-450)GCC>GTC	p.A150V	AMPD3_uc009yfw.1_Non-coding_Transcript|AMPD3_uc009yfx.1_Missense_Mutation_p.A141V|AMPD3_uc001mio.1_Missense_Mutation_p.A141V|AMPD3_uc001mip.1_Missense_Mutation_p.A148V|AMPD3_uc009yfy.1_Missense_Mutation_p.A141V	NM_000480	NP_001020560	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3 isoform 1A	141					AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)										0.4	34.795966	35.057538	12	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10456849	10456849	590	11	C	T	T	26	26	AMPD3	T	2	2
C11orf61	79684	broad.mit.edu	36	11	124149824	124149824	+	Splice_Site_SNP	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:124149824C>A	uc001qba.1	-	c.e2_splice_site			C11orf61_uc001qay.1_Intron|C11orf61_uc001qaz.1_Splice_Site_SNP	NM_024631	NP_078907			hypothetical protein LOC79684												0	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0079)										0.129032	18.542919	30.999695	12	81	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	124149824	124149824	1692	11	C	A	A	18	18	C11orf61	A	5	3
OR8K1	390157	broad.mit.edu	36	11	55870165	55870165	+	Missense_Mutation	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55870165C>A	uc001nir.1	+	c.75C>A	c.(73-75)GAC>GAA	p.D25E		NM_001002907	NP_001002907	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)													0.20354	48.365275	57.588654	23	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55870165	55870165	11654	11	C	A	A	17	17	OR8K1	A	3	3
OR5AR1	219493	broad.mit.edu	36	11	56188220	56188220	+	Silent	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56188220C>A	uc001njc.1	+	c.483C>A	c.(481-483)ACC>ACA	p.T161T		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	161	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.358974	411.527773	418.994517	154	275	CC		KEEP	---	---	---	---	capture			Silent	SNP	56188220	56188220	11555	11	C	A	A	22	22	OR5AR1	A	3	3
RIN1	9610	broad.mit.edu	36	11	65859839	65859839	+	Missense_Mutation	SNP	A	G	G			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65859839A>G	uc001ohn.1	-	c.352T>C	c.(352-354)TCC>CCC	p.S118P	RIN1_uc009yrd.1_5'UTR	NM_004292	NP_004283	Q13671	RIN1_HUMAN	ras inhibitor RIN1	118	SH2.				endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding			lung(1)	1														0.416667	8.278898	8.371236	5	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65859839	65859839	13848	11	A	G	G	11	11	RIN1	G	4	4
STYK1	55359	broad.mit.edu	36	12	10677959	10677959	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10677959G>A	uc001qys.1	-	c.84C>T	c.(82-84)ATC>ATT	p.I28I		NM_018423	NP_060893	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	28	Helical; (Potential).				protein phosphorylation	integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(1)	6										211				0.22807	92.136593	103.75003	39	132	GG		KEEP	---	---	---	---	capture			Silent	SNP	10677959	10677959	15879	12	G	A	A	37	37	STYK1	A	1	1
ACAD10	80724	broad.mit.edu	36	12	110652007	110652007	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:110652007C>T	uc009zvx.1	+	c.1351C>T	c.(1351-1353)CGC>TGC	p.R451C	ACAD10_uc001tsp.1_Missense_Mutation_p.R420C|ACAD10_uc001tsq.1_Missense_Mutation_p.R420C|ACAD10_uc001tss.1_Non-coding_Transcript	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10	420					oxidation-reduction process		acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity			ovary(2)	2														0.285714	80.804989	85.134419	30	75	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110652007	110652007	109	12	C	T	T	19	19	ACAD10	T	1	1
NCOR2	9612	broad.mit.edu	36	12	123383681	123383681	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:123383681G>A	uc009zyd.1	-	c.6733C>T	c.(6733-6735)CGG>TGG	p.R2245W	NCOR2_uc009zye.1_Missense_Mutation_p.R2229W	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1	2246					cellular lipid metabolic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity|transcription repressor activity			ovary(1)|skin(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)										0.653846	56.690059	57.240882	17	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123383681	123383681	10635	12	G	A	A	39	39	NCOR2	A	1	1
TMEM132D	121256	broad.mit.edu	36	12	128750567	128750567	+	Missense_Mutation	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:128750567C>A	uc009zyl.1	-	c.709G>T	c.(709-711)GGG>TGG	p.G237W		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	237	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.597403	148.232045	148.865454	46	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128750567	128750567	16579	12	C	A	A	24	24	TMEM132D	A	3	3
EP400	57634	broad.mit.edu	36	12	131080344	131080344	+	Missense_Mutation	SNP	A	C	C			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:131080344A>C	uc001ujn.1	+	c.5527A>C	c.(5527-5529)ACC>CCC	p.T1843P	EP400_uc001ujl.1_Missense_Mutation_p.T1842P|EP400_uc001ujm.1_Missense_Mutation_p.T1762P|SNORA49_uc001ujo.1_5'Flank	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1879					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)										0.333333	8.493306	8.789863	4	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131080344	131080344	5342	12	A	C	C	10	10	EP400	C	4	4
AQP2	359	broad.mit.edu	36	12	48635568	48635568	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:48635568G>A	uc001rvn.1	+	c.726G>A	c.(724-726)CCG>CCA	p.P242P	AQP2_uc009zll.1_5'Flank	NM_000486	NP_000477	P41181	AQP2_HUMAN	aquaporin 2	242	Cytoplasmic (Potential).				cellular response to copper ion|cellular response to mercury ion|excretion	apical plasma membrane|integral to membrane|transport vesicle membrane	glycerol transmembrane transporter activity|water channel activity			ovary(2)	2														0.25	6.587798	7.501652	4	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	48635568	48635568	837	12	G	A	A	39	39	AQP2	A	1	1
NCKAP1L	3071	broad.mit.edu	36	12	53200807	53200807	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:53200807G>A	uc001sgc.2	+	c.1688G>A	c.(1687-1689)CGT>CAT	p.R563H		NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	563					actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4														0.623468	1138.79619	1146.471335	356	215	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53200807	53200807	10621	12	G	A	A	40	40	NCKAP1L	A	1	1
PIP4K2C	79837	broad.mit.edu	36	12	56274136	56274136	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56274136G>A	uc001sot.1	+	c.236G>A	c.(235-237)AGC>AAC	p.S79N	PIP4K2C_uc001sou.1_Missense_Mutation_p.S79N	NM_024779	NP_079055	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	79	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)									258				0.341667	115.430886	118.092683	41	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56274136	56274136	12362	12	G	A	A	34	34	PIP4K2C	A	2	2
SLC2A3	6515	broad.mit.edu	36	12	7975300	7975300	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7975300G>T	uc001qtr.1	-	c.318C>A	c.(316-318)TGC>TGA	p.C106*	SLC2A3_uc001qts.1_Nonsense_Mutation_p.C106*	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose	106	Helical; Name=3; (Potential).				carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		Colon(96;424 1461 14416 20933 23688)								0.141791	25.764025	42.268029	19	115	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	7975300	7975300	15042	12	G	T	T	34	34	SLC2A3	T	5	3
