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
CCDC147	159686	broad.mit.edu	36	10	106115652	106115652	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:106115652G>A	uc001kyh.1	+	c.688G>A	c.(688-690)GCA>ACA	p.A230T		NM_001008723	NP_001008723	Q5T655	CC147_HUMAN	coiled-coil domain containing 147	230	Potential.									ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)										0.717172	225.686354	229.939908	71	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106115652	106115652	2901	10	G	A	A	42	42	CCDC147	A	2	2
ARHGAP21	57584	broad.mit.edu	36	10	24936465	24936465	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:24936465C>T	uc001isb.1	-	c.2650G>A	c.(2650-2652)GGT>AGT	p.G884S	ARHGAP21_uc009xkl.1_Missense_Mutation_p.G885S	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	884					signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8														0.123188	24.08935	43.257007	17	121	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24936465	24936465	882	10	C	T	T	22	22	ARHGAP21	T	2	2
GPR158	57512	broad.mit.edu	36	10	25927336	25927336	+	Silent	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:25927336G>A	uc001isj.1	+	c.2775G>A	c.(2773-2775)GTG>GTA	p.V925V	GPR158_uc001isk.1_Silent_p.V300V	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	925	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.266667	6.889157	7.630611	4	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	25927336	25927336	6938	10	G	A	A	47	47	GPR158	A	2	2
CCAR1	55749	broad.mit.edu	36	10	70172160	70172160	+	Missense_Mutation	SNP	A	C	C			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:70172160A>C	uc001joo.1	+	c.346A>C	c.(346-348)AGC>CGC	p.S116R	CCAR1_uc001jol.1_Non-coding_Transcript|CCAR1_uc001jom.1_5'UTR|CCAR1_uc009xpx.1_Missense_Mutation_p.S90R|CCAR1_uc001jon.1_Intron	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1	116					apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7														0.24	23.040142	27.751375	18	57	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70172160	70172160	2850	10	A	C	C	3	3	CCAR1	C	4	4
RBP4	5950	broad.mit.edu	36	10	95350505	95350505	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:95350505G>C	uc001kit.1	-	c.157C>G	c.(157-159)CTC>GTC	p.L53V		NM_006744	NP_006735	P02753	RET4_HUMAN	retinol-binding protein 4, plasma precursor	53					cardiac muscle tissue development|embryonic organ morphogenesis|embryonic retina morphogenesis in camera-type eye|embryonic skeletal system development|female genitalia morphogenesis|gluconeogenesis|glucose homeostasis|heart trabecula formation|lung development|maintenance of gastrointestinal epithelium|negative regulation of cardiac muscle cell proliferation|positive regulation of immunoglobulin secretion|positive regulation of insulin secretion|response to retinoic acid|retinol metabolic process|urinary bladder development|uterus development|vagina development	extracellular space	protein binding|retinal binding|retinol binding|retinol transporter activity				0		Colorectal(252;0.122)			Vitamin A(DB00162)	Pancreas(5;160 256 1117 46697 50185)								0.545455	15.447606	15.467543	6	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95350505	95350505	13627	10	G	C	C	35	35	RBP4	C	3	3
MFRP	83552	broad.mit.edu	36	11	118715359	118715359	+	Silent	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118715359C>T	uc001pwi.1	-	c.624G>A	c.(622-624)CAG>CAA	p.Q208Q	MFRP_uc001pwj.1_Non-coding_Transcript	NM_015645	NP_056460	Q9BXJ0	C1QT5_HUMAN	C1q and tumor necrosis factor related protein 5	208	C1q.					collagen					0		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)										0.285714	7.29465	7.871883	4	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	118715359	118715359	9916	11	C	T	T	24	24	MFRP	T	2	2
RIC8A	60626	broad.mit.edu	36	11	202647	202647	+	Silent	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:202647G>A	uc001lof.1	+	c.1116G>A	c.(1114-1116)CGG>CGA	p.R372R	RIC8A_uc001log.1_Silent_p.R366R|RIC8A_uc001loh.1_Silent_p.R359R	NM_021932	NP_068751	Q9NPQ8	RIC8A_HUMAN	resistance to inhibitors of cholinesterase 8	366						cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity				0		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)										0.333333	10.146197	10.587965	6	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	202647	202647	13830	11	G	A	A	42	42	RIC8A	A	2	2
KBTBD4	55709	broad.mit.edu	36	11	47551296	47551296	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:47551296G>T	uc001nfw.1	-	c.1394C>A	c.(1393-1395)TCC>TAC	p.S465Y	NDUFS3_uc001nft.2_Intron|KBTBD4_uc001nfx.1_Missense_Mutation_p.S440Y|KBTBD4_uc001nfy.1_Missense_Mutation_p.S440Y|KBTBD4_uc001nfz.1_Missense_Mutation_p.S456Y	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	440	Kelch 5.									ovary(1)|central_nervous_system(1)	2														0.223757	176.993689	202.331249	81	281	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47551296	47551296	8300	11	G	T	T	41	41	KBTBD4	T	3	3
P2RY6	5031	broad.mit.edu	36	11	72685999	72685999	+	Missense_Mutation	SNP	T	A	A			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:72685999T>A	uc001otm.1	+	c.788T>A	c.(787-789)CTG>CAG	p.L263Q	P2RY6_uc001otn.1_Missense_Mutation_p.L263Q|P2RY6_uc001oto.1_Missense_Mutation_p.L263Q|P2RY6_uc001otp.1_Missense_Mutation_p.L263Q|P2RY6_uc001otq.1_Missense_Mutation_p.L263Q|P2RY6_uc001otr.1_Missense_Mutation_p.L263Q|P2RY6_uc001ots.1_Missense_Mutation_p.L263Q|P2RY6_uc009ytn.1_Missense_Mutation_p.L263Q	NM_176796	NP_789768	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y6	263	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1														0.217391	6.360159	8.061047	5	18	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72685999	72685999	11767	11	T	A	A	55	55	P2RY6	A	4	4
PRDM4	11108	broad.mit.edu	36	12	106659168	106659168	+	Splice_Site_SNP	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:106659168C>T	uc001tmp.1	-	c.e10_splice_site			PRDM4_uc001tmq.1_Splice_Site_SNP	NM_012406	NP_036538			PR domain containing 4						cell proliferation|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|zinc ion binding			breast(1)	1														0.222222	15.255717	19.113	12	42	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	106659168	106659168	12901	12	C	T	T	24	24	PRDM4	T	5	2
FAR2	55711	broad.mit.edu	36	12	29341265	29341265	+	Missense_Mutation	SNP	T	A	A			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:29341265T>A	uc001ris.2	+	c.410T>A	c.(409-411)CTT>CAT	p.L137H	FAR2_uc001rit.1_Missense_Mutation_p.L137H|FAR2_uc009zjm.1_Missense_Mutation_p.L40H	NM_018099	NP_060569	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	137					ether lipid biosynthetic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0														0.294118	6.621815	7.29957	5	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29341265	29341265	5911	12	T	A	A	56	56	FAR2	A	4	4
MYO1A	4640	broad.mit.edu	36	12	55726676	55726676	+	Silent	SNP	C	A	A			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55726676C>A	uc001smw.2	-	c.567G>T	c.(565-567)GTG>GTT	p.V189V	MYO1A_uc009zpd.1_Silent_p.V189V	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	189	Myosin head-like.				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|urinary_tract(1)|skin(1)	4														0.2125	39.829268	45.945233	17	63	CC		KEEP	---	---	---	---	capture			Silent	SNP	55726676	55726676	10463	12	C	A	A	29	29	MYO1A	A	3	3
OS9	10956	broad.mit.edu	36	12	56400258	56400258	+	Missense_Mutation	SNP	A	C	C			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56400258A>C	uc001spj.1	+	c.1710A>C	c.(1708-1710)AAA>AAC	p.K570N	OS9_uc001spk.1_Missense_Mutation_p.K555N|OS9_uc001spl.1_Intron|OS9_uc001spm.1_Intron|OS9_uc001spn.1_Intron	NM_006812	NP_006803	Q13438	OS9_HUMAN	amplified in osteosarcoma isoform 1 precursor	570					ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)											0.32	14.182353	14.907123	8	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56400258	56400258	11683	12	A	C	C	2	2	OS9	C	4	4
VWF	7450	broad.mit.edu	36	12	5998362	5998363	+	Missense_Mutation	DNP	TG	GA	GA			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5998362_5998363TG>GA	uc001qnn.1	-	c.4482_4483CA>TC	c.(4480-4485)TCCATG>TCTCTG	p.M1495L		NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1495					blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.205882	10.203586	12.937924	7	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	5998362	5998363	17818	12	TG	GA	GA	51	51	VWF	GA	4	4
WNK1	65125	broad.mit.edu	36	12	733630	733631	+	Missense_Mutation	DNP	GA	CG	CG			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:733630_733631GA>CG	uc001qio.2	+	c.638_639GA>CG	c.(637-639)GGA>GCG	p.G213A	WNK1_uc001qin.2_Missense_Mutation_p.G213A|WNK1_uc001qip.2_Missense_Mutation_p.G213A	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	213					intracellular protein kinase cascade|ion transport|neuron development|protein phosphorylation	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			ovary(5)|breast(4)|large_intestine(1)|lung(1)|central_nervous_system(1)	12	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			Colon(19;451 567 6672 12618 28860)				913				0.259259	10.30502	11.730939	7	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	733630	733631	17951	12	GA	CG	CG	41	41	WNK1	CG	3	3
