Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
SFXN3	81855	broad.mit.edu	37	10	102798400	102798400	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102798400C>T	uc010qpx.1	+	c.796C>T	c.(796-798)CGC>TGC	p.R266C	SFXN3_uc001ksp.2_Missense_Mutation_p.R262C|SFXN3_uc001ksq.2_Missense_Mutation_p.R262C	NM_030971	NP_112233	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	262					iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)								OREG0020454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.234043	23.7978	26.774898	11	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102798400	102798400	14687	10	C	T	T	T	351	27	SFXN3	1	1
PDCD11	22984	broad.mit.edu	37	10	105178380	105178380	+	Missense_Mutation	SNP	G	A	A	rs61751510		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:105178380G>A	uc001kwy.1	+	c.2095G>A	c.(2095-2097)GAG>AAG	p.E699K		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	699	S1 motif 7.				mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)						545				0.111111	3.270998	8.66492	4	32	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	105178380	105178380	12038	10	G	A	A	A	481	37	PDCD11	1	1
NRAP	4892	broad.mit.edu	37	10	115389448	115389448	+	Missense_Mutation	SNP	C	T	T	rs2286734	byFrequency	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115389448C>T	uc001lal.3	-	c.1939G>A	c.(1939-1941)GCC>ACC	p.A647T	NRAP_uc009xyb.2_5'Flank|NRAP_uc001laj.2_Missense_Mutation_p.A647T|NRAP_uc001lak.2_Missense_Mutation_p.A612T	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	647	Nebulin 15.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)	9		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)										0.183099	27.337638	34.027199	13	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115389448	115389448	11043	10	C	T	T	T	351	27	NRAP	1	1
DCLRE1A	9937	broad.mit.edu	37	10	115609761	115609761	+	Missense_Mutation	SNP	C	T	T	rs34407062		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115609761C>T	uc001law.2	-	c.1103G>A	c.(1102-1104)CGG>CAG	p.R368Q		NM_014881	NP_055696	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	368					cell division|mitosis	nucleus	hydrolase activity			skin(1)	1				Epithelial(162;0.0157)|all cancers(201;0.0171)										0.176471	20.09171	25.084741	9	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115609761	115609761	4465	10	C	T	T	T	299	23	DCLRE1A	1	1
CAMK1D	57118	broad.mit.edu	37	10	12595329	12595329	+	Missense_Mutation	SNP	A	G	G	rs34194224	byFrequency;by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:12595329A>G	uc001ilo.2	+	c.198A>G	c.(196-198)ATA>ATG	p.I66M	CAMK1D_uc001iln.2_Missense_Mutation_p.I66M	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	66	Protein kinase.				protein phosphorylation	calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				GBM - Glioblastoma multiforme(1;3.16e-05)						482				0.2	42.45553	49.150014	16	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12595329	12595329	2714	10	A	G	G	G	189	15	CAMK1D	4	4
SEPHS1	22929	broad.mit.edu	37	10	13375926	13375926	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:13375926C>T	uc001imk.2	-	c.451G>A	c.(451-453)GCA>ACA	p.A151T	SEPHS1_uc001imh.2_Missense_Mutation_p.A75T|SEPHS1_uc010qbs.1_Missense_Mutation_p.A103T|SEPHS1_uc001imi.2_Missense_Mutation_p.A151T|SEPHS1_uc001imj.2_Missense_Mutation_p.A151T|SEPHS1_uc010qbt.1_Missense_Mutation_p.A84T|SEPHS1_uc009xje.2_Missense_Mutation_p.A151T	NM_012247	NP_036379	P49903	SPS1_HUMAN	selenophosphate synthetase 1	151					protein modification process		ATP binding|GTP binding|selenide, water dikinase activity				0														0.190476	9.093121	10.969685	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13375926	13375926	14540	10	C	T	T	T	351	27	SEPHS1	1	1
LRRC27	80313	broad.mit.edu	37	10	134165171	134165171	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:134165171G>A	uc010quw.1	+	c.987G>A	c.(985-987)GCG>GCA	p.A329A	LRRC27_uc001llf.2_Missense_Mutation_p.R361Q|LRRC27_uc010quv.1_Silent_p.A329A|LRRC27_uc001llg.2_Non-coding_Transcript|LRRC27_uc001lli.2_Silent_p.A329A|LRRC27_uc001llj.2_Silent_p.A267A|LRRC27_uc001llk.3_Silent_p.A202A	NM_030626	NP_085129	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27 isoform a	329	Potential.									ovary(1)	1		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)										0.162162	23.157205	31.184805	12	62	KEEP	---	---	---	---	capture		Silent	SNP	134165171	134165171	9356	10	G	A	A	A	481	37	LRRC27	1	1
DCLRE1C	64421	broad.mit.edu	37	10	14976393	14976393	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:14976393C>T	uc001inn.2	-	c.664G>A	c.(664-666)GAA>AAA	p.E222K	DCLRE1C_uc010qbx.1_Missense_Mutation_p.E222K|DCLRE1C_uc001inl.2_Missense_Mutation_p.E102K|DCLRE1C_uc009xji.2_Missense_Mutation_p.E107K|DCLRE1C_uc001inm.2_Missense_Mutation_p.E102K|DCLRE1C_uc001ino.2_Missense_Mutation_p.E107K|DCLRE1C_uc009xjh.2_Non-coding_Transcript|DCLRE1C_uc001inp.2_Missense_Mutation_p.E102K|DCLRE1C_uc001inq.2_Missense_Mutation_p.E102K|DCLRE1C_uc001inr.2_Missense_Mutation_p.E107K|DCLRE1C_uc009xjj.1_Non-coding_Transcript	NM_001033855	NP_001029027	Q96SD1	DCR1C_HUMAN	artemis protein isoform a	222					DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1														0.059801	-21.67756	39.309573	18	283	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	14976393	14976393	4467	10	C	T	T	T	416	32	DCLRE1C	2	2
ITGA8	8516	broad.mit.edu	37	10	15714695	15714695	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15714695C>T	uc001ioc.1	-	c.730G>A	c.(730-732)GAT>AAT	p.D244N	ITGA8_uc010qcb.1_Missense_Mutation_p.D244N	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	244	Extracellular (Potential).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6														0.094595	4.067402	16.283521	7	67	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	15714695	15714695	8186	10	C	T	T	T	390	30	ITGA8	2	2