TNFSF11	8600	broad.mit.edu	36	13	42078962	42078962	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:42078962G>T	uc001uyu.1	+	c.862G>T	c.(862-864)GAA>TAA	p.E288*	TNFSF11_uc001uyt.1_Nonsense_Mutation_p.E215*	NM_003701	NP_143026	O14788	TNF11_HUMAN	tumor necrosis factor ligand superfamily, member	288	Extracellular (Potential).				immune response|monocyte chemotaxis|osteoclast differentiation|positive regulation of bone resorption|positive regulation of corticotropin-releasing hormone secretion|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 homotypic cell-cell adhesion|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell activation|tumor necrosis factor-mediated signaling pathway	cytoplasm|extracellular space|integral to plasma membrane	cytokine activity|receptor activity|tumor necrosis factor receptor binding				0		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)						113				0.167247	77.802504	107.903121	48	239	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	42078962	42078962	16843	13	G	T	T	41	41	TNFSF11	T	5	3
FAM124A	220108	broad.mit.edu	36	13	50724294	50724294	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:50724294C>T	uc001vff.1	+	c.898C>T	c.(898-900)CGC>TGC	p.R300C	FAM124A_uc001vfe.2_Missense_Mutation_p.R264C|FAM124A_uc001vfg.1_Missense_Mutation_p.R264C	NM_145019	NP_659456	Q86V42	F124A_HUMAN	hypothetical protein LOC220108	264										central_nervous_system(1)	1		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)										0.268293	52.415571	56.394468	22	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50724294	50724294	5622	13	C	T	T	27	27	FAM124A	T	1	1
RALGAPA1	253959	broad.mit.edu	36	14	35289580	35289580	+	Silent	SNP	T	A	A			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:35289580T>A	uc001wtj.1	-	c.870A>T	c.(868-870)GCA>GCT	p.A290A	RALGAPA1_uc001wti.1_Silent_p.A290A|RALGAPA1_uc001wtk.1_Silent_p.A141A	NM_194301	NP_919277	Q6GYQ0	RGPA1_HUMAN	GTPase activating Rap/RanGAP domain-like 1	290					activation of Ral GTPase activity|signal transduction	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4														0.150685	18.274993	26.82062	11	62	TT		KEEP	---	---	---	---	capture			Silent	SNP	35289580	35289580	13473	14	T	A	A	63	63	RALGAPA1	A	4	4
EHD4	30844	broad.mit.edu	36	15	39980176	39980176	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39980176C>T	uc001zot.1	-	c.1585G>A	c.(1585-1587)GTG>ATG	p.V529M		NM_139265	NP_644670	Q9H223	EHD4_HUMAN	EH-domain containing 4	529	EH.				endocytic recycling|protein homooligomerization	early endosome membrane|endoplasmic reticulum|nucleus|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			ovary(2)	2		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)										0.236842	22.960831	25.362457	9	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39980176	39980176	5169	15	C	T	T	19	19	EHD4	T	1	1
UMOD	7369	broad.mit.edu	36	16	20265008	20265008	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20265008G>A	uc002dhb.1	-	c.1222C>T	c.(1222-1224)CGG>TGG	p.R408W	UMOD_uc002dgz.1_Missense_Mutation_p.R375W|UMOD_uc002dha.1_Missense_Mutation_p.R375W	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	375	ZP.				cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)	1														0.333333	35.225415	36.092545	12	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20265008	20265008	17537	16	G	A	A	39	39	UMOD	A	1	1
SLC5A11	115584	broad.mit.edu	36	16	24802934	24802934	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:24802934G>A	uc002dmu.1	+	c.645G>A	c.(643-645)GCG>GCA	p.A215A	SLC5A11_uc002dms.1_Silent_p.A151A|SLC5A11_uc002dmt.1_Silent_p.A151A|SLC5A11_uc010bxt.1_Silent_p.A151A	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	215	Helical; (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)										0.360902	124.786308	127.040501	48	85	GG		KEEP	---	---	---	---	capture			Silent	SNP	24802934	24802934	15160	16	G	A	A	38	38	SLC5A11	A	1	1
TBC1D24	57465	broad.mit.edu	36	16	2509369	2509369	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2509369G>A	uc002cqm.1	+	c.1115G>A	c.(1114-1116)CGC>CAC	p.R372H	ATP6V0C_uc002cqn.1_Missense_Mutation_p.A77T|ATP6V0C_uc002cqo.1_Missense_Mutation_p.A34T|AMDHD2_uc002cqp.1_5'Flank|AMDHD2_uc002cqq.1_5'Flank	NM_020705	NP_065756	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	Error:Variant_position_missing_in_Q9ULP9_after_alignment					neuron projection development	cytoplasm	protein binding|Rab GTPase activator activity				0														0.2	51.471975	62.292193	26	104	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2509369	2509369	16136	16	G	A	A	38	38	TBC1D24	A	1	1
NSMCE1	197370	broad.mit.edu	36	16	27145587	27145587	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27145587G>A	uc002doi.1	-	c.555C>T	c.(553-555)CCC>CCT	p.P185P	NSMCE1_uc002doj.1_Non-coding_Transcript	NM_145080	NP_659547	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog	185					DNA recombination|DNA repair|intracellular signal transduction	nucleus	zinc ion binding				0														0.307692	9.493428	9.923129	4	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	27145587	27145587	11080	16	G	A	A	39	39	NSMCE1	A	1	1
SH2B1	25970	broad.mit.edu	36	16	28791058	28791058	+	Missense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28791058G>T	uc002dri.1	+	c.1560G>T	c.(1558-1560)CAG>CAT	p.Q520H	SH2B1_uc002drj.1_Missense_Mutation_p.Q520H|SH2B1_uc002drk.1_Missense_Mutation_p.Q520H|SH2B1_uc002drl.1_Missense_Mutation_p.Q520H|SH2B1_uc002drm.1_Missense_Mutation_p.Q520H	NM_015503	NP_056318	Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	520	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation) (By similarity).				blood coagulation|intracellular signal transduction	cytosol|membrane|nucleus	signal transducer activity			ovary(2)	2														0.266667	8.389812	9.13059	4	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28791058	28791058	14718	16	G	T	T	34	34	SH2B1	T	3	3
ANKS3	124401	broad.mit.edu	36	16	4695175	4695175	+	Missense_Mutation	SNP	T	C	C			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:4695175T>C	uc002cxj.1	-	c.790A>G	c.(790-792)AGC>GGC	p.S264G	ANKS3_uc002cxl.1_Missense_Mutation_p.S91G|ANKS3_uc002cxk.1_Missense_Mutation_p.S135G|ANKS3_uc002cxm.1_Missense_Mutation_p.S58G|ANKS3_uc002cxi.1_Missense_Mutation_p.S191G	NM_133450	NP_597707	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain	264											0														0.277778	8.760766	9.565758	5	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4695175	4695175	698	16	T	C	C	55	55	ANKS3	C	4	4
CDH11	1009	broad.mit.edu	36	16	63542410	63542410	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:63542410C>T	uc002eoi.1	-	c.1655G>A	c.(1654-1656)GGC>GAC	p.G552D	CDH11_uc010cdn.1_Non-coding_Transcript|CDH11_uc002eoj.1_Missense_Mutation_p.G552D	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	552	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(7)|ovary(2)	9		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)						239	TSP Lung(24;0.17)			0.421687	101.008529	101.452571	35	48	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63542410	63542410	3226	16	C	T	T	26	26	CDH11	T	2	2