COL4A2	1284	broad.mit.edu	36	13	109919603	109919603	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:109919603G>T	uc001vqx.1	+	c.2134G>T	c.(2134-2136)GCT>TCT	p.A712S		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	712	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)											0.210526	9.09114	10.563333	4	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109919603	109919603	3828	13	G	T	T	34	34	COL4A2	T	3	3
ISL2	64843	broad.mit.edu	36	15	74417344	74417344	+	Missense_Mutation	SNP	T	C	C			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:74417344T>C	uc002bbw.1	+	c.229T>C	c.(229-231)TGC>CGC	p.C77R		NM_145805	NP_665804	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	77	LIM zinc-binding 1.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding				0						GBM(97;953 1391 16164 31496 36951)								0.1875	7.136155	10.06546	6	26	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74417344	74417344	8161	15	T	C	C	55	55	ISL2	C	4	4
AKAP13	11214	broad.mit.edu	36	15	83924739	83924739	+	Silent	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:83924739A>T	uc002blu.1	+	c.2436A>T	c.(2434-2436)GGA>GGT	p.G812G	AKAP13_uc002blt.1_Silent_p.G812G|AKAP13_uc002blv.1_Silent_p.G812G|AKAP13_uc010bne.1_5'Flank	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	812					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|ovary(1)|liver(1)	8						Melanoma(94;603 1453 3280 32295 32951)								0.26087	9.632752	10.82981	6	17	AA		KEEP	---	---	---	---	capture			Silent	SNP	83924739	83924739	452	15	A	T	T	9	9	AKAP13	T	4	4
IFT140	9742	broad.mit.edu	36	16	1500989	1500989	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1500989T>G	uc002cma.1	-	c.4346A>C	c.(4345-4347)GAG>GCG	p.E1449A	IFT140_uc002cmb.1_Missense_Mutation_p.E1449A|IFT140_uc002clz.1_Missense_Mutation_p.E659A	NM_014714	NP_055529	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1449										ovary(3)|pancreas(1)	4		Hepatocellular(780;0.219)												0.6	6.621127	6.664066	3	2	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1500989	1500989	7857	16	T	G	G	54	54	IFT140	G	4	4
MYH11	4629	broad.mit.edu	36	16	15726091	15726091	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:15726091C>T	uc002ddx.1	-	c.4051G>A	c.(4051-4053)GAG>AAG	p.E1351K	MYH11_uc002ddv.1_Missense_Mutation_p.E1351K|MYH11_uc002ddw.1_Missense_Mutation_p.E1344K|MYH11_uc002ddy.1_Missense_Mutation_p.E1344K|MYH11_uc010bvg.1_Missense_Mutation_p.E1176K|NDE1_uc002dds.1_3'UTR|MYH11_uc010bvh.1_Missense_Mutation_p.E50K|NDE1_uc002ddz.1_Non-coding_Transcript	NM_001040114	NP_001035203	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	1344	Potential.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(4)|skin(2)|lung(1)	7										1257				0.25	13.748353	15.804275	9	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15726091	15726091	10426	16	C	T	T	30	30	MYH11	T	2	2
PRSS22	64063	broad.mit.edu	36	16	2846184	2846184	+	Missense_Mutation	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2846184A>T	uc002cry.1	-	c.181T>A	c.(181-183)TGG>AGG	p.W61R	PRSS22_uc002crz.1_Missense_Mutation_p.W61R	NM_022119	NP_071402	Q9GZN4	BSSP4_HUMAN	protease, serine, 22	61	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			central_nervous_system(1)	1														0.272727	9.032833	10.064467	6	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2846184	2846184	13069	16	A	T	T	6	6	PRSS22	T	4	4
NOD2	64127	broad.mit.edu	36	16	49302501	49302501	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49302501G>T	uc002egm.1	+	c.1178G>T	c.(1177-1179)CGC>CTC	p.R393L	NOD2_uc010cbk.1_Missense_Mutation_p.R366L|NOD2_uc002egl.1_Missense_Mutation_p.R171L|NOD2_uc010cbl.1_Missense_Mutation_p.R171L|NOD2_uc010cbm.1_Missense_Mutation_p.R171L|NOD2_uc010cbn.1_Non-coding_Transcript|NOD2_uc010cbo.1_Non-coding_Transcript|NOD2_uc010cbp.1_5'Flank|NOD2_uc010cbq.1_5'Flank|NOD2_uc010cbr.1_5'Flank	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	393	NACHT.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)	3		all_cancers(37;0.0156)												0.272727	9.938248	10.96592	6	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49302501	49302501	10920	16	G	T	T	38	38	NOD2	T	3	3
SLC38A7	55238	broad.mit.edu	36	16	57269746	57269746	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:57269746T>G	uc002eod.1	-	c.603A>C	c.(601-603)AAA>AAC	p.K201N	SLC38A7_uc002eob.1_Non-coding_Transcript|SLC38A7_uc002eoc.1_Missense_Mutation_p.K201N|SLC38A7_uc002eoe.1_Missense_Mutation_p.K201N	NM_018231	NP_060701	Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	201					amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1														0.555556	10.968621	10.992151	5	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57269746	57269746	15106	16	T	G	G	52	52	SLC38A7	G	4	4
C17orf76	388341	broad.mit.edu	36	17	16288037	16288037	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:16288037G>C	uc010cph.1	-	c.625C>G	c.(625-627)CTG>GTG	p.L209V	NCRNA00188_uc010cpe.1_Intron|C17orf76_uc002gqg.1_3'UTR|C17orf76_uc002gqh.2_Missense_Mutation_p.A123G	NM_001113567	NP_001107039	Q8NAA5	CQ076_HUMAN	hypothetical protein LOC388341 isoform 1	209	LRR 1.										0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)										0.277778	7.757311	8.565484	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16288037	16288037	1939	17	G	C	C	34	34	C17orf76	C	3	3
LGALS9C	654346	broad.mit.edu	36	17	18330119	18330119	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:18330119T>G	uc002gtw.1	+	c.278T>G	c.(277-279)TTC>TGC	p.F93C		NM_001040078	NP_001035167	Q6DKI2	LEG9C_HUMAN	galectin 9 like	93	Galectin 1.						sugar binding			ovary(1)	1														0.151163	8.31183	18.384843	13	73	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18330119	18330119	9076	17	T	G	G	62	62	LGALS9C	G	4	4
DHRS11	79154	broad.mit.edu	36	17	32029577	32029577	+	Silent	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:32029577C>T	uc002hnd.1	+	c.567C>T	c.(565-567)ACC>ACT	p.T189T	MRM1_uc002hne.1_5'Flank|MRM1_uc002hnf.1_5'Flank	NM_024308	NP_077284	Q6UWP2	DHR11_HUMAN	short-chain dehydrogenase/reductase	189					oxidation-reduction process	extracellular region	binding|oxidoreductase activity				0														0.227848	22.221427	27.617359	18	61	CC		KEEP	---	---	---	---	capture			Silent	SNP	32029577	32029577	4666	17	C	T	T	22	22	DHRS11	T	2	2
GPATCH8	23131	broad.mit.edu	36	17	39833980	39833980	+	Nonsense_Mutation	SNP	C	A	A			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39833980C>A	uc002igw.1	-	c.991G>T	c.(991-993)GGA>TGA	p.G331*	GPATCH8_uc002igv.1_Nonsense_Mutation_p.G253*	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	331						intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)								OREG0024461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.123967	22.476428	39.176581	15	106	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	39833980	39833980	6868	17	C	A	A	21	21	GPATCH8	A	5	3
KIAA0195	9772	broad.mit.edu	36	17	71006375	71006375	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71006375G>C	uc002jnz.2	+	c.3804G>C	c.(3802-3804)TGG>TGC	p.W1268C	KIAA0195_uc002joa.2_Missense_Mutation_p.W908C|KIAA0195_uc002job.2_Missense_Mutation_p.W306C	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	1268	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)											0.333333	37.067277	38.549753	20	40	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71006375	71006375	8467	17	G	C	C	44	44	KIAA0195	C	3	3
NEURL4	84461	broad.mit.edu	36	17	7169415	7169415	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7169415G>T	uc002gga.1	-	c.1468C>A	c.(1468-1470)CGT>AGT	p.R490S	NEURL4_uc002ggb.1_Missense_Mutation_p.R490S|NEURL4_uc002ggc.1_5'UTR	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	490							protein binding			ovary(1)	1														0.424242	26.820072	26.989281	14	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7169415	7169415	10747	17	G	T	T	39	39	NEURL4	T	3	3
ST6GALNAC1	55808	broad.mit.edu	36	17	72133549	72133549	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:72133549G>A	uc002jsh.1	-	c.1552C>T	c.(1552-1554)CGC>TGC	p.R518C	ST6GALNAC1_uc002jsi.1_Missense_Mutation_p.R386C|ST6GALNAC1_uc002jsj.1_Non-coding_Transcript	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	GalNAc alpha-2, 6-sialyltransferase I	518	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0														0.4375	21.323989	21.378117	7	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72133549	72133549	15741	17	G	A	A	39	39	ST6GALNAC1	A	1	1
MGAT5B	146664	broad.mit.edu	36	17	72448181	72448182	+	Missense_Mutation	DNP	TC	AT	AT			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:72448181_72448182TC>AT	uc002jti.1	+	c.1714_1715TC>AT	c.(1714-1716)TCC>ATC	p.S572I	MGAT5B_uc002jth.1_Missense_Mutation_p.S561I	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	beta(1,6)-N-acetylglucosaminyltransferase V	563	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)	2														0.291667	22.025283	23.899338	14	34	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	72448181	72448182	9939	17	TC	AT	AT	54	54	MGAT5B	AT	4	4