CUBN	8029	broad.mit.edu	37	10	17113512	17113512	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:17113512G>T	uc001ioo.2	-	c.2538C>A	c.(2536-2538)ATC>ATA	p.I846I		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	846	CUB 4.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)	18					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)					2704				0.09375	1.600617	12.221726	6	58	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	17113512	17113512	4211	10	G	T	T	T	525	41	CUBN	2	2
PLXDC2	84898	broad.mit.edu	37	10	20335869	20335869	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:20335869G>T	uc001iqg.1	+	c.396G>T	c.(394-396)TGG>TGT	p.W132C	PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor	132	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3														0.107692	5.874213	15.799737	7	58	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	20335869	20335869	12544	10	G	T	T	T	559	43	PLXDC2	2	2
GPR158	57512	broad.mit.edu	37	10	25861798	25861798	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25861798G>T	uc001isj.2	+	c.1735G>T	c.(1735-1737)GAC>TAC	p.D579Y		NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	579	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.126984	10.553667	19.106419	8	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25861798	25861798	6938	10	G	T	T	T	533	41	GPR158	2	2
GAD2	2572	broad.mit.edu	37	10	26559611	26559611	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:26559611G>T	uc001isp.2	+	c.1018G>T	c.(1018-1020)GTG>TTG	p.V340L	GAD2_uc001isq.2_Missense_Mutation_p.V340L	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	glutamate decarboxylase 2	340					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)	1					L-Glutamic Acid(DB00142)									0.114286	16.533198	31.924306	12	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26559611	26559611	6431	10	G	T	T	T	520	40	GAD2	1	1
ZNF239	8187	broad.mit.edu	37	10	44053339	44053339	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:44053339A>G	uc001jaw.3	-	c.189T>C	c.(187-189)TAT>TAC	p.Y63Y	ZNF239_uc001jax.3_Silent_p.Y63Y|ZNF239_uc009xmj.2_Silent_p.Y63Y|ZNF239_uc009xmk.2_Silent_p.Y63Y	NM_005674	NP_005665	Q16600	ZN239_HUMAN	zinc finger protein 239	63					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|RNA binding|zinc ion binding				0														0.122449	7.814981	14.655905	6	43	KEEP	---	---	---	---	capture		Silent	SNP	44053339	44053339	18382	10	A	G	G	G	50	4	ZNF239	4	4
RASSF4	83937	broad.mit.edu	37	10	45480383	45480383	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:45480383C>T	uc001jbo.2	+	c.496C>T	c.(496-498)CGG>TGG	p.R166W	RASSF4_uc001jbp.2_Missense_Mutation_p.R197W|RASSF4_uc009xmn.2_Missense_Mutation_p.R96W|RASSF4_uc001jbq.2_Missense_Mutation_p.R63W|RASSF4_uc001jbt.2_Missense_Mutation_p.R123W	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	166					cell cycle|signal transduction		protein binding			large_intestine(1)	1														0.192308	11.863365	14.159291	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45480383	45480383	13549	10	C	T	T	T	295	23	RASSF4	1	1
NET1	10276	broad.mit.edu	37	10	5498572	5498572	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:5498572G>A	uc001iia.2	+	c.1406G>A	c.(1405-1407)CGC>CAC	p.R469H	NET1_uc010qar.1_Missense_Mutation_p.R288H|NET1_uc001iib.2_Missense_Mutation_p.R415H|NET1_uc010qas.1_Missense_Mutation_p.R288H	NM_001047160	NP_001040625	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming gene 1 isoform	469	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	Rho guanyl-nucleotide exchange factor activity			breast(1)	1														0.138614	20.800129	33.53754	14	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5498572	5498572	10737	10	G	A	A	A	494	38	NET1	1	1
TMEM26	219623	broad.mit.edu	37	10	63170221	63170221	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:63170221C>G	uc001jlo.2	-	c.966G>C	c.(964-966)CTG>CTC	p.L322L	TMEM26_uc010qij.1_Non-coding_Transcript|TMEM26_uc001jlp.1_Non-coding_Transcript	NM_178505	NP_848600	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	322						integral to membrane					0	Prostate(12;0.0112)													0.125	15.124	25.015293	9	63	KEEP	---	---	---	---	capture		Silent	SNP	63170221	63170221	16690	10	C	G	G	G	366	29	TMEM26	3	3
MYPN	84665	broad.mit.edu	37	10	69881880	69881880	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:69881880G>A	uc001jnm.3	+	c.685G>A	c.(685-687)GAA>AAA	p.E229K	MYPN_uc001jnl.1_Missense_Mutation_p.E229K|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Missense_Mutation_p.E229K|MYPN_uc001jnp.1_Missense_Mutation_p.E229K|MYPN_uc009xps.2_Missense_Mutation_p.E229K|MYPN_uc009xpt.2_Missense_Mutation_p.E229K|MYPN_uc010qit.1_5'UTR|MYPN_uc010qiu.1_Non-coding_Transcript	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	229	Potential.|Interaction with CARP.					nucleus|sarcomere	actin binding			ovary(3)	3														0.15625	9.454816	13.063822	5	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69881880	69881880	10493	10	G	A	A	A	533	41	MYPN	2	2
TAF3	83860	broad.mit.edu	37	10	7866437	7866437	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7866437A>T	uc010qbd.1	+	c.323A>T	c.(322-324)CAG>CTG	p.Q108L		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	108					maintenance of protein location in nucleus|regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1														0.101124	8.11001	22.238322	9	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7866437	7866437	16046	10	A	T	T	T	91	7	TAF3	3	3
NRG3	10718	broad.mit.edu	37	10	84498358	84498358	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:84498358C>T	uc001kco.2	+	c.979C>T	c.(979-981)CGT>TGT	p.R327C	NRG3_uc010qlz.1_Missense_Mutation_p.R327C|NRG3_uc001kcp.2_Missense_Mutation_p.R106C|NRG3_uc001kcq.2_5'UTR	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	327	EGF-like.|Extracellular (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity				0				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)										0.0875	4.167482	17.934198	7	73	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	84498358	84498358	11054	10	C	T	T	T	299	23	NRG3	1	1
LARP4B	23185	broad.mit.edu	37	10	875638	875638	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:875638G>C	uc001ifs.1	-	c.898C>G	c.(898-900)CAA>GAA	p.Q300E		NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	300	RRM.						nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3														0.15625	11.454552	15.063207	5	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	875638	875638	8954	10	G	C	C	C	585	45	LARP4B	3	3