TERF2IP	54386	broad.mit.edu	36	16	74247742	74247742	+	Missense_Mutation	SNP	T	G	G			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:74247742T>G	uc002fet.1	+	c.932T>G	c.(931-933)GTG>GGG	p.V311G		NM_018975	NP_061848	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting	311					negative regulation of DNA recombination at telomere|negative regulation of telomere maintenance|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of double-strand break repair via homologous recombination|telomere maintenance via telomerase|transcription, DNA-dependent	cytoplasm|nuclear telomere cap complex|nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1														0.5	7.628229	7.628229	5	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74247742	74247742	16290	16	T	G	G	59	59	TERF2IP	G	4	4
C17orf71	55181	broad.mit.edu	36	17	54642203	54642203	+	Silent	SNP	T	G	G			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:54642203T>G	uc002ixi.1	+	c.9T>G	c.(7-9)GGT>GGG	p.G3G		NM_018149	NP_060619	Q8ND04	SMG8_HUMAN	hypothetical protein LOC55181	3					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of protein kinase activity		protein binding			ovary(3)	3	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)													0.318182	10.541545	11.232655	7	15	TT		KEEP	---	---	---	---	capture			Silent	SNP	54642203	54642203	1935	17	T	G	G	58	58	C17orf71	G	4	4
BPTF	2186	broad.mit.edu	36	17	63339006	63339006	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:63339006C>T	uc002jgf.1	+	c.4544C>T	c.(4543-4545)ACG>ATG	p.T1515M	BPTF_uc002jge.1_Missense_Mutation_p.T1641M	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1641					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|transcription regulator activity|zinc ion binding			ovary(2)	2	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)											0.432836	173.82899	174.355166	58	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63339006	63339006	1523	17	C	T	T	19	19	BPTF	T	1	1
ABCA6	23460	broad.mit.edu	36	17	64619996	64619996	+	Silent	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64619996G>T	uc002jhw.1	-	c.2055C>A	c.(2053-2055)ATC>ATA	p.I685I	ABCA6_uc002jhx.1_Silent_p.I138I	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	685	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			large_intestine(2)|ovary(2)	4	Breast(10;5.65e-12)													0.194357	128.602758	156.391701	62	257	GG		KEEP	---	---	---	---	capture			Silent	SNP	64619996	64619996	37	17	G	T	T	45	45	ABCA6	T	3	3
ITGB4	3691	broad.mit.edu	36	17	71250071	71250071	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71250071G>A	uc002jpg.1	+	c.2688G>A	c.(2686-2688)CCG>CCA	p.P896P	ITGB4_uc002jph.1_Silent_p.P896P|ITGB4_uc002jpi.2_Silent_p.P896P|ITGB4_uc010dgp.1_Missense_Mutation_p.G909S|ITGB4_uc002jpj.1_Silent_p.P896P	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	896	Cytoplasmic (Potential).				cell communication|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development	integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)							754				0.461538	13.745341	13.762274	6	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	71250071	71250071	8201	17	G	A	A	39	39	ITGB4	A	1	1
MRPL4	51073	broad.mit.edu	36	19	10230167	10230167	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10230167C>T	uc002mnp.1	+	c.631C>T	c.(631-633)CGC>TGC	p.R211C	MRPL4_uc002mnm.1_Missense_Mutation_p.R211C|MRPL4_uc002mnn.1_Missense_Mutation_p.R211C|MRPL4_uc002mno.1_Missense_Mutation_p.R211C	NM_146388	NP_666500	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4 isoform b	211					translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)										0.5	84.081193	84.081193	25	25	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10230167	10230167	10196	19	C	T	T	23	23	MRPL4	T	1	1
CRTC1	23373	broad.mit.edu	36	19	18740332	18740332	+	Missense_Mutation	SNP	T	G	G			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18740332T>G	uc010ebv.1	+	c.1097T>G	c.(1096-1098)CTG>CGG	p.L366R	CRTC1_uc002nkb.2_Missense_Mutation_p.L350R|CRTC1_uc010ebw.1_Missense_Mutation_p.L215R|CRTC1_uc002nkc.2_Intron	NM_001098482	NP_001091952	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform	350	Ser-rich.				interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding			ovary(1)|lung(1)|breast(1)	3										173				0.428571	7.322554	7.353914	3	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18740332	18740332	4038	19	T	G	G	55	55	CRTC1	G	4	4
NCAN	1463	broad.mit.edu	36	19	19198413	19198413	+	Missense_Mutation	SNP	A	T	T			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19198413A>T	uc002nlz.1	+	c.1191A>T	c.(1189-1191)GAA>GAT	p.E397D	NCAN_uc010ecc.1_De_novo_Start_OutOfFrame	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3	397					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)											0.428571	6.319564	6.351418	3	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19198413	19198413	10603	19	A	T	T	3	3	NCAN	T	4	4
FCGBP	8857	broad.mit.edu	36	19	45103811	45103811	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45103811G>A	uc002omp.2	-	c.3657C>T	c.(3655-3657)GGC>GGT	p.G1219G		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1219	Cys-rich.					extracellular region	protein binding			ovary(4)|central_nervous_system(1)	5	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)											0.409091	23.268873	23.427786	9	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	45103811	45103811	6015	19	G	A	A	38	38	FCGBP	A	1	1
LILRA2	11027	broad.mit.edu	36	19	59778731	59778731	+	Silent	SNP	T	C	C			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59778731T>C	uc002qgg.2	+	c.852T>C	c.(850-852)CCT>CCC	p.P284P	LILRA2_uc010ern.1_Silent_p.P284P|LILRA2_uc002qgf.1_Silent_p.P284P|LILRA2_uc010ero.1_Silent_p.P272P	NM_006866	NP_006857	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	284	Ig-like C2-type 3.|Extracellular (Potential).				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)										0.384615	34.465692	34.968613	15	24	TT		KEEP	---	---	---	---	capture			Silent	SNP	59778731	59778731	9111	19	T	C	C	55	55	LILRA2	C	4	4
CELSR2	1952	broad.mit.edu	36	1	109595746	109595746	+	Missense_Mutation	SNP	A	C	C			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:109595746A>C	uc001dxa.2	+	c.1522A>C	c.(1522-1524)ACC>CCC	p.T508P		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	508	Cadherin 4.|Extracellular (Potential).				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of gene-specific transcription|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)	3		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		NSCLC(158;1285 2011 34800 34852 42084)								0.212121	8.870566	11.449909	7	26	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109595746	109595746	3355	1	A	C	C	6	6	CELSR2	C	4	4
IGSF9	57549	broad.mit.edu	36	1	158167643	158167643	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158167643C>T	uc001fur.1	-	c.1546G>A	c.(1546-1548)GTG>ATG	p.V516M	IGSF9_uc001fup.1_De_novo_Start_InFrame|IGSF9_uc001fuq.1_Missense_Mutation_p.V500M	NM_020789	NP_065840	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform b	516	Fibronectin type-III 1.|Extracellular (Potential).					cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)											0.345865	129.61479	132.402092	46	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	158167643	158167643	7906	1	C	T	T	19	19	IGSF9	T	1	1
PIGM	93183	broad.mit.edu	36	1	158267658	158267658	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158267658C>T	uc001fuv.1	-	c.496G>A	c.(496-498)GTC>ATC	p.V166I		NM_145167	NP_660150	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	166	Lumenal (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane				ovary(2)|skin(1)	3	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.191939	214.665133	260.838428	100	421	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	158267658	158267658	12316	1	C	T	T	19	19	PIGM	T	1	1