RNF213	57674	broad.mit.edu	36	17	75946709	75946709	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75946709G>A	uc002jyh.1	+	c.5108G>A	c.(5107-5109)GGT>GAT	p.G1703D	RNF213_uc010dhw.1_Missense_Mutation_p.G85D	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	12	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)											0.235294	10.889695	13.071073	8	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75946709	75946709	13955	17	G	A	A	44	44	RNF213	A	2	2
TSHZ1	10194	broad.mit.edu	36	18	71127228	71127228	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:71127228C>T	uc002lly.1	+	c.743C>T	c.(742-744)TCC>TTC	p.S248F	TSHZ1_uc002llz.2_Missense_Mutation_p.S248F	NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	293					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)										0.176471	7.142153	10.493574	6	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71127228	71127228	17174	18	C	T	T	30	30	TSHZ1	T	2	2
ZNF433	163059	broad.mit.edu	36	19	11987807	11987807	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11987807C>A	uc002msy.1	-	c.875G>T	c.(874-876)AGC>ATC	p.S292I	ZNF433_uc002msz.1_Missense_Mutation_p.S257I	NM_001080411	NP_001073880	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	292	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.28	11.805948	12.900975	7	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11987807	11987807	18500	19	C	A	A	28	28	ZNF433	A	3	3
DLL3	10683	broad.mit.edu	36	19	44687745	44687745	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44687745G>A	uc002olx.2	+	c.907G>A	c.(907-909)GGG>AGG	p.G303R	DLL3_uc010egq.1_Missense_Mutation_p.G303R|DLL3_uc002olw.2_Missense_Mutation_p.G303R	NM_016941	NP_058637	Q9NYJ7	DLL3_HUMAN	delta-like 3 protein isoform 1 precursor	303	EGF-like 2.|Extracellular (Potential).				Notch signaling pathway|skeletal system development	integral to membrane	Notch binding			central_nervous_system(2)|breast(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)											0.555556	8.315167	8.332932	5	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44687745	44687745	4747	19	G	A	A	47	47	DLL3	A	2	2
LILRA3	11026	broad.mit.edu	36	19	59495074	59495074	+	Missense_Mutation	SNP	C	G	G			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59495074C>G	uc002qfd.1	-	c.415G>C	c.(415-417)GGG>CGG	p.G139R	LILRA6_uc002qew.1_Intron|LILRA3_uc010erk.1_Missense_Mutation_p.G139R	NM_006865	NP_006856	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor,	139	Ig-like C2-type 2.				defense response	extracellular region|plasma membrane	antigen binding|receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.170213	7.563726	12.421018	8	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59495074	59495074	9112	19	C	G	G	24	24	LILRA3	G	3	3
U2AF2	11338	broad.mit.edu	36	19	60872637	60872637	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60872637A>G	uc002qlu.1	+	c.1060A>G	c.(1060-1062)ACG>GCG	p.T354A	U2AF2_uc002qlt.1_Missense_Mutation_p.T350A	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2	354					mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)										0.333333	8.863369	9.2357	5	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60872637	60872637	17380	19	A	G	G	10	10	U2AF2	G	4	4
SPAG17	200162	broad.mit.edu	36	1	118443931	118443931	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118443931T>G	uc001ehk.1	-	c.650A>C	c.(649-651)GAT>GCT	p.D217A		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	217						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)										0.130435	8.717801	14.835681	6	40	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118443931	118443931	15482	1	T	G	G	50	50	SPAG17	G	4	4
FLG	2312	broad.mit.edu	36	1	150550136	150550136	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150550136C>T	uc001ezu.1	-	c.3850G>A	c.(3850-3852)GAG>AAG	p.E1284K		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1284	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.397849	105.653821	106.502442	37	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150550136	150550136	6160	1	C	T	T	31	31	FLG	T	1	1
FLG2	388698	broad.mit.edu	36	1	150592174	150592174	+	Missense_Mutation	SNP	C	G	G			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150592174C>G	uc001ezw.2	-	c.4712G>C	c.(4711-4713)AGA>ACA	p.R1571T		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1571							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.111111	8.580301	63.863159	41	328	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150592174	150592174	6161	1	C	G	G	32	32	FLG2	G	3	3
KCNN3	3782	broad.mit.edu	36	1	153011345	153011345	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153011345G>T	uc001ffp.1	-	c.1178C>A	c.(1177-1179)TCC>TAC	p.S393Y	KCNN3_uc001ffo.1_Missense_Mutation_p.S88Y|KCNN3_uc009wox.1_Missense_Mutation_p.S393Y	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	398						integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)											0.09589	9.493887	57.565868	28	264	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153011345	153011345	8385	1	G	T	T	41	41	KCNN3	T	3	3
HCN3	57657	broad.mit.edu	36	1	153519066	153519066	+	Silent	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153519066C>T	uc001fjz.1	+	c.519C>T	c.(517-519)TTC>TTT	p.F173F		NM_020897	NP_065948	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic	173	Helical; Name=Segment S3; (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)|breast(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)											0.796296	141.744673	146.150916	43	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	153519066	153519066	7280	1	C	T	T	30	30	HCN3	T	2	2
CLCNKA	1187	broad.mit.edu	36	1	16230898	16230898	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16230898A>G	uc001axu.1	+	c.1729A>G	c.(1729-1731)ACC>GCC	p.T577A	CLCNKB_uc001axw.2_Intron|CLCNKA_uc001axt.1_Non-coding_Transcript|CLCNKA_uc001axv.1_Missense_Mutation_p.T577A	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1	577	CBS 1.				excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		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)	Niflumic Acid(DB04552)									0.285714	13.437604	14.306242	6	15	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16230898	16230898	3605	1	A	G	G	10	10	CLCNKA	G	4	4
LAMB3	3914	broad.mit.edu	36	1	207870589	207870589	+	Missense_Mutation	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:207870589A>T	uc001hhg.1	-	c.937T>A	c.(937-939)TGC>AGC	p.C313S	LAMB3_uc009xco.1_Missense_Mutation_p.C313S|LAMB3_uc001hhh.1_Missense_Mutation_p.C313S|LAMB3_uc009xcp.1_Missense_Mutation_p.C249S	NM_001017402	NP_001121113	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	313	Laminin EGF-like 1.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|large_intestine(1)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(81;0.0519)										0.184211	13.71005	20.889679	14	62	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	207870589	207870589	8935	1	A	T	T	8	8	LAMB3	T	4	4
CNR2	1269	broad.mit.edu	36	1	24074150	24074150	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24074150A>G	uc001bif.1	-	c.545T>C	c.(544-546)CTT>CCT	p.L182P	CNR2_uc009vqu.1_Missense_Mutation_p.L182P	NM_001841	NP_001832	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	182	Extracellular (Potential).				behavior|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response	dendrite|integral to plasma membrane|perikaryon	cannabinoid receptor activity			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Nabilone(DB00486)									0.2	7.324858	9.849445	6	24	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24074150	24074150	3770	1	A	G	G	3	3	CNR2	G	4	4
SLC30A2	7780	broad.mit.edu	36	1	26244132	26244132	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:26244132G>T	uc001blg.1	-	c.214C>A	c.(214-216)CGC>AGC	p.R72S	SLC30A2_uc001blh.1_Missense_Mutation_p.R72S	NM_001004434	NP_001004434	Q9BRI3	ZNT2_HUMAN	solute carrier family 30, member 2 isoform 1	72	Cytoplasmic (Potential).				positive regulation of sequestering of zinc ion|zinc ion transport	integral to membrane|late endosome|lysosomal membrane	cation transmembrane transporter activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)										0.11039	15.99454	39.033026	17	137	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26244132	26244132	15052	1	G	T	T	38	38	SLC30A2	T	3	3
NR0B2	8431	broad.mit.edu	36	1	27112573	27112573	+	Missense_Mutation	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:27112573A>T	uc001bnf.1	-	c.446T>A	c.(445-447)CTT>CAT	p.L149H		NM_021969	NP_068804	Q15466	NR0B2_HUMAN	short heterodimer partner	149	Ligand-binding (By similarity).				cholesterol metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	DNA binding|protein domain specific binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity				0		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)										0.263158	16.630022	18.563226	10	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27112573	27112573	11019	1	A	T	T	3	3	NR0B2	T	4	4