OPN4	94233	broad.mit.edu	37	10	88419700	88419700	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:88419700G>T	uc010qmk.1	+	c.882G>T	c.(880-882)TGG>TGT	p.W294C	OPN4_uc001kdp.2_Missense_Mutation_p.W294C|OPN4_uc001kdq.2_Missense_Mutation_p.W283C|OPN4_uc009xsx.1_5'Flank	NM_001030015	NP_001025186	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 2	283	Cytoplasmic (Potential).				phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1														0.25	7.619564	8.30108	3	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88419700	88419700	11288	10	G	T	T	T	546	42	OPN4	2	2
PDLIM1	9124	broad.mit.edu	37	10	97031411	97031411	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:97031411T>C	uc001kkh.2	-	c.227A>G	c.(226-228)AAC>AGC	p.N76S	PDLIM1_uc001kki.2_Missense_Mutation_p.N76S|PDLIM1_uc009xuv.2_Missense_Mutation_p.N76S|PDLIM1_uc001kkj.1_Missense_Mutation_p.N76S	NM_020992	NP_066272	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	76	PDZ.				response to oxidative stress	cytoplasm|cytoskeleton	zinc ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)										0.187845	74.884299	91.494462	34	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97031411	97031411	12100	10	T	C	C	C	780	60	PDLIM1	4	4
CASP5	838	broad.mit.edu	37	11	104879560	104879560	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:104879560G>A	uc010ruz.1	-	c.194C>T	c.(193-195)ACG>ATG	p.T65M	CASP5_uc010rva.1_Missense_Mutation_p.T52M|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_001136112	NP_001129584	P51878	CASP5_HUMAN	caspase 5 isoform f precursor	52					apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)										0.112903	6.305393	15.467919	7	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104879560	104879560	2793	11	G	A	A	A	520	40	CASP5	1	1
NPAT	4863	broad.mit.edu	37	11	108047778	108047778	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108047778A>G	uc001pjz.3	-	c.946T>C	c.(946-948)TTG>CTG	p.L316L	NPAT_uc001pka.2_Silent_p.L111L	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	316	Mediates transcriptional activation.|Interaction with MIZF.				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				0.193548	14.632966	17.348935	6	25	KEEP	---	---	---	---	capture		Silent	SNP	108047778	108047778	10970	11	A	G	G	G	50	4	NPAT	4	4
CEP164	22897	broad.mit.edu	37	11	117232638	117232638	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117232638C>A	uc001prc.2	+	c.481C>A	c.(481-483)CTT>ATT	p.L161I	CEP164_uc001prb.2_Missense_Mutation_p.L161I|CEP164_uc010rxk.1_Missense_Mutation_p.L161I|CEP164_uc001prf.2_Non-coding_Transcript|CEP164_uc009yzp.1_5'Flank	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	161	Interaction with ATRIP.				cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)										0.078431	-1.572573	16.947266	8	94	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	117232638	117232638	3382	11	C	A	A	A	416	32	CEP164	2	2
PHLDB1	23187	broad.mit.edu	37	11	118516232	118516232	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118516232C>T	uc001ptr.1	+	c.3280C>T	c.(3280-3282)CAC>TAC	p.H1094Y	PHLDB1_uc001pts.2_Missense_Mutation_p.H1094Y|PHLDB1_uc001ptt.2_Missense_Mutation_p.H1047Y|PHLDB1_uc001ptu.1_Non-coding_Transcript|PHLDB1_uc001ptv.1_Missense_Mutation_p.H909Y|PHLDB1_uc001ptw.1_Missense_Mutation_p.H449Y|PHLDB1_uc009zai.1_Missense_Mutation_p.H130Y|PHLDB1_uc001ptx.1_Missense_Mutation_p.H130Y|PHLDB1_uc010ryi.1_Missense_Mutation_p.H237Y	NM_015157	NP_055972	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B,	1094											0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)										0.259259	18.812399	20.229699	7	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118516232	118516232	12275	11	C	T	T	T	273	21	PHLDB1	2	2
SLC37A4	2542	broad.mit.edu	37	11	118895962	118895962	+	Silent	SNP	G	A	A	rs61730035		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118895962G>A	uc010ryr.1	-	c.1128C>T	c.(1126-1128)AAC>AAT	p.N376N	SLC37A4_uc009zam.2_Non-coding_Transcript|SLC37A4_uc009zan.2_Non-coding_Transcript|SLC37A4_uc010rys.1_Silent_p.N354N|SLC37A4_uc010ryt.1_Silent_p.N281N|SLC37A4_uc001pus.2_Silent_p.N354N	NM_001164278	NP_001157750	O43826	G6PT1_HUMAN	solute carrier family 37 (glucose-6-phosphate	354					glucose homeostasis|glucose metabolic process	endoplasmic reticulum membrane|integral to endoplasmic reticulum membrane|integral to membrane	glucose-6-phosphate transmembrane transporter activity|glucose-6-phosphate transmembrane transporter activity	p.N375N(1)		large_intestine(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)										0.2	10.46116	12.553748	5	20	KEEP	---	---	---	---	capture		Silent	SNP	118895962	118895962	15097	11	G	A	A	A	516	40	SLC37A4	1	1
PDZD3	79849	broad.mit.edu	37	11	119059200	119059200	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:119059200G>A	uc001pvz.2	+	c.999G>A	c.(997-999)GGG>GGA	p.G333G	PDZD3_uc001pvy.2_Silent_p.G319G|PDZD3_uc010rzd.1_Silent_p.G320G|PDZD3_uc001pwa.2_Silent_p.G29G|PDZD3_uc001pwb.2_Silent_p.G399G	NM_024791	NP_079067	Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	399	PDZ 3.				cGMP-mediated signaling|ion transport|negative regulation of cGMP biosynthetic process|receptor guanylyl cyclase signaling pathway|response to toxin|water transport	apical part of cell|brush border|cytosol|membrane fraction|subapical complex	guanylate cyclase inhibitor activity|ion channel inhibitor activity|protein C-terminus binding			breast(1)	1	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)										0.307692	10.395024	10.823677	4	9	KEEP	---	---	---	---	capture		Silent	SNP	119059200	119059200	12123	11	G	A	A	A	535	42	PDZD3	2	2