CLCNKB	1188	broad.mit.edu	36	1	16244681	16244681	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16244681G>T	uc001axw.2	+	c.142G>T	c.(142-144)GAG>TAG	p.E48*	CLCNKB_uc001axx.2_Nonsense_Mutation_p.E48*	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb	48	Cytoplasmic (Potential).				excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)										0.315789	15.342209	15.916257	6	13	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	16244681	16244681	3606	1	G	T	T	37	37	CLCNKB	T	5	3
GPA33	10223	broad.mit.edu	36	1	165290226	165290226	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165290226C>T	uc001gea.1	-	c.929G>A	c.(928-930)GGG>GAG	p.G310E		NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor	310	Cytoplasmic (Potential).					integral to plasma membrane	receptor activity				0														0.231214	96.844167	108.287889	40	133	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165290226	165290226	6860	1	C	T	T	22	22	GPA33	T	2	2
RFWD2	64326	broad.mit.edu	36	1	174182965	174182965	+	Missense_Mutation	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:174182965C>A	uc001gku.1	-	c.2167G>T	c.(2167-2169)GGT>TGT	p.G723C	RFWD2_uc009wwv.1_Missense_Mutation_p.G498C|RFWD2_uc001gkt.1_Missense_Mutation_p.G562C|RFWD2_uc001gkv.1_Missense_Mutation_p.G699C|RFWD2_uc001gkw.1_Missense_Mutation_p.G483C	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a	723	WD 7.				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						Ovarian(134;1413 1765 5706 35534 51541)								0.153846	77.349154	105.596031	38	209	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	174182965	174182965	13732	1	C	A	A	22	22	RFWD2	A	3	3
CACNA1S	779	broad.mit.edu	36	1	199327810	199327810	+	Missense_Mutation	SNP	T	C	C			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199327810T>C	uc001gvv.1	-	c.454A>G	c.(454-456)ATG>GTG	p.M152V		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	152	Extracellular (Potential).|I.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.303571	50.460316	52.384907	17	39	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199327810	199327810	2663	1	T	C	C	52	52	CACNA1S	C	4	4
C4BPA	722	broad.mit.edu	36	1	205384652	205384652	+	Silent	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205384652C>T	uc001hfo.1	+	c.1761C>T	c.(1759-1761)AGC>AGT	p.S587S		NM_000715	NP_000706	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	587					complement activation, classical pathway|innate immune response	extracellular region	protein binding			large_intestine(1)|ovary(1)	2														0.438776	127.913776	128.232659	43	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	205384652	205384652	2344	1	C	T	T	27	27	C4BPA	T	1	1
MOSC2	54996	broad.mit.edu	36	1	219001666	219001666	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:219001666G>A	uc001hmq.1	+	c.490G>A	c.(490-492)GCA>ACA	p.A164T	MOSC2_uc001hmr.1_Missense_Mutation_p.A164T|MOSC2_uc009xdx.1_Missense_Mutation_p.A164T	NM_017898	NP_060368	Q969Z3	MOSC2_HUMAN	MOCO sulphurase C-terminal domain containing 2	164					oxidation-reduction process	mitochondrial outer membrane	molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.00499)|all cancers(67;0.204)										0.607143	108.45406	109.015743	34	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	219001666	219001666	10106	1	G	A	A	42	42	MOSC2	A	2	2
LEFTY1	10637	broad.mit.edu	36	1	224141287	224141287	+	Missense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:224141287G>T	uc001hpo.1	-	c.864C>A	c.(862-864)TTC>TTA	p.F288L		NM_020997	NP_066277	O75610	LFTY1_HUMAN	left-right determination, factor B	288					cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)													0.153846	15.511157	22.96111	10	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	224141287	224141287	9039	1	G	T	T	41	41	LEFTY1	T	3	3
NUP133	55746	broad.mit.edu	36	1	227667792	227667792	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:227667792G>A	uc001htn.1	-	c.2297C>T	c.(2296-2298)ACG>ATG	p.T766M		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	766					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|ovary(1)	5	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)								578				0.464286	38.571343	38.602433	13	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	227667792	227667792	11159	1	G	A	A	40	40	NUP133	A	1	1
URB2	9816	broad.mit.edu	36	1	227838947	227838947	+	Missense_Mutation	SNP	A	G	G			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:227838947A>G	uc001hts.1	+	c.1964A>G	c.(1963-1965)CAT>CGT	p.H655R	URB2_uc009xfd.1_Missense_Mutation_p.H655R	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	655						nucleolus				central_nervous_system(2)|ovary(1)	3										340				0.230769	9.631631	11.365122	6	20	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	227838947	227838947	17587	1	A	G	G	8	8	URB2	G	4	4
CYP4A22	284541	broad.mit.edu	36	1	47382146	47382146	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:47382146G>A	uc001cqv.1	+	c.761G>A	c.(760-762)CGC>CAC	p.R254H	CYP4A22_uc009vyo.1_Missense_Mutation_p.R254H|CYP4A22_uc009vyp.1_Intron	NM_001010969	NP_001010969	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A,	254					oxidation-reduction process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding			ovary(1)|breast(1)	2						Pancreas(88;1240 1470 2099 14214 37557)								0.466667	224.442694	224.601553	77	88	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47382146	47382146	4349	1	G	A	A	38	38	CYP4A22	A	1	1
PODN	127435	broad.mit.edu	36	1	53316955	53316955	+	Silent	SNP	T	C	C			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:53316955T>C	uc001cuv.1	+	c.1329T>C	c.(1327-1329)ATT>ATC	p.I443I	PODN_uc001cuw.1_Silent_p.I424I	NM_153703	NP_714914	Q7Z5L7	PODN_HUMAN	podocan	395	LRR 13.				negative regulation of cell migration|negative regulation of cell proliferation	cytoplasm|extracellular space|proteinaceous extracellular matrix	collagen binding			ovary(1)|pancreas(1)	2														0.333333	12.706933	13.2291	7	14	TT		KEEP	---	---	---	---	capture			Silent	SNP	53316955	53316955	12606	1	T	C	C	63	63	PODN	C	4	4
PRKAA2	5563	broad.mit.edu	36	1	56934355	56934355	+	Silent	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:56934355C>T	uc001cyk.2	+	c.723C>T	c.(721-723)GTC>GTT	p.V241V		NM_006252	NP_006243	P54646	AAPK2_HUMAN	AMP-activated protein kinase alpha 2 catalytic	241	Protein kinase.				carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|protein phosphorylation|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleoplasm	ATP binding|metal ion binding			breast(4)|ovary(1)|stomach(1)	6										168				0.157895	22.854084	31.334893	12	64	CC		KEEP	---	---	---	---	capture			Silent	SNP	56934355	56934355	12937	1	C	T	T	31	31	PRKAA2	T	1	1
FUBP1	8880	broad.mit.edu	36	1	78208217	78208217	+	Missense_Mutation	SNP	T	C	C			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:78208217T>C	uc001dii.1	-	c.191A>G	c.(190-192)AAA>AGA	p.K64R	FUBP1_uc001dih.2_Non-coding_Transcript	NM_003902	NP_003893	Q96AE4	FUBP1_HUMAN	far upstream element-binding protein	64					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(2)|lung(1)	3														0.392157	65.192466	65.71059	20	31	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78208217	78208217	6343	1	T	C	C	64	64	FUBP1	C	4	4