HMGB4	127540	broad.mit.edu	36	1	34102648	34102648	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:34102648C>T	uc001bxp.1	+	c.269C>T	c.(268-270)CCC>CTC	p.P90L	CSMD2_uc001bxm.1_Intron|CSMD2_uc001bxn.1_Intron|HMGB4_uc001bxq.1_Missense_Mutation_p.P16L|HMGB4_uc009vuj.1_Missense_Mutation_p.P90L	NM_145205	NP_001008728	B2R4X7	B2R4X7_HUMAN	HMG2 like isoform 1	90						nucleus	DNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)												0.266667	6.588649	7.330567	4	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34102648	34102648	7519	1	C	T	T	22	22	HMGB4	T	2	2
HIVEP3	59269	broad.mit.edu	36	1	41818471	41818471	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:41818471C>T	uc001cgz.2	-	c.4585G>A	c.(4585-4587)GAA>AAA	p.E1529K	HIVEP3_uc001cha.2_Missense_Mutation_p.E1529K|HIVEP3_uc001cgy.1_Non-coding_Transcript	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1529					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription activator activity|zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)												0.235294	6.891377	7.982614	4	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41818471	41818471	7479	1	C	T	T	32	32	HIVEP3	T	2	2
MYH7B	57644	broad.mit.edu	36	20	33052915	33052915	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33052915C>A	uc002xbi.1	+	c.5727C>A	c.(5725-5727)AAC>AAA	p.N1909K		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	1867	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)											0.6	8.22419	8.268061	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33052915	33052915	10435	20	C	A	A	18	18	MYH7B	A	3	3
LPIN3	64900	broad.mit.edu	36	20	39412287	39412287	+	Missense_Mutation	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39412287A>T	uc010ggh.1	+	c.941A>T	c.(940-942)GAT>GTT	p.D314V	LPIN3_uc002xjx.1_Missense_Mutation_p.D313V	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	313					fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)												0.357143	7.001661	7.282082	5	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39412287	39412287	9293	20	A	T	T	12	12	LPIN3	T	4	4
CASS4	57091	broad.mit.edu	36	20	54445802	54445802	+	Missense_Mutation	SNP	T	C	C			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:54445802T>C	uc002xxp.1	+	c.212T>C	c.(211-213)CTC>CCC	p.L71P	CASS4_uc002xxq.2_Missense_Mutation_p.L71P|CASS4_uc002xxr.1_Missense_Mutation_p.L71P|CASS4_uc010gio.1_Missense_Mutation_p.L71P	NM_020356	NP_065089	Q9NQ75	CASS4_HUMAN	HEF-like protein	71	SH3.				cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)	2														0.363636	8.108451	8.283342	4	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54445802	54445802	2802	20	T	C	C	54	54	CASS4	C	4	4
SON	6651	broad.mit.edu	36	21	33845267	33845267	+	Silent	SNP	T	A	A			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:33845267T>A	uc002yse.1	+	c.1860T>A	c.(1858-1860)CTT>CTA	p.L620L	SON_uc002ysb.1_Silent_p.L620L|SON_uc002ysc.1_Silent_p.L620L|SON_uc002ysd.2_5'UTR|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	620					anti-apoptosis	nuclear speck	DNA binding|double-stranded RNA binding			ovary(3)	3														0.4	7.390385	7.479466	4	6	TT		KEEP	---	---	---	---	capture			Silent	SNP	33845267	33845267	15426	21	T	A	A	64	64	SON	A	4	4
RRP1B	23076	broad.mit.edu	36	21	43932230	43932230	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43932230G>A	uc002zdk.1	+	c.1547G>A	c.(1546-1548)GGT>GAT	p.G516D	RRP1B_uc002zdl.1_Missense_Mutation_p.G49D	NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B	516					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding				0				STAD - Stomach adenocarcinoma(101;0.178)										0.357143	10.471662	10.722889	5	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43932230	43932230	14168	21	G	A	A	44	44	RRP1B	A	2	2
APOBEC3B	9582	broad.mit.edu	36	22	37718016	37718016	+	Nonsense_Mutation	SNP	C	A	A			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:37718016C>A	uc003awo.1	+	c.1050C>A	c.(1048-1050)TAC>TAA	p.Y350*	APOBEC3B_uc003awp.1_Nonsense_Mutation_p.Y325*|APOBEC3B_uc003awq.1_Non-coding_Transcript	NM_004900	NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	350							hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)													0.220588	12.22985	17.340503	15	53	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	37718016	37718016	801	22	C	A	A	18	18	APOBEC3B	A	5	3
CHST10	9486	broad.mit.edu	36	2	100385460	100385460	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:100385460T>G	uc002tam.1	-	c.190A>C	c.(190-192)AAG>CAG	p.K64Q		NM_004854	NP_004845	O43529	CHSTA_HUMAN	HNK-1 sulfotransferase	64	Lumenal (Potential).				carbohydrate biosynthetic process|cell adhesion	Golgi membrane|integral to membrane|membrane fraction				ovary(1)	1														0.333333	7.490723	7.788572	4	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100385460	100385460	3532	2	T	G	G	62	62	CHST10	G	4	4
GPR148	344561	broad.mit.edu	36	2	131203885	131203885	+	Missense_Mutation	SNP	T	A	A			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131203885T>A	uc002trv.1	+	c.691T>A	c.(691-693)TGC>AGC	p.C231S		NM_207364	NP_997247	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	231	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Colorectal(110;0.1)													0.186441	9.965993	15.447612	11	48	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131203885	131203885	6928	2	T	A	A	55	55	GPR148	A	4	4
COL6A3	1293	broad.mit.edu	36	2	237898955	237898955	+	Silent	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237898955C>T	uc002vwl.2	-	c.9480G>A	c.(9478-9480)AAG>AAA	p.K3160K	COL6A3_uc002vwj.2_Silent_p.K541K|COL6A3_uc002vwk.2_Silent_p.K2993K|COL6A3_uc002vwm.2_Silent_p.K2959K|COL6A3_uc002vwn.2_Silent_p.K2960K|COL6A3_uc002vwo.2_Silent_p.K2954K	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	3160	Nonhelical region.|BPTI/Kunitz inhibitor.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.104478	27.461	69.11716	28	240	CC		KEEP	---	---	---	---	capture			Silent	SNP	237898955	237898955	3839	2	C	T	T	24	24	COL6A3	T	2	2
TCF23	150921	broad.mit.edu	36	2	27226502	27226502	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27226502C>A	uc002rjc.1	+	c.230C>A	c.(229-231)GCC>GAC	p.A77D		NM_175769	NP_786951	Q7RTU1	TCF23_HUMAN	transcription factor 23	77	Basic motif (By similarity).				cell differentiation|muscle organ development	nucleus	transcription regulator activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.217391	10.35382	11.984262	5	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27226502	27226502	16218	2	C	A	A	26	26	TCF23	A	3	3
C2orf71	388939	broad.mit.edu	36	2	29147436	29147437	+	Missense_Mutation	DNP	CA	AT	AT			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:29147436_29147437CA>AT	uc002rmt.1	-	c.3195_3196TG>AT	c.(3193-3198)CCTGCT>CCATCT	p.A1066S		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	1066	Pro-rich.				response to stimulus|visual perception	photoreceptor outer segment					0														0.625	11.270214	11.378919	5	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	29147436	29147437	2279	2	CA	AT	AT	25	25	C2orf71	AT	3	3
GFPT1	2673	broad.mit.edu	36	2	69428933	69428933	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:69428933C>T	uc002sfh.1	-	c.829G>A	c.(829-831)GAA>AAA	p.E277K		NM_002056	NP_002047	Q06210	GFPT1_HUMAN	glucosamine-fructose-6-phosphate	295	Glutamine amidotransferase type-2.				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding				0														0.368509	639.730924	648.802265	220	377	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69428933	69428933	6613	2	C	T	T	30	30	GFPT1	T	2	2
ITGB5	3693	broad.mit.edu	36	3	125975380	125975380	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:125975380G>T	uc003eho.1	-	c.1763C>A	c.(1762-1764)TCG>TAG	p.S588*	ITGB5_uc010hrx.1_Non-coding_Transcript|ITGB5_uc003ehp.1_Non-coding_Transcript	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5	588	III.|Extracellular (Potential).|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.163)										0.122951	21.56627	38.522285	15	107	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	125975380	125975380	8202	3	G	T	T	37	37	ITGB5	T	5	3
PLXNA1	5361	broad.mit.edu	36	3	128190722	128190722	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:128190722C>T	uc003ejg.1	+	c.527C>T	c.(526-528)CCC>CTC	p.P176L		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	199	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(114;0.155)										0.142857	8.091114	12.362109	5	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128190722	128190722	12545	3	C	T	T	22	22	PLXNA1	T	2	2
SOX2	6657	broad.mit.edu	36	3	182913218	182913218	+	Missense_Mutation	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:182913218A>T	uc003fkx.1	+	c.376A>T	c.(376-378)ACG>TCG	p.T126S	SOX2OT_uc003fkv.1_Intron|SOX2OT_uc003fkw.2_Intron	NM_003106	NP_003097	P48431	SOX2_HUMAN	sex-determining region Y-box 2	126					cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|promoter binding|protein binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)							27				0.5	6.427571	6.427567	3	3	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	182913218	182913218	15449	3	A	T	T	6	6	SOX2	T	4	4