CBL	867	broad.mit.edu	37	11	119169085	119169085	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:119169085G>A	uc001pwe.2	+	c.2269G>A	c.(2269-2271)GCA>ACA	p.A757T		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	757	Interaction with CD2AP.|Asp/Glu-rich (acidic).				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(133)|lung(9)|central_nervous_system(2)|ovary(1)	145		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)					p.A757T(MG63-Tumor)|p.A757T(CALU1-Tumor)|p.A757T(VMRCLCP-Tumor)|p.A757T(NCIH1792-Tumor)|p.A757T(CAL51-Tumor)	309				0.237288	35.031476	38.74466	14	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119169085	119169085	2819	11	G	A	A	A	494	38	CBL	1	1
GRAMD1B	57476	broad.mit.edu	37	11	123480927	123480927	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123480927G>A	uc001pyw.2	+	c.1392G>A	c.(1390-1392)GAG>GAA	p.E464E	GRAMD1B_uc001pyx.2_Silent_p.E457E|GRAMD1B_uc010rzw.1_Silent_p.E417E|GRAMD1B_uc010rzx.1_Silent_p.E417E|GRAMD1B_uc001pyy.2_Silent_p.E148E	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	457						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)						1503				0.092105	4.272838	16.999361	7	69	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	123480927	123480927	7024	11	G	A	A	A	425	33	GRAMD1B	2	2
GRAMD1B	57476	broad.mit.edu	37	11	123480977	123480977	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123480977A>T	uc001pyw.2	+	c.1442A>T	c.(1441-1443)TAC>TTC	p.Y481F	GRAMD1B_uc001pyx.2_Missense_Mutation_p.Y474F|GRAMD1B_uc010rzw.1_Missense_Mutation_p.Y434F|GRAMD1B_uc010rzx.1_Missense_Mutation_p.Y434F|GRAMD1B_uc001pyy.2_Missense_Mutation_p.Y165F	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	474						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)						1503				0.078261	-0.000549	20.891603	9	106	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	123480977	123480977	7024	11	A	T	T	T	182	14	GRAMD1B	3	3
MICALCL	84953	broad.mit.edu	37	11	12379966	12379966	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12379966C>T	uc001mkg.1	+	c.2028C>T	c.(2026-2028)GCC>GCT	p.A676A		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	676					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.144404	70.06265	103.78	40	237	KEEP	---	---	---	---	capture		Silent	SNP	12379966	12379966	9962	11	C	T	T	T	288	23	MICALCL	1	1
OR4D5	219875	broad.mit.edu	37	11	123810376	123810376	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123810376C>G	uc001pzk.1	+	c.53C>G	c.(52-54)TCT>TGT	p.S18C		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)										0.156627	25.818234	35.160443	13	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123810376	123810376	11464	11	C	G	G	G	416	32	OR4D5	3	3
ARHGAP32	9743	broad.mit.edu	37	11	128839217	128839217	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128839217C>T	uc009zcp.2	-	c.5849G>A	c.(5848-5850)CGA>CAA	p.R1950Q	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Missense_Mutation_p.R909Q|ARHGAP32_uc001qez.2_Missense_Mutation_p.R1601Q	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1950	Interaction with FYN.				cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5														0.12	9.016989	19.671897	9	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128839217	128839217	893	11	C	T	T	T	403	31	ARHGAP32	1	1
APLP2	334	broad.mit.edu	37	11	129980466	129980466	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:129980466G>T	uc010sby.1	+	c.313G>T	c.(313-315)GAG>TAG	p.E105*	APLP2_uc001qfp.2_Nonsense_Mutation_p.E105*|APLP2_uc001qfq.2_Nonsense_Mutation_p.E105*|APLP2_uc010sbz.1_Intron|APLP2_uc001qfr.2_Intron|APLP2_uc001qfs.2_Nonsense_Mutation_p.E105*|APLP2_uc001qfv.2_Nonsense_Mutation_p.E52*	NM_001642	NP_001633	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	105	Extracellular (Potential).				G-protein coupled receptor protein signaling pathway	integral to membrane|nucleus|plasma membrane	DNA binding|identical protein binding|serine-type endopeptidase inhibitor activity			ovary(3)	3	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)										0.0875	1.27104	15.037932	7	73	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	129980466	129980466	790	11	G	T	T	T	533	41	APLP2	5	2
PDHX	8050	broad.mit.edu	37	11	35016541	35016541	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:35016541G>T	uc001mvt.2	+	c.1328G>T	c.(1327-1329)GGG>GTG	p.G443V	PDHX_uc010rep.1_Missense_Mutation_p.G428V|PDHX_uc010req.1_Missense_Mutation_p.G216V	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	443					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)											0.096774	2.800024	17.968852	9	84	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	35016541	35016541	12088	11	G	T	T	T	559	43	PDHX	2	2
ACCSL	390110	broad.mit.edu	37	11	44069884	44069884	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:44069884G>A	uc001mxw.1	+	c.298G>A	c.(298-300)GAC>AAC	p.D100N	ACCSL_uc009ykr.2_5'UTR	NM_001031854	NP_001027025	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase	100							1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups	p.D100N(1)		ovary(5)	5														0.116279	6.347694	12.575453	5	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44069884	44069884	135	11	G	A	A	A	533	41	ACCSL	2	2
ACCSL	390110	broad.mit.edu	37	11	44080126	44080126	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:44080126C>T	uc001mxw.1	+	c.1501C>T	c.(1501-1503)CGG>TGG	p.R501W	ACCSL_uc009ykr.2_Missense_Mutation_p.R320W	NM_001031854	NP_001027025	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase	501							1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5														0.135135	12.908258	22.45376	10	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44080126	44080126	135	11	C	T	T	T	243	19	ACCSL	1	1
KIAA0652	9776	broad.mit.edu	37	11	46685569	46685569	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46685569C>T	uc001nda.2	+	c.812C>T	c.(811-813)GCA>GTA	p.A271V	KIAA0652_uc009yld.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_014741	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 2	262					autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)										0.144144	17.307379	30.9095	16	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46685569	46685569	8495	11	C	T	T	T	313	25	KIAA0652	2	2