TGM3	7053	broad.mit.edu	36	20	2263830	2263830	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2263830C>T	uc002wfx.2	+	c.1711C>T	c.(1711-1713)CGG>TGG	p.R571W		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	571					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)	8					L-Glutamine(DB00130)									0.179191	63.461928	80.190165	31	142	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2263830	2263830	16359	20	C	T	T	23	23	TGM3	T	1	1
PYGB	5834	broad.mit.edu	36	20	25203280	25203280	+	Missense_Mutation	SNP	G	C	C			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:25203280G>C	uc002wup.1	+	c.581G>C	c.(580-582)CGG>CCG	p.R194P		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	194					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)	1					Pyridoxal Phosphate(DB00114)									0.4	8.495086	8.583178	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25203280	25203280	13318	20	G	C	C	39	39	PYGB	C	3	3
TMC2	117532	broad.mit.edu	36	20	2545805	2545805	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2545805G>A	uc002wgf.1	+	c.2028G>A	c.(2026-2028)ATG>ATA	p.M676I	TMC2_uc002wgg.1_Missense_Mutation_p.M660I	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	676	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3														0.113158	38.355266	94.570787	43	337	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2545805	2545805	16515	20	G	A	A	45	45	TMC2	A	2	2
USP25	29761	broad.mit.edu	36	21	16172162	16172162	+	Silent	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:16172162C>T	uc002yjz.1	+	c.3072C>T	c.(3070-3072)TAC>TAT	p.Y1024Y	USP25_uc002yjy.1_Silent_p.Y992Y|USP25_uc010gla.1_Silent_p.Y387Y	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific protease 25	992					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)										0.142857	14.852447	22.579661	9	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	16172162	16172162	17619	21	C	T	T	18	18	USP25	T	2	2
RIPK4	54101	broad.mit.edu	36	21	42034461	42034461	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42034461C>T	uc002yzn.1	-	c.1961G>A	c.(1960-1962)AGG>AAG	p.R654K		NM_020639	NP_065690	Q9H4D1	Q9H4D1_HUMAN	ankyrin repeat domain 3	654					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7										268				0.214286	6.822256	7.874127	3	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42034461	42034461	13860	21	C	T	T	24	24	RIPK4	T	2	2
APOL1	8542	broad.mit.edu	36	22	34980948	34980948	+	Missense_Mutation	SNP	A	T	T			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:34980948A>T	uc003ape.1	+	c.49A>T	c.(49-51)ATG>TTG	p.M17L	APOL1_uc003apc.1_Non-coding_Transcript|APOL1_uc003apf.1_Missense_Mutation_p.M1L|APOL1_uc010gwx.1_5'UTR	NM_145343	NP_003652	O14791	APOL1_HUMAN	apolipoprotein L1 isoform b precursor	1					cholesterol metabolic process|cytolysis|innate immune response|killing of cells of other organism|lipid transport|lipoprotein metabolic process	high-density lipoprotein particle|intrinsic to membrane|very-low-density lipoprotein particle	chloride channel activity|lipid binding|protein binding			breast(2)|ovary(1)	3														0.182243	85.718897	105.998646	39	175	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34980948	34980948	816	22	A	T	T	8	8	APOL1	T	4	4
REV1	51455	broad.mit.edu	36	2	99422039	99422039	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:99422039G>A	uc002tad.1	-	c.669C>T	c.(667-669)GCC>GCT	p.A223A	REV1_uc002tac.1_Silent_p.A223A|REV1_uc002tae.1_Silent_p.A202A	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1	223					DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2														0.460526	106.516668	106.619361	35	41	GG		KEEP	---	---	---	---	capture			Silent	SNP	99422039	99422039	13709	2	G	A	A	47	47	REV1	A	2	2
TOMM70A	9868	broad.mit.edu	36	3	101574254	101574254	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:101574254G>T	uc003dtw.1	-	c.1338C>A	c.(1336-1338)TAC>TAA	p.Y446*		NM_014820	NP_055635	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70	446	Cytoplasmic (Potential).|TPR 7.				protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1														0.142857	9.838677	17.545271	9	54	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	101574254	101574254	16904	3	G	T	T	44	44	TOMM70A	T	5	3
SIAH2	6478	broad.mit.edu	36	3	151963106	151963106	+	Missense_Mutation	SNP	A	C	C			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:151963106A>C	uc003eyi.1	-	c.221T>G	c.(220-222)CTG>CGG	p.L74R		NM_005067	NP_005058	O43255	SIAH2_HUMAN	seven in absentia homolog 2	74					apoptosis|axon guidance|cell cycle|negative regulation of canonical Wnt receptor signaling pathway|small GTPase mediated signal transduction|ubiquitin-dependent protein catabolic process	cytosol|nucleus	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)											0.28	12.708074	13.801049	7	18	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151963106	151963106	14795	3	A	C	C	7	7	SIAH2	C	4	4
CCDC50	152137	broad.mit.edu	36	3	192575544	192575544	+	Splice_Site_SNP	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:192575544G>A	uc003fsv.1	+	c.e6_splice_site			CCDC50_uc003fsw.1_Intron	NM_178335	NP_848018			Ymer protein long isoform							cytoplasm	protein binding				0	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)						161				0.164557	11.907021	20.386968	13	66	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	192575544	192575544	2943	3	G	A	A	33	33	CCDC50	A	5	2
NISCH	11188	broad.mit.edu	36	3	52497025	52497025	+	Missense_Mutation	SNP	G	C	C			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52497025G>C	uc003ded.2	+	c.2477G>C	c.(2476-2478)GGC>GCC	p.G826A	NISCH_uc003dee.2_Missense_Mutation_p.G315A|NISCH_uc003deg.1_Non-coding_Transcript	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	826	Interaction with LIMK (By similarity).|Interaction with PAK1 (By similarity).				apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)										0.277778	6.719391	7.561706	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52497025	52497025	10833	3	G	C	C	42	42	NISCH	C	3	3
NAA11	84779	broad.mit.edu	36	4	80465909	80465909	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:80465909G>A	uc003hlt.2	-	c.147C>T	c.(145-147)GAC>GAT	p.D49D		NM_032693	NP_116082	Q9BSU3	NAA11_HUMAN	ARD1 homolog B protein	49	Interaction with NAA15 (By similarity).|N-acetyltransferase.					cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2														0.309524	37.562909	38.918646	13	29	GG		KEEP	---	---	---	---	capture			Silent	SNP	80465909	80465909	10512	4	G	A	A	40	40	NAA11	A	1	1
LARS	51520	broad.mit.edu	36	5	145488442	145488442	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:145488442G>A	uc003lnx.1	-	c.2866C>T	c.(2866-2868)CGT>TGT	p.R956C	LARS_uc003lnw.1_Missense_Mutation_p.R114C	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	956					leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)									0.24	109.739741	120.486002	42	133	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	145488442	145488442	8957	5	G	A	A	40	40	LARS	A	1	1