ZNF662	389114	broad.mit.edu	36	3	42931197	42931197	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42931197C>T	uc003cmi.1	+	c.628C>T	c.(628-630)CAC>TAC	p.H210Y	CCBP2_uc010hie.1_Intron|ZNF662_uc003cmj.1_Missense_Mutation_p.H102Y|ZNF662_uc003cmk.1_Missense_Mutation_p.H175Y	NM_207404	NP_997287	Q6ZS27	ZN662_HUMAN	zinc finger protein 662 isoform 1	210	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)										0.346734	199.981563	204.123186	69	130	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42931197	42931197	18666	3	C	T	T	17	17	ZNF662	T	2	2
MAP4	4134	broad.mit.edu	36	3	47888544	47888544	+	Silent	SNP	T	C	C			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:47888544T>C	uc003csb.1	-	c.2373A>G	c.(2371-2373)CCA>CCG	p.P791P	MAP4_uc003csc.2_Silent_p.P791P|MAP4_uc003crw.1_5'Flank|MAP4_uc003crx.1_Silent_p.P51P|MAP4_uc003cry.1_Silent_p.P526P|MAP4_uc003csa.2_Silent_p.P526P|MAP4_uc003crz.2_Non-coding_Transcript|MAP4_uc003csd.1_Silent_p.P526P	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1	791					negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)										0.163934	9.201027	15.77064	10	51	TT		KEEP	---	---	---	---	capture			Silent	SNP	47888544	47888544	9641	3	T	C	C	55	55	MAP4	C	4	4
GPR27	2850	broad.mit.edu	36	3	71886705	71886705	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:71886705T>G	uc003doy.1	+	c.815T>G	c.(814-816)GTG>GGG	p.V272G	EIF4E3_uc003dox.1_5'Flank|EIF4E3_uc010hoc.1_5'Flank	NM_018971	NP_061844	Q9NS67	GPR27_HUMAN	G protein-coupled receptor 27	272	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.78e-05)|Epithelial(33;5.75e-05)|Lung(16;0.0012)|LUSC - Lung squamous cell carcinoma(21;0.00156)										0.75	6.731868	6.947096	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71886705	71886705	6960	3	T	G	G	59	59	GPR27	G	4	4
GPR27	2850	broad.mit.edu	36	3	71886707	71886708	+	Missense_Mutation	DNP	CT	AA	AA			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:71886707_71886708CT>AA	uc003doy.1	+	c.817_818CT>AA	c.(817-819)CTG>AAG	p.L273K	EIF4E3_uc003dox.1_5'Flank|EIF4E3_uc010hoc.1_5'Flank	NM_018971	NP_061844	Q9NS67	GPR27_HUMAN	G protein-coupled receptor 27	273	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.78e-05)|Epithelial(33;5.75e-05)|Lung(16;0.0012)|LUSC - Lung squamous cell carcinoma(21;0.00156)										0.8	8.999912	9.410086	4	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	71886707	71886708	6960	3	CT	AA	AA	28	28	GPR27	AA	3	3
PALLD	23022	broad.mit.edu	36	4	169866871	169866871	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:169866871C>T	uc003iru.1	+	c.1619C>T	c.(1618-1620)TCA>TTA	p.S540L	PALLD_uc003irv.1_Missense_Mutation_p.S158L	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin	540					cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		Esophageal Squamous(109;1482 1532 18347 40239 51172)								0.32	13.371773	14.102445	8	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	169866871	169866871	11823	4	C	T	T	29	29	PALLD	T	2	2
TUBB4Q	56604	broad.mit.edu	36	4	191141485	191141485	+	Missense_Mutation	SNP	T	C	C			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:191141485T>C	uc003izt.1	-	c.489A>G	c.(487-489)ATA>ATG	p.I163M		NM_020040	NP_064424	Q99867	TBB4Q_HUMAN	tubulin, beta polypeptide 4, member Q	164					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;4.1e-31)|Epithelial(3;1.44e-30)|OV - Ovarian serous cystadenocarcinoma(60;2.03e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00839)|READ - Rectum adenocarcinoma(43;0.155)										0.366667	18.18411	18.664835	11	19	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	191141485	191141485	17314	4	T	C	C	61	61	TUBB4Q	C	4	4
PCDH7	5099	broad.mit.edu	36	4	30334945	30334945	+	Missense_Mutation	SNP	A	C	C			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:30334945A>C	uc010iez.1	+	c.2662A>C	c.(2662-2664)AAA>CAA	p.K888Q	PCDH7_uc003gsj.1_Missense_Mutation_p.K935Q|PCDH7_uc003gsk.1_Missense_Mutation_p.K935Q	NM_032457	NP_115833	O60245	PCDH7_HUMAN	protocadherin 7 isoform c precursor	935	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4														0.416667	8.758804	8.834401	5	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30334945	30334945	11936	4	A	C	C	13	13	PCDH7	C	4	4
UGT2B17	7367	broad.mit.edu	36	4	69116219	69116219	+	Silent	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:69116219G>C	uc003hea.1	-	c.579C>G	c.(577-579)TCC>TCG	p.S193S		NM_001077	NP_001068	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family,	193					steroid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)	1						Melanoma(18;649 833 28984 37818 38500)								0.160494	10.901027	19.845284	13	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	69116219	69116219	17517	4	G	C	C	35	35	UGT2B17	C	3	3
SLC4A4	8671	broad.mit.edu	36	4	72482209	72482209	+	Missense_Mutation	SNP	T	A	A			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:72482209T>A	uc003hfy.1	+	c.782T>A	c.(781-783)ATT>AAT	p.I261N	SLC4A4_uc010iib.1_Missense_Mutation_p.I261N|SLC4A4_uc003hfz.1_Missense_Mutation_p.I261N|SLC4A4_uc010iic.1_Missense_Mutation_p.I261N|SLC4A4_uc003hga.1_Missense_Mutation_p.I139N|SLC4A4_uc003hgb.2_Missense_Mutation_p.I217N|SLC4A4_uc003hgc.2_Missense_Mutation_p.I217N	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate	261	Cytoplasmic (Potential).					basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)	4			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)											0.098901	7.107137	21.755231	9	82	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72482209	72482209	15153	4	T	A	A	52	52	SLC4A4	A	4	4
ANKRD17	26057	broad.mit.edu	36	4	74176260	74176260	+	Silent	SNP	T	A	A			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74176260T>A	uc003hgp.1	-	c.5949A>T	c.(5947-5949)ACA>ACT	p.T1983T	ANKRD17_uc003hgo.1_Silent_p.T1870T|ANKRD17_uc003hgq.1_Silent_p.T1732T|ANKRD17_uc003hgr.1_Silent_p.T1982T	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	1983	Ser-rich.|Thr-rich.				interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(2)|lung(1)	8	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)											0.091329	44.988376	190.471998	79	786	TT		KEEP	---	---	---	---	capture			Silent	SNP	74176260	74176260	649	4	T	A	A	51	51	ANKRD17	A	4	4
WDFY3	23001	broad.mit.edu	36	4	85882042	85882042	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:85882042T>G	uc003hpd.1	-	c.6130A>C	c.(6130-6132)AAT>CAT	p.N2044H		NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2044						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)										0.190476	9.263817	13.046085	8	34	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85882042	85882042	17842	4	T	G	G	63	63	WDFY3	G	4	4
WDR36	134430	broad.mit.edu	36	5	110474437	110474437	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:110474437C>T	uc003kpd.1	+	c.1661C>T	c.(1660-1662)ACA>ATA	p.T554I	WDR36_uc010jbu.1_Non-coding_Transcript	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	554	WD 7.				response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)	1		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)										0.166667	9.086802	11.613216	4	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110474437	110474437	17863	5	C	T	T	17	17	WDR36	T	2	2
CLPTM1L	81037	broad.mit.edu	36	5	1394882	1394882	+	Silent	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1394882G>A	uc003jch.1	-	c.357C>T	c.(355-357)CAC>CAT	p.H119H	CLPTM1L_uc003jcg.1_De_novo_Start_OutOfFrame	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like	119	Extracellular (Potential).				apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)						276				0.238994	88.393445	98.273027	38	121	GG		KEEP	---	---	---	---	capture			Silent	SNP	1394882	1394882	3693	5	G	A	A	40	40	CLPTM1L	A	1	1
FAT2	2196	broad.mit.edu	36	5	150909059	150909059	+	Silent	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150909059G>C	uc003lue.2	-	c.4779C>G	c.(4777-4779)TCC>TCG	p.S1593S		NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1593	Extracellular (Potential).|Cadherin 14.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.228571	10.166939	12.551233	8	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	150909059	150909059	5926	5	G	C	C	43	43	FAT2	C	3	3
C1QTNF2	114898	broad.mit.edu	36	5	159709322	159709322	+	Missense_Mutation	SNP	C	G	G			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:159709322C>G	uc003lyd.1	-	c.424G>C	c.(424-426)GGC>CGC	p.G142R		NM_031908	NP_114114	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	97	Collagen-like.					collagen					0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.333333	7.227944	7.507406	4	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159709322	159709322	2030	5	C	G	G	22	22	C1QTNF2	G	3	3