PTPRJ	5795	broad.mit.edu	37	11	48186000	48186000	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48186000A>T	uc001ngp.3	+	c.3788A>T	c.(3787-3789)AAC>ATC	p.N1263I		NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	1263	Tyrosine-protein phosphatase.|Cytoplasmic (Potential).				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8														0.077586	-1.906875	19.258733	9	107	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	48186000	48186000	13261	11	A	T	T	T	26	2	PTPRJ	3	3
OR4S1	256148	broad.mit.edu	37	11	48328098	48328098	+	Silent	SNP	T	C	C	rs117933983	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48328098T>C	uc010rhu.1	+	c.324T>C	c.(322-324)ACT>ACC	p.T108T		NM_001004725	NP_001004725	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.152542	16.245913	23.055772	9	50	KEEP	---	---	---	---	capture		Silent	SNP	48328098	48328098	11492	11	T	C	C	C	704	55	OR4S1	4	4
FOLH1	2346	broad.mit.edu	37	11	49168410	49168410	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:49168410G>T	uc001ngy.2	-	c.2151C>A	c.(2149-2151)AGC>AGA	p.S717R	FOLH1_uc001ngx.2_Missense_Mutation_p.A117E|FOLH1_uc001ngz.2_Missense_Mutation_p.S686R|FOLH1_uc009yly.2_Missense_Mutation_p.S702R|FOLH1_uc009ylz.2_Missense_Mutation_p.S671R|FOLH1_uc009yma.2_Missense_Mutation_p.S409R	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1	717	Extracellular (Probable).				proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)	1					Capromab(DB00089)|L-Glutamic Acid(DB00142)									0.126984	11.053309	19.606164	8	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49168410	49168410	6221	11	G	T	T	T	594	46	FOLH1	2	2
OR51A4	401666	broad.mit.edu	37	11	4968172	4968172	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4968172T>C	uc010qys.1	-	c.159A>G	c.(157-159)ACA>ACG	p.T53T		NM_001005329	NP_001005329	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A,	53	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.078652	-3.293964	29.009449	14	164	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	4968172	4968172	11497	11	T	C	C	C	704	55	OR51A4	4	4
SPRYD5	84767	broad.mit.edu	37	11	55658706	55658706	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55658706C>T	uc010rip.1	+	c.957C>T	c.(955-957)CCC>CCT	p.P319P	SPRYD5_uc010riq.1_Silent_p.P176P	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	319	B30.2/SPRY.					intracellular	zinc ion binding				0		all_epithelial(135;0.226)												0.178082	56.279575	70.513205	26	120	KEEP	---	---	---	---	capture		Silent	SNP	55658706	55658706	15625	11	C	T	T	T	288	23	SPRYD5	1	1
OR8K5	219453	broad.mit.edu	37	11	55927704	55927704	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55927704G>A	uc010rja.1	-	c.90C>T	c.(88-90)GTC>GTT	p.V30V		NM_001004058	NP_001004058	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K,	30	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)												0.132653	21.606072	34.447623	13	85	KEEP	---	---	---	---	capture		Silent	SNP	55927704	55927704	11656	11	G	A	A	A	418	33	OR8K5	2	2
OR5R1	219479	broad.mit.edu	37	11	56185153	56185153	+	Missense_Mutation	SNP	C	T	T	rs61901985	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56185153C>T	uc010rji.1	-	c.556G>A	c.(556-558)GCT>ACT	p.A186T		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.136364	17.936002	29.207491	12	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56185153	56185153	11590	11	C	T	T	T	364	28	OR5R1	2	2
OR5R1	219479	broad.mit.edu	37	11	56185651	56185651	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56185651G>T	uc010rji.1	-	c.58C>A	c.(58-60)CGG>AGG	p.R20R		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.075862	-2.083168	24.650715	11	134	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	56185651	56185651	11590	11	G	T	T	T	506	39	OR5R1	1	1
TNKS1BP1	85456	broad.mit.edu	37	11	57077132	57077132	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57077132C>T	uc001njr.2	-	c.3053G>A	c.(3052-3054)CGG>CAG	p.R1018Q	TNKS1BP1_uc001njs.2_Missense_Mutation_p.R1018Q|TNKS1BP1_uc009ymd.1_Missense_Mutation_p.R469Q	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	1018	Gly-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)												0.145455	14.970404	21.613442	8	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57077132	57077132	16861	11	C	T	T	T	299	23	TNKS1BP1	1	1
SLC43A3	29015	broad.mit.edu	37	11	57175355	57175355	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57175355G>A	uc010rjr.1	-	c.1425C>T	c.(1423-1425)TTC>TTT	p.F475F	PRG2_uc001nke.2_Intron|SLC43A3_uc001nkg.2_Silent_p.F462F|SLC43A3_uc001nkh.2_Silent_p.F462F|SLC43A3_uc009yme.2_Silent_p.F462F|SLC43A3_uc001nki.2_Silent_p.F462F	NM_199329	NP_955361	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	462	Helical; (Potential).				transmembrane transport	integral to membrane				central_nervous_system(1)	1														0.078652	-0.749063	15.398597	7	82	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	57175355	57175355	15131	11	G	A	A	A	581	45	SLC43A3	2	2
PYGM	5837	broad.mit.edu	37	11	64527201	64527201	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64527201G>A	uc001oax.3	-	c.170C>T	c.(169-171)GCC>GTC	p.A57V	PYGM_uc001oay.3_Missense_Mutation_p.A57V	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	57					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)									0.102041	3.742699	11.476326	5	44	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	64527201	64527201	13320	11	G	A	A	A	546	42	PYGM	2	2
ALDH3B2	222	broad.mit.edu	37	11	67434391	67434391	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:67434391G>A	uc001omr.2	-	c.16C>T	c.(16-18)CGG>TGG	p.R6W	ALDH3B2_uc001oms.2_Missense_Mutation_p.R6W|ALDH3B2_uc009ysa.1_Missense_Mutation_p.R6W	NM_000695	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3B2	6					alcohol metabolic process|cellular aldehyde metabolic process|lipid metabolic process|oxidation-reduction process		3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase			lung(1)|kidney(1)	2					NADH(DB00157)									0.173077	18.654247	23.89347	9	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67434391	67434391	503	11	G	A	A	A	519	40	ALDH3B2	1	1