NDST1	3340	broad.mit.edu	36	5	149901334	149901334	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149901334G>A	uc003lsk.2	+	c.1759G>A	c.(1759-1761)GAG>AAG	p.E587K	NDST1_uc003lsm.1_Missense_Mutation_p.E587K	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	587	Heparan sulfate N-deacetylase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.4	143.819795	144.913126	50	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	149901334	149901334	10654	5	G	A	A	37	37	NDST1	A	1	1
SH3PXD2B	285590	broad.mit.edu	36	5	171699087	171699087	+	Missense_Mutation	SNP	G	C	C			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:171699087G>C	uc003mbr.1	-	c.1627C>G	c.(1627-1629)CGG>GGG	p.R543G		NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	543					adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)											0.25	21.925492	23.926552	9	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	171699087	171699087	14749	5	G	C	C	38	38	SH3PXD2B	C	3	3
DAB2	1601	broad.mit.edu	36	5	39412931	39412931	+	Missense_Mutation	SNP	A	C	C			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:39412931A>C	uc003jlx.2	-	c.1715T>G	c.(1714-1716)GTC>GGC	p.V572G	DAB2_uc003jlw.2_Missense_Mutation_p.V551G	NM_001343	NP_001334	P98082	DAB2_HUMAN	disabled homolog 2	572					cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding			kidney(2)|skin(1)	3	all_lung(31;0.000197)		Epithelial(62;0.137)									OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.222222	11.88362	15.135119	10	35	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39412931	39412931	4384	5	A	C	C	10	10	DAB2	C	4	4
POPDC3	64208	broad.mit.edu	36	6	105714366	105714366	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:105714366G>A	uc003prb.1	-	c.507C>T	c.(505-507)GGC>GGT	p.G169G	POPDC3_uc003pra.1_Non-coding_Transcript	NM_022361	NP_071756	Q9HBV1	POPD3_HUMAN	popeye protein 3	169						integral to membrane				ovary(2)|skin(1)	3		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)												0.483516	128.520463	128.539757	44	47	GG		KEEP	---	---	---	---	capture			Silent	SNP	105714366	105714366	12685	6	G	A	A	38	38	POPDC3	A	1	1
THEMIS	387357	broad.mit.edu	36	6	128175812	128175812	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:128175812C>T	uc003qbi.1	-	c.1667G>A	c.(1666-1668)CGC>CAC	p.R556H	THEMIS_uc010kfa.1_Missense_Mutation_p.R459H|THEMIS_uc010kfb.1_Missense_Mutation_p.R521H	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	hypothetical protein LOC387357	556					negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)	2														0.203463	79.64483	98.650058	47	184	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128175812	128175812	16388	6	C	T	T	27	27	THEMIS	T	1	1
GRM1	2911	broad.mit.edu	36	6	146797430	146797430	+	Silent	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:146797430C>T	uc010khw.1	+	c.3390C>T	c.(3388-3390)GAC>GAT	p.D1130D	GRM1_uc010khv.1_3'UTR|GRM1_uc003qll.2_3'UTR	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	1130	Asp/Glu-rich (acidic).|Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.265432	105.778802	113.756288	43	119	CC		KEEP	---	---	---	---	capture			Silent	SNP	146797430	146797430	7075	6	C	T	T	18	18	GRM1	T	2	2
MAP3K4	4216	broad.mit.edu	36	6	161389644	161389644	+	Missense_Mutation	SNP	T	G	G			TCGA-19-0957-01	TCGA-19-0957-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:161389644T>G	uc003qtn.1	+	c.350T>G	c.(349-351)ATG>AGG	p.M117R	MAP3K4_uc010kkc.1_Missense_Mutation_p.M117R|MAP3K4_uc003qto.1_Missense_Mutation_p.M117R	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	117					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				0.235294	6.491169	7.582829	4	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	161389644	161389644	9635	6	T	G	G	51	51	MAP3K4	G	4	4
ZNF318	24149	broad.mit.edu	36	6	43433076	43433076	+	Silent	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43433076C>T	uc003oux.1	-	c.954G>A	c.(952-954)CTG>CTA	p.L318L	ZNF318_uc003ouw.2_Non-coding_Transcript	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	318	Potential.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(2)|breast(2)|central_nervous_system(1)	5			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)											0.245125	202.653259	223.888257	88	271	CC		KEEP	---	---	---	---	capture			Silent	SNP	43433076	43433076	18428	6	C	T	T	21	21	ZNF318	T	2	2
PGK2	5232	broad.mit.edu	36	6	49861934	49861934	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:49861934G>A	uc003ozu.1	-	c.926C>T	c.(925-927)CCT>CTT	p.P309L		NM_138733	NP_620061	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	309					glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1	Lung NSC(77;0.0402)													0.395954	388.163097	391.449302	137	209	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49861934	49861934	12214	6	G	A	A	35	35	PGK2	A	2	2
FAM83B	222584	broad.mit.edu	36	6	54914485	54914485	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:54914485G>A	uc003pck.1	+	c.2757G>A	c.(2755-2757)ACG>ACA	p.T919T		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	919										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)													0.335227	157.325035	161.575854	59	117	GG		KEEP	---	---	---	---	capture			Silent	SNP	54914485	54914485	5860	6	G	A	A	40	40	FAM83B	A	1	1
COL12A1	1303	broad.mit.edu	36	6	75856599	75856599	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:75856599C>T	uc010kbb.1	-	c.8888G>A	c.(8887-8889)GGG>GAG	p.G2963E	COL12A1_uc010kbc.1_Missense_Mutation_p.G1799E|COL12A1_uc003phs.1_Missense_Mutation_p.G2963E|COL12A1_uc003pht.1_Missense_Mutation_p.G1799E	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2963	Triple-helical region (COL1) with 2 imperfections.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)	8														0.311927	84.199683	87.63969	34	75	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75856599	75856599	3807	6	C	T	T	22	22	COL12A1	T	2	2
TFR2	7036	broad.mit.edu	36	7	100062949	100062949	+	Silent	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100062949G>T	uc003uvv.1	-	c.1869C>A	c.(1867-1869)GCC>GCA	p.A623A	TFR2_uc010lhc.1_Silent_p.A164A|TFR2_uc003uvu.1_Silent_p.A452A	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2	623	Extracellular (Potential).				cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)								p.AVAQ621del(LI7-Tumor)	219				0.290323	13.672663	14.892619	9	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	100062949	100062949	16339	7	G	T	T	43	43	TFR2	T	3	3
PIK3CG	5294	broad.mit.edu	36	7	106295328	106295328	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106295328C>T	uc003vdv.2	+	c.86C>T	c.(85-87)GCG>GTG	p.A29V	PIK3CG_uc003vdu.1_Missense_Mutation_p.A29V|PIK3CG_uc003vdw.1_Missense_Mutation_p.A29V	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	29					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.25974	44.873103	48.894453	20	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106295328	106295328	12340	7	C	T	T	27	27	PIK3CG	T	1	1
TRPV6	55503	broad.mit.edu	36	7	142283008	142283008	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142283008C>T	uc003wbx.1	-	c.1154G>A	c.(1153-1155)CGG>CAG	p.R385Q	TRPV6_uc003wbw.1_Missense_Mutation_p.R171Q|TRPV6_uc010lou.1_Missense_Mutation_p.R256Q	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel,	385	Extracellular (Potential).				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(1)	1	Melanoma(164;0.059)													0.103896	8.054451	20.069374	8	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142283008	142283008	17151	7	C	T	T	23	23	TRPV6	T	1	1