NKX2-5	1482	broad.mit.edu	36	5	172592313	172592313	+	Silent	SNP	T	C	C			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:172592313T>C	uc003mcm.1	-	c.840A>G	c.(838-840)CCA>CCG	p.P280P		NM_004387	NP_004378	P52952	NKX25_HUMAN	NK2 transcription factor related, locus 5	280	Ala/Pro-rich.				adult heart development|atrial cardiac muscle cell development|atrial septum morphogenesis|heart looping|hemopoiesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell apoptosis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of myotube differentiation|pharyngeal system development|positive regulation of calcium ion transport via voltage-gated calcium channel activity|positive regulation of cardioblast differentiation|positive regulation of cell proliferation|positive regulation of heart contraction|positive regulation of neuron differentiation|positive regulation of sodium ion transport|positive regulation of survival gene product expression|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription via serum response element binding|regulation of cardiac muscle contraction|septum secundum development|spleen development|thyroid gland development|tongue development|vasculogenesis|ventricular septum morphogenesis	transcription factor complex	chromatin binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|serum response element binding|transcription activator activity|transcription factor binding|transcription repressor activity			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			Esophageal Squamous(72;810 1219 2387 13420 44943)								0.294118	8.461826	9.111418	5	12	TT		KEEP	---	---	---	---	capture			Silent	SNP	172592313	172592313	10855	5	T	C	C	55	55	NKX2-5	C	4	4
ERBB2IP	55914	broad.mit.edu	36	5	65407958	65407958	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:65407958G>C	uc010iwx.1	+	c.4031G>C	c.(4030-4032)GGG>GCG	p.G1344A	ERBB2IP_uc003jui.1_Missense_Mutation_p.G1300A|ERBB2IP_uc003juj.1_Missense_Mutation_p.G1231A|ERBB2IP_uc003juk.1_Missense_Mutation_p.G1341A|ERBB2IP_uc003jul.1_Missense_Mutation_p.G1296A	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	1341	PDZ.				basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(1)	6		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)										0.24031	77.260139	85.201508	31	98	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65407958	65407958	5400	5	G	C	C	43	43	ERBB2IP	C	3	3
POPDC3	64208	broad.mit.edu	36	6	105713115	105713115	+	Nonsense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:105713115G>A	uc003prb.1	-	c.799C>T	c.(799-801)CAA>TAA	p.Q267*	POPDC3_uc003pra.1_Non-coding_Transcript	NM_022361	NP_071756	Q9HBV1	POPD3_HUMAN	popeye protein 3	267						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)												0.619718	291.524229	293.31145	88	54	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	105713115	105713115	12685	6	G	A	A	45	45	POPDC3	A	5	2
ROS1	6098	broad.mit.edu	36	6	117806943	117806943	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117806943G>T	uc003pxp.1	-	c.2569C>A	c.(2569-2571)CTG>ATG	p.L857M	GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	857	Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(5)|central_nervous_system(3)|stomach(2)|large_intestine(1)|lung(1)	12		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)						1038				0.198718	70.64892	83.820221	31	125	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117806943	117806943	14010	6	G	T	T	35	35	ROS1	T	3	3
ID4	3400	broad.mit.edu	36	6	19946294	19946295	+	Missense_Mutation	DNP	GC	TG	TG			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:19946294_19946295GC>TG	uc003ncw.1	+	c.330_331GC>TG	c.(328-333)ACGCAC>ACTGAC	p.H111D		NM_001546	NP_001537	P47928	ID4_HUMAN	inhibitor of DNA binding 4, dominant negative	111						nucleus	transcription corepressor activity|transcription repressor activity				0	Ovarian(93;0.0355)|Breast(50;0.0654)|all_epithelial(95;0.12)		OV - Ovarian serous cystadenocarcinoma(7;0.00659)|all cancers(50;0.0327)|Epithelial(50;0.0621)			Esophageal Squamous(13;105 518 19978 28644 46870)								0.8	9.762958	10.116948	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	19946294	19946295	7792	6	GC	TG	TG	38	38	ID4	TG	3	3
BRD2	6046	broad.mit.edu	36	6	33053259	33053259	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:33053259G>A	uc010juh.1	+	c.1263G>A	c.(1261-1263)ATG>ATA	p.M421I	BRD2_uc003ocn.2_Missense_Mutation_p.M421I|BRD2_uc003oco.2_Non-coding_Transcript|BRD2_uc003ocq.2_Missense_Mutation_p.M421I|BRD2_uc003ocp.2_Missense_Mutation_p.M301I	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	421	Bromo 2.				spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5										227				0.396292	957.813271	965.966118	342	521	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33053259	33053259	1533	6	G	A	A	48	48	BRD2	A	2	2
KLF10	7071	broad.mit.edu	36	8	103732764	103732764	+	Silent	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:103732764G>C	uc003ykv.1	-	c.972C>G	c.(970-972)CCC>CCG	p.P324P	KLF10_uc003yku.1_Silent_p.P313P	NM_005655	NP_005646	Q13118	KLF10_HUMAN	Kruppel-like factor 10 isoform a	324					cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			Esophageal Squamous(16;495 519 2144 16528 44005)								0.285714	6.497971	7.073743	4	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	103732764	103732764	8650	8	G	C	C	39	39	KLF10	C	3	3
KLHL38	340359	broad.mit.edu	36	8	124727327	124727327	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:124727327C>T	uc003yqs.1	-	c.1579G>A	c.(1579-1581)GGC>AGC	p.G527S		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	527	Kelch 6.										0														0.2	97.376845	117.025471	47	188	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124727327	124727327	8704	8	C	T	T	22	22	KLHL38	T	2	2
DLC1	10395	broad.mit.edu	36	8	13001867	13001867	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:13001867G>C	uc003wwm.1	-	c.2350C>G	c.(2350-2352)CAG>GAG	p.Q784E	DLC1_uc003wwl.1_Missense_Mutation_p.Q381E|DLC1_uc003wwk.1_Missense_Mutation_p.Q347E	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	784					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7										739				0.207792	21.452346	27.560768	16	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13001867	13001867	4730	8	G	C	C	45	45	DLC1	C	3	3
SLC7A13	157724	broad.mit.edu	36	8	87311048	87311048	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:87311048C>T	uc003ydq.1	-	c.575G>A	c.(574-576)CGA>CAA	p.R192Q	SLC7A13_uc003ydr.1_Missense_Mutation_p.R192Q	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	192	Extracellular (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1														0.432466	1058.764001	1061.959734	349	458	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87311048	87311048	15192	8	C	T	T	31	31	SLC7A13	T	1	1
UGCG	7357	broad.mit.edu	36	9	113728597	113728597	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:113728597G>T	uc004bft.1	+	c.558G>T	c.(556-558)CAG>CAT	p.Q186H		NM_003358	NP_003349	Q16739	CEGT_HUMAN	ceramide glucosyltransferase	186	Cytoplasmic (Potential).				epidermis development|glucosylceramide biosynthetic process	Golgi membrane|integral to membrane|membrane fraction	ceramide glucosyltransferase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)									0.2	7.024084	9.549886	6	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113728597	113728597	17497	9	G	T	T	35	35	UGCG	T	3	3
DBH	1621	broad.mit.edu	36	9	135502863	135502863	+	Silent	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135502863C>T	uc004cel.1	+	c.1099C>T	c.(1099-1101)CTG>TTG	p.L367L		NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta-hydroxylase precursor	367	Intragranular (Potential).				hormone biosynthetic process|oxidation-reduction process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)									0.2	6.456043	8.556983	5	20	CC		KEEP	---	---	---	---	capture			Silent	SNP	135502863	135502863	4421	9	C	T	T	28	28	DBH	T	2	2
C9orf64	84267	broad.mit.edu	36	9	85749671	85749671	+	Missense_Mutation	SNP	C	G	G			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:85749671C>G	uc004anb.1	-	c.651G>C	c.(649-651)TGG>TGC	p.W217C	C9orf64_uc004anc.1_Missense_Mutation_p.W76C	NM_032307	NP_115683	Q5T6V5	CI064_HUMAN	hypothetical protein LOC84267	217											0														0.4	162.719505	163.900362	54	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85749671	85749671	2605	9	C	G	G	30	30	C9orf64	G	3	3
DRP2	1821	broad.mit.edu	36	X	100383450	100383451	+	Missense_Mutation	DNP	CT	AA	AA			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100383450_100383451CT>AA	uc004egz.2	+	c.697_698CT>AA	c.(697-699)CTC>AAC	p.L233N		NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	233	Spectrin 2.				central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2														0.333333	7.612168	7.899413	4	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	100383450	100383451	4948	23	CT	AA	AA	28	28	DRP2	AA	3	3
DRP2	1821	broad.mit.edu	36	X	100396160	100396160	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100396160G>A	uc004egz.2	+	c.2068G>A	c.(2068-2070)GGT>AGT	p.G690S		NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	690					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2														0.238095	6.757167	8.082913	5	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100396160	100396160	4948	23	G	A	A	35	35	DRP2	A	2	2