TCIRG1	10312	broad.mit.edu	37	11	67815003	67815003	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:67815003G>A	uc001one.2	+	c.1269G>A	c.(1267-1269)GCG>GCA	p.A423A	TCIRG1_uc001ong.2_Silent_p.A207A|TCIRG1_uc001onh.2_Silent_p.A125A|TCIRG1_uc001oni.2_5'UTR|TCIRG1_uc009ysd.2_5'Flank	NM_006019	NP_006010	Q13488	VPP3_HUMAN	T-cell, immune regulator 1 isoform a	423	Lumenal (Potential).				ATP hydrolysis coupled proton transport|cellular defense response|cellular iron ion homeostasis|insulin receptor signaling pathway|positive regulation of cell proliferation|transferrin transport	apical plasma membrane|endosome membrane|integral to plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity			ovary(1)	1														0.5	9.826143	9.826143	3	3	KEEP	---	---	---	---	capture		Silent	SNP	67815003	67815003	16229	11	G	A	A	A	496	39	TCIRG1	1	1
DNAJB13	374407	broad.mit.edu	37	11	73675980	73675980	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:73675980G>A	uc001ouo.2	+	c.392G>A	c.(391-393)CGA>CAA	p.R131Q		NM_153614	NP_705842	P59910	DJB13_HUMAN	testis spermatogenesis apoptosis-related protein	131					apoptosis|protein folding|spermatogenesis		heat shock protein binding|unfolded protein binding				0	Breast(11;7.42e-05)											OREG0021218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.083333	0.070184	14.883989	7	77	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	73675980	73675980	4801	11	G	A	A	A	481	37	DNAJB13	1	1
SLCO2B1	11309	broad.mit.edu	37	11	74907574	74907574	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:74907574G>A	uc001owb.2	+	c.1449G>A	c.(1447-1449)CTG>CTA	p.L483L	SLCO2B1_uc010rrq.1_Silent_p.L228L|SLCO2B1_uc010rrr.1_Silent_p.L339L|SLCO2B1_uc010rrs.1_Silent_p.L367L|SLCO2B1_uc001owc.2_Silent_p.L256L|SLCO2B1_uc001owd.2_Silent_p.L461L	NM_007256	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family,	483	Extracellular (Potential).|Kazal-like.				sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)									0.151515	8.353004	12.191738	5	28	KEEP	---	---	---	---	capture		Silent	SNP	74907574	74907574	15224	11	G	A	A	A	600	47	SLCO2B1	2	2
PRKRIR	5612	broad.mit.edu	37	11	76062159	76062159	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:76062159C>A	uc001oxh.1	-	c.2035G>T	c.(2035-2037)GCA>TCA	p.A679S	PRKRIR_uc010rrz.1_Missense_Mutation_p.A504S	NM_004705	NP_004696	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double	679					negative regulation of cell proliferation|response to stress|signal transduction		DNA binding|metal ion binding|protein dimerization activity			ovary(2)|pancreas(1)	3														0.089744	2.561959	15.81639	7	71	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	76062159	76062159	12969	11	C	A	A	A	325	25	PRKRIR	2	2
CCDC81	60494	broad.mit.edu	37	11	86133743	86133743	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:86133743C>T	uc001pbx.1	+	c.1945C>T	c.(1945-1947)CGG>TGG	p.R649W	CCDC81_uc001pbw.1_Missense_Mutation_p.R559W|CCDC81_uc010rtq.1_Missense_Mutation_p.R432W|CCDC81_uc001pby.1_Missense_Mutation_p.R384W	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	649											0		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)												0.096774	4.410917	14.50617	6	56	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	86133743	86133743	2979	11	C	T	T	T	295	23	CCDC81	1	1
GRM5	2915	broad.mit.edu	37	11	88780384	88780384	+	Silent	SNP	T	G	G	rs76850190		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:88780384T>G	uc001pcq.2	-	c.657A>C	c.(655-657)ACA>ACC	p.T219T	GRM5_uc009yvm.2_Silent_p.T219T|GRM5_uc009yvn.1_Silent_p.T219T	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	219	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(1)	5		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)									0.173913	14.769543	19.389254	8	38	KEEP	---	---	---	---	capture		Silent	SNP	88780384	88780384	7079	11	T	G	G	G	704	55	GRM5	4	4
MTNR1B	4544	broad.mit.edu	37	11	92714636	92714636	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92714636G>A	uc001pdk.1	+	c.247G>A	c.(247-249)GCA>ACA	p.A83T		NM_005959	NP_005950	P49286	MTR1B_HUMAN	melatonin receptor 1B	83	Helical; Name=2; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|glucose homeostasis|regulation of insulin secretion|synaptic transmission	integral to plasma membrane	melatonin receptor activity			central_nervous_system(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Ramelteon(DB00980)									0.080769	-5.535439	40.992874	21	239	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	92714636	92714636	10345	11	G	A	A	A	546	42	MTNR1B	2	2
HEPHL1	341208	broad.mit.edu	37	11	93822102	93822102	+	Silent	SNP	C	T	T	rs116956001	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:93822102C>T	uc001pep.2	+	c.2262C>T	c.(2260-2262)TTC>TTT	p.F754F		NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	754	Plastocyanin-like 5.|Extracellular (Potential).				copper ion transport|oxidation-reduction process	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)												0.101852	7.589291	24.627731	11	97	KEEP	---	---	---	---	capture		Silent	SNP	93822102	93822102	7338	11	C	T	T	T	402	31	HEPHL1	1	1
CWC15	51503	broad.mit.edu	37	11	94704179	94704179	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94704179G>A	uc001pfd.3	-	c.295C>T	c.(295-297)CCT>TCT	p.P99S	CWC15_uc009ywl.1_3'UTR|KDM4D_uc001pfe.2_5'Flank	NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog	99					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												0.07767	-4.574689	33.068585	16	190	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	94704179	94704179	4227	11	G	A	A	A	533	41	CWC15	2	2
GIT2	9815	broad.mit.edu	37	12	110376292	110376292	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:110376292G>A	uc001tps.2	-	c.1896C>T	c.(1894-1896)GCC>GCT	p.A632A	TCHP_uc001tpo.1_Intron|GIT2_uc001tpr.2_Silent_p.A172A|GIT2_uc001tpq.2_Silent_p.A602A|GIT2_uc001tpv.2_Silent_p.A554A|GIT2_uc001tpu.2_Silent_p.A552A|GIT2_uc001tpt.2_Silent_p.A504A|GIT2_uc010sxu.1_Silent_p.A540A	NM_057169	NP_476510	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting	632					regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1														0.11	12.009245	27.011413	11	89	KEEP	---	---	---	---	capture		Silent	SNP	110376292	110376292	6665	12	G	A	A	A	548	43	GIT2	2	2