PTPRN2	5799	broad.mit.edu	36	7	157802317	157802317	+	Missense_Mutation	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:157802317C>A	uc003wno.1	-	c.232G>T	c.(232-234)GCC>TCC	p.A78S	PTPRN2_uc003wnp.1_Missense_Mutation_p.A61S|PTPRN2_uc003wnq.1_Missense_Mutation_p.A78S|PTPRN2_uc003wnr.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	78	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.145631	26.306658	38.704072	15	88	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	157802317	157802317	13265	7	C	A	A	26	26	PTPRN2	A	3	3
IGFBP1	3484	broad.mit.edu	36	7	45898086	45898086	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:45898086G>A	uc003tnp.1	+	c.550G>A	c.(550-552)GTA>ATA	p.V184I	IGFBP1_uc003tno.2_Missense_Mutation_p.V184I|IGFBP1_uc010kyn.1_Intron	NM_000596	NP_000587	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	184	Thyroglobulin type-1.					extracellular space	insulin-like growth factor binding				0												OREG0018048	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.117391	30.101221	63.099776	27	203	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45898086	45898086	7879	7	G	A	A	40	40	IGFBP1	A	1	1
ZNF804B	219578	broad.mit.edu	36	7	88801269	88801269	+	Missense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:88801269G>T	uc003uju.1	+	c.1037G>T	c.(1036-1038)AGA>ATA	p.R346I		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	346						intracellular	zinc ion binding			ovary(5)|pancreas(2)	7	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)											0.520833	77.268554	77.286378	25	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88801269	88801269	18769	7	G	T	T	33	33	ZNF804B	T	3	3
RGS22	26166	broad.mit.edu	36	8	101152829	101152829	+	Missense_Mutation	SNP	C	G	G			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:101152829C>G	uc003yjb.1	-	c.538G>C	c.(538-540)GCC>CCC	p.A180P	RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Missense_Mutation_p.A180P|RGS22_uc010mbo.1_Non-coding_Transcript	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	180					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				0.402778	89.22614	89.829725	29	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101152829	101152829	13779	8	C	G	G	25	25	RGS22	G	3	3
ZHX1	11244	broad.mit.edu	36	8	124337359	124337359	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:124337359G>A	uc003yqe.1	-	c.9C>T	c.(7-9)AGC>AGT	p.S3S	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.1_Silent_p.S3S|ZHX1_uc003yqg.1_Intron|ZHX1_uc010mdi.1_Silent_p.S3S|ZHX1_uc010mdj.1_Silent_p.S3S	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	3					negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)											0.138801	56.844945	96.826613	44	273	GG		KEEP	---	---	---	---	capture			Silent	SNP	124337359	124337359	18266	8	G	A	A	46	46	ZHX1	A	2	2
COL22A1	169044	broad.mit.edu	36	8	139728093	139728093	+	Silent	SNP	A	G	G			TCGA-19-0957-01	TCGA-19-0957-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:139728093A>G	uc003yvd.1	-	c.3462T>C	c.(3460-3462)CCT>CCC	p.P1154P	COL22A1_uc003yvc.1_Silent_p.P272P	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1154	Pro-rich.|Gly-rich.|Collagen-like 10.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.3125	7.482634	8.037517	5	11	AA		KEEP	---	---	---	---	capture			Silent	SNP	139728093	139728093	3819	8	A	G	G	11	11	COL22A1	G	4	4
ZMAT4	79698	broad.mit.edu	36	8	40673973	40673973	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:40673973G>A	uc003xnr.1	-	c.297C>T	c.(295-297)CAC>CAT	p.H99H	ZMAT4_uc003xns.1_Silent_p.H99H	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a	99	Matrin-type 2.					nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)											0.557319	976.932789	978.55974	316	251	GG		KEEP	---	---	---	---	capture			Silent	SNP	40673973	40673973	18285	8	G	A	A	40	40	ZMAT4	A	1	1
SLC27A4	10999	broad.mit.edu	36	9	130162519	130162519	+	Silent	SNP	C	A	A			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:130162519C>A	uc004but.1	+	c.1860C>A	c.(1858-1860)GCC>GCA	p.A620A	SLC27A4_uc004buu.1_Silent_p.A214A	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid	620					long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0						Pancreas(107;1554 2241 10946 12953)								0.192308	10.429738	15.038046	10	42	CC		KEEP	---	---	---	---	capture			Silent	SNP	130162519	130162519	15025	9	C	A	A	22	22	SLC27A4	A	3	3
PMPCA	23203	broad.mit.edu	36	9	138436231	138436231	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138436231G>T	uc004chl.1	+	c.1390G>T	c.(1390-1392)GAG>TAG	p.E464*	PMPCA_uc010nbl.1_Nonsense_Mutation_p.E364*|PMPCA_uc004chn.1_Nonsense_Mutation_p.E61*	NM_015160	NP_055975	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	464					proteolysis	mitochondrial inner membrane|mitochondrial matrix	metalloendopeptidase activity|zinc ion binding				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)										0.307692	6.793884	7.223642	4	9	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	138436231	138436231	12566	9	G	T	T	37	37	PMPCA	T	5	3
FRMPD1	22844	broad.mit.edu	36	9	37727217	37727217	+	Missense_Mutation	SNP	C	T	T			TCGA-19-0957-01	TCGA-19-0957-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:37727217C>T	uc004aag.1	+	c.1526C>T	c.(1525-1527)GCG>GTG	p.A509V	FRMPD1_uc004aah.1_Missense_Mutation_p.A509V	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	509						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|breast(1)	7				GBM - Glioblastoma multiforme(29;0.00655)										0.460937	185.329992	185.496844	59	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37727217	37727217	6307	9	C	T	T	27	27	FRMPD1	T	1	1
PTCH1	5727	broad.mit.edu	36	9	97249455	97249455	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:97249455G>A	uc004avk.2	-	c.3904C>T	c.(3904-3906)CCC>TCC	p.P1302S	PTCH1_uc010mro.1_Missense_Mutation_p.P1151S|PTCH1_uc010mrp.1_Missense_Mutation_p.P1151S|PTCH1_uc010mrq.1_Missense_Mutation_p.P1151S|PTCH1_uc004avl.2_Missense_Mutation_p.P1151S|PTCH1_uc010mrr.1_Missense_Mutation_p.P1236S|PTCH1_uc004avm.2_Missense_Mutation_p.P1301S|PTCH1_uc010mrn.1_Missense_Mutation_p.P94S	NM_000264	NP_001077076	Q13635	PTC1_HUMAN	patched isoform L	1302	Cytoplasmic (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(229)|central_nervous_system(43)|bone(33)|upper_aerodigestive_tract(10)|lung(5)|large_intestine(4)|oesophagus(3)|ovary(3)|breast(2)|vulva(1)	333		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)								509				0.433333	36.170919	36.286666	13	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97249455	97249455	13184	9	G	A	A	42	42	PTCH1	A	2	2
TCEAL5	340543	broad.mit.edu	36	X	102415595	102415595	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:102415595G>A	uc004ejz.1	-	c.553C>T	c.(553-555)CGG>TGG	p.R185W	TCEAL5_uc010nol.1_Missense_Mutation_p.R185W	NM_001012979	NP_001012997	Q5H9L2	TCAL5_HUMAN	transcription elongation factor A (SII)-like 5	185					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(1)|breast(1)	2														0.318318	295.802805	305.53577	106	227	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102415595	102415595	16200	23	G	A	A	40	40	TCEAL5	A	1	1
TLR7	51284	broad.mit.edu	36	X	12813752	12813752	+	Silent	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:12813752G>A	uc004cvc.1	+	c.204G>A	c.(202-204)ACG>ACA	p.T68T		NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	68	Extracellular (Potential).|LRR 2.				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				0.102635	60.809235	174.10668	74	647	GG		KEEP	---	---	---	---	capture			Silent	SNP	12813752	12813752	16486	23	G	A	A	37	37	TLR7	A	1	1