TXLNG	55787	broad.mit.edu	36	X	16769612	16769612	+	Silent	SNP	G	A	A			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:16769612G>A	uc004cxq.1	+	c.1389G>A	c.(1387-1389)GCG>GCA	p.A463A	TXLNG_uc010ney.1_Silent_p.A331A	NM_018360	NP_060830	Q9NUQ3	TXLNG_HUMAN	gamma-taxilin	463	Potential.				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane				lung(1)	1														0.171875	9.095231	15.632593	11	53	GG		KEEP	---	---	---	---	capture			Silent	SNP	16769612	16769612	17345	23	G	A	A	39	39	TXLNG	A	1	1
NHS	4810	broad.mit.edu	36	X	17653850	17653850	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:17653850A>G	uc004cxx.1	+	c.1640A>G	c.(1639-1641)CAT>CGT	p.H547R	NHS_uc004cxy.1_Missense_Mutation_p.H391R|NHS_uc004cxz.1_Missense_Mutation_p.H370R|NHS_uc004cya.1_Missense_Mutation_p.H270R	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	547						nucleus				ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6	Hepatocellular(33;0.183)													0.268293	18.198449	20.194102	11	30	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17653850	17653850	10811	23	A	G	G	8	8	NHS	G	4	4
PHF16	9767	broad.mit.edu	36	X	46798605	46798605	+	Silent	SNP	C	T	T			TCGA-19-1385-01	TCGA-19-1385-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46798605C>T	uc004dgx.1	+	c.1074C>T	c.(1072-1074)TTC>TTT	p.F358F	PHF16_uc004dgy.1_Silent_p.F358F	NM_001077445	NP_055550	Q92613	JADE3_HUMAN	PHD finger protein 16	358					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.277778	13.26992	14.068065	5	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	46798605	46798605	12250	23	C	T	T	29	29	PHF16	T	2	2
ZNF182	7569	broad.mit.edu	36	X	47720694	47720694	+	Missense_Mutation	SNP	A	T	T			TCGA-19-1385-01	TCGA-19-1385-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47720694A>T	uc004dir.1	-	c.1736T>A	c.(1735-1737)TTC>TAC	p.F579Y	ZNF182_uc004dis.1_Missense_Mutation_p.F560Y|ZNF182_uc004dit.1_Missense_Mutation_p.F579Y	NM_006962	NP_008893	P17025	ZN182_HUMAN	zinc finger protein 21 isoform 1	579	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3														0.166667	7.126439	12.849239	9	45	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47720694	47720694	18341	23	A	T	T	9	9	ZNF182	T	4	4
CCNB3	85417	broad.mit.edu	36	X	50054608	50054608	+	Silent	SNP	T	G	G			TCGA-19-1385-01	TCGA-19-1385-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:50054608T>G	uc004dox.2	+	c.210T>G	c.(208-210)TCT>TCG	p.S70S	CCNB3_uc004doy.1_Silent_p.S70S|CCNB3_uc004doz.1_Intron|CCNB3_uc010njq.1_5'UTR	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	70					cell division|meiosis	nucleus				ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)													0.25	9.431807	10.802521	6	18	TT		KEEP	---	---	---	---	capture			Silent	SNP	50054608	50054608	3041	23	T	G	G	54	54	CCNB3	G	4	4
MAGEE1	57692	broad.mit.edu	36	X	75566420	75566420	+	Nonsense_Mutation	SNP	G	T	T			TCGA-19-1385-01	TCGA-19-1385-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:75566420G>T	uc004ecm.1	+	c.1693G>T	c.(1693-1695)GGA>TGA	p.G565*		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	565	MAGE 1.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6														0.25	6.389787	7.302638	4	12	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	75566420	75566420	9568	23	G	T	T	43	43	MAGEE1	T	5	3
TET1	80312	broad.mit.edu	36	10	70003389	70003390	+	Frame_Shift_Ins	INS	-	G	G			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70003389_70003390insG	uc001jok.2	+	c.1288_1289insG	c.(1288-1290)CCTfs	p.P430fs		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	430					DNA demethylation|inner cell mass cell differentiation|oxidation-reduction process|stem cell maintenance	nucleus	iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)	5										280				0.32			16	34				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	70003389	70003390	16296	10	-	G	G	26	26	TET1	G	5	5
C10orf12	26148	broad.mit.edu	36	10	98731313	98731314	+	Frame_Shift_Ins	INS	-	A	A			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98731313_98731314insA	uc001kmv.1	+	c.176_177insA	c.(175-177)ACTfs	p.T59fs	C10orf12_uc009xvg.1_Frame_Shift_Ins_p.T369fs	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	59											0		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)										0.38			22	36				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	98731313	98731314	1624	10	-	A	A	20	20	C10orf12	A	5	5
UBTD1	80019	broad.mit.edu	36	10	99317765	99317770	+	In_Frame_Del	DEL	CCTGCC	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:99317765_99317770delCCTGCC	uc001knv.1	+	c.175_180delCCTGCC	c.(175-180)CCTGCCdel	p.PA59del		NM_024954	NP_079230	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	59_60											0		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		Pancreas(100;169 2668 32720)								0.58			7	5				---	---	---	---	capture_indel			In_Frame_Del	DEL	99317765	99317770	17465	10	CCTGCC	-	-	26	26	UBTD1	-	5	5
NPAT	4863	broad.mit.edu	36	11	107548735	107548735	+	Frame_Shift_Del	DEL	G	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:107548735_107548735delG	uc001pjz.2	-	c.2186_2186delC	c.(2185-2187)TCAfs	p.S729fs	NPAT_uc001pka.2_Frame_Shift_Del_p.S524fs	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	729					regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)						345				0.63			116	69				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	107548735	107548735	10970	11	G	-	-	45	45	NPAT	-	5	5
KCNA4	3739	broad.mit.edu	36	11	29990152	29990153	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:29990152_29990153delTT	uc001msk.1	-	c.649_650delAA	c.(649-651)AATfs	p.N217fs	KCNA4_uc009yjh.1_Frame_Shift_Del_p.N217fs	NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	217						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.37			41	69				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	29990152	29990153	8310	11	TT	-	-	52	52	KCNA4	-	5	5
LRRC43	254050	broad.mit.edu	36	12	121238269	121238269	+	Frame_Shift_Del	DEL	G	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121238269_121238269delG	uc009zxm.1	+	c.591_591delG	c.(589-591)CTGfs	p.L197fs	LRRC43_uc001ubw.2_Frame_Shift_Del_p.L12fs|LRRC43_uc009zxn.1_5'Flank|LRRC43_uc009zxl.1_Non-coding_Transcript	NM_001098519	NP_001091989	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43 isoform 1	197	LRR 3.										0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)										0.47			73	83				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	121238269	121238269	9376	12	G	-	-	46	46	LRRC43	-	5	5
NR2C1	7181	broad.mit.edu	36	12	93946323	93946324	+	Frame_Shift_Ins	INS	-	G	G			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:93946323_93946324insG	uc001tdm.2	-	c.1501_1502insC	c.(1501-1503)TACfs	p.Y501fs		NM_003297	NP_003288	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	501					regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1														0.34			18	35				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	93946323	93946324	11027	12	-	G	G	57	57	NR2C1	G	5	5
UPF3A	65110	broad.mit.edu	36	13	114088448	114088463	+	Frame_Shift_Del	DEL	CAGAAGGTTCGGGGAC	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:114088448_114088463delCAGAAGGTTCGGGGAC	uc001vup.1	+	c.1385_1400delCAGAAGGTTCGGGGAC	c.(1384-1401)GCAGAAGGTTCGGGGACTfs	p.A462fs	UPF3A_uc001vuq.1_Frame_Shift_Del_p.A429fs|UPF3A_uc001vur.1_Non-coding_Transcript|UPF3A_uc001vus.1_Non-coding_Transcript|UPF3A_uc001vut.1_Frame_Shift_Del_p.A261fs|UPF3A_uc001vuu.1_Frame_Shift_Del_p.Q116fs	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	462_467					mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)										0.35			34	64				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	114088448	114088463	17565	13	CAGAAGGTTCGGGGAC	-	-	25	25	UPF3A	-	5	5
CDC42BPB	9578	broad.mit.edu	36	14	102517068	102517073	+	In_Frame_Del	DEL	TCTTCA	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:102517068_102517073delTCTTCA	uc001ymi.1	-	c.930_935delTGAAGA	c.(928-936)TCTGAAGAA>TCA	p.EE311del		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	311_312	Protein kinase.				actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction|protein phosphorylation	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|lung(2)|ovary(1)|breast(1)|skin(1)	8		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)						1085				0.78			97	28				---	---	---	---	capture_indel			In_Frame_Del	DEL	102517068	102517073	3201	14	TCTTCA	-	-	62	62	CDC42BPB	-	5	5
SLC5A11	115584	broad.mit.edu	36	16	24827795	24827797	+	In_Frame_Del	DEL	AGA	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24827795_24827797delAGA	uc002dmu.1	+	c.1527_1529delAGA	c.(1525-1530)CCAGAT>CCT	p.D510del	SLC5A11_uc002dms.1_In_Frame_Del_p.D446del|SLC5A11_uc002dmt.1_In_Frame_Del_p.D354del|SLC5A11_uc010bxt.1_In_Frame_Del_p.D446del|SLC5A11_uc002dmv.1_In_Frame_Del_p.D133del	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	510	Extracellular (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)										0.55			38	31				---	---	---	---	capture_indel			In_Frame_Del	DEL	24827795	24827797	15160	16	AGA	-	-	7	7	SLC5A11	-	5	5