TAOK3	51347	broad.mit.edu	37	12	118627674	118627674	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:118627674G>A	uc001twx.2	-	c.1267C>T	c.(1267-1269)CAG>TAG	p.Q423*	TAOK3_uc001twv.2_5'UTR|TAOK3_uc001tww.2_Nonsense_Mutation_p.Q253*|TAOK3_uc001twy.3_Nonsense_Mutation_p.Q423*	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	423					MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)									500				0.125	10.818933	20.727403	9	63	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	118627674	118627674	16070	12	G	A	A	A	585	45	TAOK3	5	2
SIRT4	23409	broad.mit.edu	37	12	120750374	120750374	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120750374G>A	uc001tyc.2	+	c.613G>A	c.(613-615)GTC>ATC	p.V205I		NM_012240	NP_036372	Q9Y6E7	SIRT4_HUMAN	sirtuin 4	205	Deacetylase sirtuin-type.				chromatin silencing|negative regulation of insulin secretion|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.173913	15.408408	19.996776	8	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120750374	120750374	14835	12	G	A	A	A	520	40	SIRT4	1	1
PIWIL1	9271	broad.mit.edu	37	12	130851740	130851740	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:130851740G>A	uc001uik.2	+	c.2258G>A	c.(2257-2259)GGA>GAA	p.G753E	PIWIL1_uc001uij.1_Missense_Mutation_p.G753E	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	753	Piwi.				gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)										0.088235	3.796357	21.279055	9	93	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	130851740	130851740	12381	12	G	A	A	A	533	41	PIWIL1	2	2
SFRS8	6433	broad.mit.edu	37	12	132199433	132199434	+	Missense_Mutation	DNP	CT	AC	AC			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:132199433_132199434CT>AC	uc010tbn.1	+	c.455_456CT>AC	c.(454-456)ACT>AAC	p.T152N	SFRS8_uc001uja.1_Missense_Mutation_p.T152N|SFRS8_uc001ujb.1_5'UTR|SFRS8_uc001uiz.1_Missense_Mutation_p.T26N	NM_004592	NP_004583	Q12872	SFSWA_HUMAN	splicing factor, arginine/serine-rich 8	152					mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)										0.192308	10.670833	12.961438	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	132199433	132199434	14673	12	CT	AC	AC	AC	260	20	SFRS8	2	2
C12orf60	144608	broad.mit.edu	37	12	14976375	14976375	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:14976375C>T	uc001rcj.3	+	c.506C>T	c.(505-507)ACA>ATA	p.T169I		NM_175874	NP_787070	Q5U649	CL060_HUMAN	hypothetical protein LOC144608	169										ovary(1)|central_nervous_system(1)	2														0.196429	22.989869	27.801492	11	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14976375	14976375	1747	12	C	T	T	T	221	17	C12orf60	2	2
SLCO1B3	28234	broad.mit.edu	37	12	21032563	21032563	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21032563T>G	uc001rek.2	+	c.1329T>G	c.(1327-1329)GAT>GAG	p.D443E	SLCO1B3_uc001rel.2_Missense_Mutation_p.D443E|SLCO1B3_uc010sil.1_Missense_Mutation_p.D443E|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_Missense_Mutation_p.D268E	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,	443	Extracellular (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)	3	Esophageal squamous(101;0.149)													0.1	5.238653	13.228275	5	45	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	21032563	21032563	15221	12	T	G	G	G	660	51	SLCO1B3	4	4
BCAT1	586	broad.mit.edu	37	12	24995032	24995032	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:24995032C>T	uc010six.1	-	c.837G>A	c.(835-837)TGG>TGA	p.W279*	BCAT1_uc001rgc.2_Nonsense_Mutation_p.W266*|BCAT1_uc001rgd.3_Nonsense_Mutation_p.W267*|BCAT1_uc010siy.1_Nonsense_Mutation_p.W230*|BCAT1_uc001rge.3_Nonsense_Mutation_p.W206*	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic	267					branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity				0	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)									0.077778	-1.033314	15.365751	7	83	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	24995032	24995032	1375	12	C	T	T	T	390	30	BCAT1	5	2
ITPR2	3709	broad.mit.edu	37	12	26709168	26709168	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:26709168C>T	uc001rhg.2	-	c.4962G>A	c.(4960-4962)TCG>TCA	p.S1654S		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	1654	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	13	Colorectal(261;0.0847)									1600				0.176471	42.600864	54.341757	21	98	KEEP	---	---	---	---	capture		Silent	SNP	26709168	26709168	8225	12	C	T	T	T	392	31	ITPR2	1	1
C12orf11	55726	broad.mit.edu	37	12	27081688	27081688	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:27081688C>T	uc001rhk.3	-	c.451G>A	c.(451-453)GCA>ACA	p.A151T	C12orf11_uc010sjk.1_Missense_Mutation_p.A50T	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	151					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)													0.116667	6.47906	15.158906	7	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27081688	27081688	1719	12	C	T	T	T	325	25	C12orf11	2	2
FOXM1	2305	broad.mit.edu	37	12	2968544	2968544	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:2968544T>C	uc001qle.2	-	c.1666A>G	c.(1666-1668)AGT>GGT	p.S556G	FOXM1_uc001qlf.2_Missense_Mutation_p.S518G|FOXM1_uc001qlg.2_Missense_Mutation_p.S503G|FOXM1_uc009zea.2_Missense_Mutation_p.S503G|FOXM1_uc009zeb.2_Missense_Mutation_p.S502G	NM_202002	NP_973731	Q08050	FOXM1_HUMAN	forkhead box M1 isoform 1	518					cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of stress-activated MAPK cascade|pattern specification process|positive regulation of cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.000622)											0.163265	12.965829	18.249951	8	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2968544	2968544	6264	12	T	C	C	C	715	55	FOXM1	4	4
KCNA1	3736	broad.mit.edu	37	12	5021039	5021039	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5021039C>T	uc001qnh.2	+	c.495C>T	c.(493-495)CCC>CCT	p.P165P		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	165					synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)	1					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.166667	11.429587	15.221322	6	30	KEEP	---	---	---	---	capture		Silent	SNP	5021039	5021039	8306	12	C	T	T	T	288	23	KCNA1	1	1