TLR7	51284	broad.mit.edu	36	X	12813838	12813838	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:12813838G>A	uc004cvc.1	+	c.290G>A	c.(289-291)AGA>AAA	p.R97K		NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	97	Extracellular (Potential).				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				0.118497	95.690119	194.573654	82	610	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12813838	12813838	16486	23	G	A	A	33	33	TLR7	A	2	2
MAP7D3	79649	broad.mit.edu	36	X	135141910	135141910	+	Missense_Mutation	SNP	G	A	A			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:135141910G>A	uc004ezt.2	-	c.872C>T	c.(871-873)CCC>CTC	p.P291L	MAP7D3_uc004ezs.2_Missense_Mutation_p.P255L|MAP7D3_uc010nsa.1_Missense_Mutation_p.P249L	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	291						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)													0.230769	16.351277	18.946863	9	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135141910	135141910	9652	23	G	A	A	43	43	MAP7D3	A	2	2
MAP7D3	79649	broad.mit.edu	36	X	135141911	135141911	+	Missense_Mutation	SNP	G	T	T			TCGA-19-0957-01	TCGA-19-0957-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:135141911G>T	uc004ezt.2	-	c.871C>A	c.(871-873)CCC>ACC	p.P291T	MAP7D3_uc004ezs.2_Missense_Mutation_p.P255T|MAP7D3_uc010nsa.1_Missense_Mutation_p.P249T	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	291						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)													0.236842	14.346404	16.762325	9	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135141911	135141911	9652	23	G	T	T	41	41	MAP7D3	T	3	3
ABCC2	1244	broad.mit.edu	36	10	101595523	101595534	+	Splice_Site_Del	DEL	CCCCCAGGTGAG	-	-			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101595523_101595534delCCCCCAGGTGAG	uc001kqf.2	+	c.e29_splice_site				NM_000392	NP_000383			ATP-binding cassette, sub-family C (CFTR/MRP),							apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)							OREG0020434	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.54			13	11				---	---	---	---	capture_indel			Splice_Site_Del	DEL	101595523	101595534	54	10	CCCCCAGGTGAG	-	-	30	30	ABCC2	-	5	5
ZNF195	7748	broad.mit.edu	36	11	3337991	3337992	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:3337991_3337992delCA	uc001lxt.1	-	c.822_823delTG	c.(820-825)TGTGGAfs	p.C274fs	ZNF195_uc001lxs.1_Frame_Shift_Del_p.C202fs|ZNF195_uc009ydz.1_Frame_Shift_Del_p.C229fs|ZNF195_uc001lxu.1_Frame_Shift_Del_p.C206fs|ZNF195_uc001lxv.1_Frame_Shift_Del_p.C251fs	NM_007152	NP_009083	O14628	ZN195_HUMAN	zinc finger protein 195 isoform 3	274_275	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)										0.36			98	175				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	3337991	3337992	18349	11	CA	-	-	21	21	ZNF195	-	5	5
IGFBP4	3487	broad.mit.edu	36	17	35853629	35853630	+	Frame_Shift_Ins	INS	-	C	C			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:35853629_35853630insC	uc002hus.1	+	c.116_117insC	c.(115-117)CGCfs	p.R39fs		NM_001552	NP_001543	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	39	IGFBP N-terminal.				DNA metabolic process|signal transduction|skeletal system development						0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GBM(160;940 3581 26177)								0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	35853629	35853630	7882	17	-	C	C	38	38	IGFBP4	C	5	5
NEFH	4744	broad.mit.edu	36	22	28214962	28214977	+	Frame_Shift_Del	DEL	AAAGTGGTGGAGAAGT	-	-			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:28214962_28214977delAAAGTGGTGGAGAAGT	uc003afo.1	+	c.1333_1348delAAAGTGGTGGAGAAGT	c.(1333-1350)AAAGTGGTGGAGAAGTCTfs	p.K445fs	NEFH_uc003afp.2_5'Flank	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	445_450	Tail.				cell death|nervous system development	neurofilament					0														0.44			71	91				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	28214962	28214977	10713	22	AAAGTGGTGGAGAAGT	-	-	5	5	NEFH	-	5	5
PHLDB2	90102	broad.mit.edu	36	3	113086627	113086636	+	Frame_Shift_Del	DEL	CTCGGAAGAT	-	-			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113086627_113086636delCTCGGAAGAT	uc010hqa.1	+	c.1013_1022delCTCGGAAGAT	c.(1012-1023)GCTCGGAAGATGfs	p.A338fs	PHLDB2_uc003dyc.1_Frame_Shift_Del_p.A365fs|PHLDB2_uc003dyd.1_Frame_Shift_Del_p.A338fs|PHLDB2_uc003dyf.2_Frame_Shift_Del_p.A338fs|PHLDB2_uc003dyg.1_Frame_Shift_Del_p.A338fs|PHLDB2_uc003dyh.1_Frame_Shift_Del_p.A338fs|PHLDB2_uc003dye.2_Frame_Shift_Del_p.A338fs	NM_145753	NP_665696	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,	338_341						cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)	4														0.48			142	153				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	113086627	113086636	12276	3	CTCGGAAGAT	-	-	28	28	PHLDB2	-	5	5
HYAL2	8692	broad.mit.edu	36	3	50332429	50332430	+	Frame_Shift_Ins	INS	-	C	C			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:50332429_50332430insC	uc003czu.1	-	c.495_496insG	c.(493-498)GACTGGfs	p.D165fs	HYAL2_uc003czv.1_Frame_Shift_Ins_p.D165fs|HYAL2_uc003czw.1_Frame_Shift_Ins_p.D165fs|HYAL2_uc003czx.1_Frame_Shift_Ins_p.D165fs|HYAL2_uc010hlj.1_Frame_Shift_Ins_p.D165fs	NM_033158	NP_149348	Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	165_166						anchored to membrane|lysosome|plasma membrane	hyalurononglucosaminidase activity|receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)	Hyaluronidase(DB00070)									0.78			364	105				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	50332429	50332430	7764	3	-	C	C	7	7	HYAL2	C	5	5
TXNDC5	81567	broad.mit.edu	36	6	7844901	7844901	+	Frame_Shift_Del	DEL	G	-	-			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:7844901_7844901delG	uc003mxv.1	-	c.426_426delC	c.(424-426)TTCfs	p.F142fs	TXNDC5_uc003mxw.1_Frame_Shift_Del_p.F99fs|TXNDC5_uc010jnz.1_Frame_Shift_Del_p.F34fs|TXNDC5_uc010joa.1_Frame_Shift_Del_p.F34fs	NM_030810	NP_110437	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 1	142	Thioredoxin 1.				anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					Ovarian(119;1430 1625 3928 26125 34589)								0.49			85	89				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	7844901	7844901	17355	6	G	-	-	45	45	TXNDC5	-	5	5
CPSF1	29894	broad.mit.edu	36	8	145593673	145593674	+	Frame_Shift_Ins	INS	-	C	C			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145593673_145593674insC	uc003zcj.1	-	c.2221_2222insG	c.(2221-2223)GATfs	p.D741fs		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	741					mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			NSCLC(133;1088 1848 27708 34777 35269)								0.55			50	41				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	145593673	145593674	3962	8	-	C	C	50	50	CPSF1	C	5	5
EGR3	1960	broad.mit.edu	36	8	22606392	22606407	+	Start_Codon_Del	DEL	TTGCCGGTCATAGCAC	-	-			TCGA-19-0957-01	TCGA-19-0957-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:22606392_22606407delTTGCCGGTCATAGCAC	uc003xcm.1	-					NM_004430	NP_004421			early growth response 3						circadian rhythm|muscle organ development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)										0.41			11	16				---	---	---	---	capture_indel			Start_Codon_Del	DEL	22606392	22606407	5162	8	TTGCCGGTCATAGCAC	-	-	64	64	EGR3	-	5	5