DDX19B	11269	broad.mit.edu	36	16	68921258	68921259	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68921258_68921259delTG	uc002eyo.1	+	c.809_810delTG	c.(808-810)ATGfs	p.M270fs	DDX19A_uc002eys.1_Intron|DDX19B_uc002eyp.1_Frame_Shift_Del_p.M239fs|DDX19B_uc002eyq.1_Frame_Shift_Del_p.M161fs|DDX19B_uc002eyr.1_Frame_Shift_Del_p.M119fs	NM_007242	NP_001014449	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform	270	Helicase ATP-binding.				mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			kidney(1)	1		Ovarian(137;0.0694)				Esophageal Squamous(26;382 757 1343 9728 15939)								0.32			31	67				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	68921258	68921259	4518	16	TG	-	-	51	51	DDX19B	-	5	5
ZNF287	57336	broad.mit.edu	36	17	16397242	16397244	+	In_Frame_Del	DEL	TTT	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16397242_16397244delTTT	uc002gqi.1	-	c.916_918delAAA	c.(916-918)AAAdel	p.K306del		NM_020653	NP_065704	Q9HBT7	ZN287_HUMAN	zinc finger protein 287	306					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)										0.37			56	95				---	---	---	---	capture_indel			In_Frame_Del	DEL	16397242	16397244	18417	17	TTT	-	-	52	52	ZNF287	-	5	5
DNAH2	146754	broad.mit.edu	36	17	7611953	7611955	+	In_Frame_Del	DEL	CCC	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7611953_7611955delCCC	uc002giu.1	+	c.3686_3688delCCC	c.(3685-3690)GCCCTC>GTC	p.1229_1230AL>V		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1229_1230	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.54			84	73				---	---	---	---	capture_indel			In_Frame_Del	DEL	7611953	7611955	4785	17	CCC	-	-	26	26	DNAH2	-	5	5
ZSWIM4	65249	broad.mit.edu	36	19	13776773	13776774	+	Frame_Shift_Ins	INS	-	CCCT	CCCT			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13776773_13776774insCCCT	uc002mxh.1	+	c.523_524insCCCT	c.(523-525)CGCfs	p.R175fs		NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	175	SWIM-type.						zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)									OREG0025298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.60			90	61				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	13776773	13776774	18847	19	-	CCCT	CCCT	23	23	ZSWIM4	CCCT	5	5
EMR1	2015	broad.mit.edu	36	19	6877520	6877520	+	Frame_Shift_Del	DEL	G	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6877520_6877520delG	uc002mfw.1	+	c.2130_2130delG	c.(2128-2130)ATGfs	p.M710fs	EMR1_uc010dvb.1_Frame_Shift_Del_p.M658fs|EMR1_uc010dvc.1_Frame_Shift_Del_p.M645fs	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	710	Helical; Name=4; (Potential).				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)	3	all_hematologic(4;0.166)													0.30			181	420				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	6877520	6877520	5297	19	G	-	-	46	46	EMR1	-	5	5
GPR89A	653519	broad.mit.edu	36	1	144483066	144483067	+	Frame_Shift_Ins	INS	-	A	A			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:144483066_144483067insA	uc001eot.2	-	c.930_931insT	c.(928-933)TTTGATfs	p.F310fs	GPR89A_uc001eop.2_Frame_Shift_Ins_p.F8fs|GPR89A_uc001eoq.2_Non-coding_Transcript|GPR89A_uc001eor.2_Frame_Shift_Ins_p.F234fs|GPR89A_uc001eos.2_Frame_Shift_Ins_p.F190fs	NM_001097612	NP_001091082	B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89A isoform 1	310_311					intracellular pH reduction|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein transport	Golgi cisterna membrane|Golgi-associated vesicle membrane|integral to membrane	signal transducer activity|voltage-gated anion channel activity				0	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	144483066	144483067	6993	1	-	A	A	29	29	GPR89A	A	5	5
EDEM1	9695	broad.mit.edu	36	3	5221751	5221751	+	Splice_Site_Del	DEL	G	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:5221751_5221751delG	uc003bqi.1	+	c.e6_splice_site			EDEM1_uc003bqh.1_Splice_Site_Del	NM_014674	NP_055489			ER degradation enhancer, mannosidase alpha-like						ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			ovary(2)|breast(1)	3				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)										0.76			272	87				---	---	---	---	capture_indel			Splice_Site_Del	DEL	5221751	5221751	5098	3	G	-	-	35	35	EDEM1	-	5	5
C5orf54	63920	broad.mit.edu	36	5	159754981	159754988	+	Frame_Shift_Del	DEL	AACACACA	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:159754981_159754988delAACACACA	uc003lye.1	-	c.88_95delTGTGTGTT	c.(88-96)TGTGTGTTGfs	p.C30fs	C5orf54_uc003lyf.1_Frame_Shift_Del_p.C30fs|C5orf54_uc010jis.1_Frame_Shift_Del_p.C30fs	NM_022090	NP_071373	Q8IZ13	CE054_HUMAN	transposon-derived Buster3 transposase-like	30_32										pancreas(1)	1														0.34			61	121				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	159754981	159754988	2410	5	AACACACA	-	-	5	5	C5orf54	-	5	5
AIM1	202	broad.mit.edu	36	6	107074737	107074747	+	Frame_Shift_Del	DEL	AACTTGTCACA	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:107074737_107074747delAACTTGTCACA	uc003prh.1	+	c.1737_1747delAACTTGTCACA	c.(1735-1749)CCAACTTGTCACAGTfs	p.P579fs		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	579_583							sugar binding			breast(4)|ovary(2)|large_intestine(1)	7	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)					p.P579fs(CW2-Tumor)	659				0.31			48	107				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	107074737	107074747	433	6	AACTTGTCACA	-	-	5	5	AIM1	-	5	5
FLNC	2318	broad.mit.edu	36	7	128258087	128258093	+	Frame_Shift_Del	DEL	GGCAAGC	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128258087_128258093delGGCAAGC	uc003vnz.2	+	c.160_166delGGCAAGC	c.(160-168)GGCAAGCGCfs	p.G54fs	FLNC_uc003voa.2_Frame_Shift_Del_p.G54fs	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	54_56	CH 1.|Actin-binding.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)	10										892				0.73			11	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	128258087	128258093	6177	7	GGCAAGC	-	-	43	43	FLNC	-	5	5
ZKSCAN1	7586	broad.mit.edu	36	7	99469432	99469433	+	Frame_Shift_Ins	INS	-	TCACA	TCACA			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99469432_99469433insTCACA	uc003usk.1	+	c.1368_1369insTCACA	c.(1366-1371)TCTGGAfs	p.S456fs	ZKSCAN1_uc003usl.1_Frame_Shift_Ins_p.S420fs|ZKSCAN1_uc003usm.1_Frame_Shift_Ins_p.S243fs	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36	456_457					regulation of transcription, DNA-dependent|viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)											0.34			17	33				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	99469432	99469433	18277	7	-	TCACA	TCACA	55	55	ZKSCAN1	TCACA	5	5
AP3M2	10947	broad.mit.edu	36	8	42131437	42131452	+	Frame_Shift_Del	DEL	CCGTTCTGTTTGTGAT	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42131437_42131452delCCGTTCTGTTTGTGAT	uc003xoo.1	+	c.75_90delCCGTTCTGTTTGTGAT	c.(73-90)AGCCGTTCTGTTTGTGATfs	p.S25fs	AP3M2_uc003xop.1_Frame_Shift_Del_p.S25fs|AP3M2_uc010lxe.1_Non-coding_Transcript|AP3M2_uc003xoq.1_5'UTR|AP3M2_uc003xor.1_Frame_Shift_Del_p.S25fs	NM_006803	NP_006794	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	25_30					intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)											0.64			37	21				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	42131437	42131452	758	8	CCGTTCTGTTTGTGAT	-	-	26	26	AP3M2	-	5	5
SH2D3C	10044	broad.mit.edu	36	9	129547116	129547116	+	Frame_Shift_Del	DEL	G	-	-			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:129547116_129547116delG	uc004bsc.1	-	c.1348_1348delC	c.(1348-1350)CAGfs	p.Q450fs	SH2D3C_uc010mxo.1_Frame_Shift_Del_p.Q290fs|SH2D3C_uc004bry.1_Frame_Shift_Del_p.Q292fs|SH2D3C_uc004brz.2_Frame_Shift_Del_p.Q89fs|SH2D3C_uc004bsb.1_Frame_Shift_Del_p.Q382fs|SH2D3C_uc004bsa.1_Frame_Shift_Del_p.Q293fs	NM_170600	NP_733745	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C isoform a	450					JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	129547116	129547116	14725	9	G	-	-	47	47	SH2D3C	-	5	5
GBGT1	26301	broad.mit.edu	36	9	135019270	135019271	+	Frame_Shift_Ins	INS	-	GG	GG			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135019270_135019271insGG	uc004ccw.1	-	c.558_559insCC	c.(556-561)ACCATCfs	p.T186fs	GBGT1_uc004ccx.1_Frame_Shift_Ins_p.T139fs|GBGT1_uc010nab.1_3'UTR|GBGT1_uc004ccy.1_3'UTR|GBGT1_uc010nac.1_Frame_Shift_Ins_p.T50fs	NM_021996	NP_068836	Q8N5D6	GBGT1_HUMAN	globoside	186_187	Lumenal (Potential).				carbohydrate metabolic process|glycolipid biosynthetic process	Golgi membrane|integral to membrane	metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)										0.36			10	18				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	135019270	135019271	6538	9	-	GG	GG	51	51	GBGT1	GG	5	5
IL1RAPL2	26280	broad.mit.edu	36	X	104365300	104365301	+	In_Frame_Ins	INS	-	AGT	AGT			TCGA-19-1385-01	TCGA-19-1385-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:104365300_104365301insAGT	uc004elz.1	+	c.499_500insAGT	c.(499-501)GAC>GAGTAC	p.167_167D>EY		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	167	Ig-like C2-type 2.|Extracellular (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3														0.30			24	55				---	---	---	---	capture_indel			In_Frame_Ins	INS	104365300	104365301	7963	23	-	AGT	AGT	45	45	IL1RAPL2	AGT	5	5