KCNA5	3741	broad.mit.edu	37	12	5153883	5153883	+	Silent	SNP	C	T	T	rs12720444		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5153883C>T	uc001qni.2	+	c.570C>T	c.(568-570)AAC>AAT	p.N190N		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	190						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4														0.147059	7.657444	11.723033	5	29	KEEP	---	---	---	---	capture		Silent	SNP	5153883	5153883	8311	12	C	T	T	T	246	19	KCNA5	1	1
HOXC4	3221	broad.mit.edu	37	12	54448008	54448008	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54448008C>T	uc001seu.2	+	c.302C>T	c.(301-303)GCG>GTG	p.A101V	HOXC4_uc001sex.2_Missense_Mutation_p.A101V	NM_014620	NP_055435	P09017	HXC4_HUMAN	homeobox C4	101					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.5	8.524504	8.524504	3	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54448008	54448008	7605	12	C	T	T	T	351	27	HOXC4	1	1
STAT2	6773	broad.mit.edu	37	12	56742722	56742722	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56742722C>G	uc001slc.2	-	c.1562G>C	c.(1561-1563)AGA>ACA	p.R521T	STAT2_uc001slb.2_Missense_Mutation_p.R63T|STAT2_uc001sld.2_Missense_Mutation_p.R517T|STAT2_uc010sqn.1_3'UTR	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	521					interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3														0.12844	21.473455	36.137066	14	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56742722	56742722	15785	12	C	G	G	G	416	32	STAT2	3	3
GLI1	2735	broad.mit.edu	37	12	57864766	57864766	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57864766C>A	uc001snx.2	+	c.2243C>A	c.(2242-2244)CCA>CAA	p.P748Q	GLI1_uc009zpq.2_Missense_Mutation_p.P620Q	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	748					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of gene-specific transcription|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	promoter binding|transcription activator activity|zinc ion binding			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	14			GBM - Glioblastoma multiforme(3;3.99e-32)			Pancreas(157;841 1936 10503 41495 50368)				277				0.108696	4.740017	11.720655	5	41	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	57864766	57864766	6705	12	C	A	A	A	273	21	GLI1	2	2
LLPH	84298	broad.mit.edu	37	12	66522855	66522855	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:66522855C>A	uc010ssw.1	-	c.32G>T	c.(31-33)AGA>ATA	p.R11I	LLPH_uc010ssx.1_Non-coding_Transcript	NM_032338	NP_115714	Q9BRT6	LLPH_HUMAN	LLP homolog	11	Lys-rich.										0														0.098214	6.952738	25.036255	11	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66522855	66522855	9164	12	C	A	A	A	416	32	LLPH	2	2
IRAK3	11213	broad.mit.edu	37	12	66639014	66639014	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:66639014G>A	uc001sth.2	+	c.1286G>A	c.(1285-1287)CGG>CAG	p.R429Q	IRAK3_uc010ssy.1_Missense_Mutation_p.R368Q	NM_007199	NP_009130	Q9Y616	IRAK3_HUMAN	interleukin-1 receptor-associated kinase 3	429	Protein kinase.		R -> Q (may be associated with ASRT5).		interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of cytokine-mediated signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan|response to virus	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity			ovary(2)|lung(1)|central_nervous_system(1)	4				GBM - Glioblastoma multiforme(28;0.0203)						206				0.197674	40.343962	47.649438	17	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66639014	66639014	8127	12	G	A	A	A	507	39	IRAK3	1	1
BEST3	144453	broad.mit.edu	37	12	70048924	70048924	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70048924C>T	uc001svg.2	-	c.1770G>A	c.(1768-1770)TGG>TGA	p.W590*	BEST3_uc001svd.1_Intron|BEST3_uc001sve.1_Intron|BEST3_uc001svf.2_Nonsense_Mutation_p.W377*|BEST3_uc010stm.1_Nonsense_Mutation_p.W484*	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform	590	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)											0.097087	6.583596	23.32521	10	93	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	70048924	70048924	1429	12	C	T	T	T	390	30	BEST3	5	2
PTPRB	5787	broad.mit.edu	37	12	70949014	70949014	+	Missense_Mutation	SNP	G	A	A	rs61758735	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70949014G>A	uc001swc.3	-	c.5069C>T	c.(5068-5070)ACT>ATT	p.T1690I	PTPRB_uc001swb.3_Missense_Mutation_p.T1472I|PTPRB_uc010sto.1_Missense_Mutation_p.T1382I|PTPRB_uc010stp.1_Missense_Mutation_p.T1382I|PTPRB_uc001swa.3_Missense_Mutation_p.T1602I	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1472	Fibronectin type-III 17.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)											0.155738	33.744402	47.554199	19	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70949014	70949014	13253	12	G	A	A	A	468	36	PTPRB	2	2
LGR5	8549	broad.mit.edu	37	12	71947005	71947005	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:71947005C>A	uc001swl.2	+	c.581C>A	c.(580-582)GCC>GAC	p.A194D	LGR5_uc001swm.2_Missense_Mutation_p.A194D|LGR5_uc001swn.1_Non-coding_Transcript	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	194	Extracellular (Potential).|LRR 6.					integral to plasma membrane	protein-hormone receptor activity			ovary(1)|pancreas(1)	2										516				0.073529	-3.916378	21.46975	10	126	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	71947005	71947005	9083	12	C	A	A	A	338	26	LGR5	2	2
LRRIQ1	84125	broad.mit.edu	37	12	85517881	85517881	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85517881C>T	uc001tac.2	+	c.3591C>T	c.(3589-3591)CTC>CTT	p.L1197L	LRRIQ1_uc001tab.1_Silent_p.L1197L	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1197										ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(134;0.212)										0.25	8.018994	8.700849	3	9	KEEP	---	---	---	---	capture		Silent	SNP	85517881	85517881	9405	12	C	T	T	T	405	32	LRRIQ1	2	2
MGAT4C	25834	broad.mit.edu	37	12	86373796	86373796	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:86373796G>T	uc010sum.1	-	c.780C>A	c.(778-780)GCC>GCA	p.A260A	MGAT4C_uc001tal.3_Silent_p.A236A|MGAT4C_uc001taj.3_Silent_p.A236A|MGAT4C_uc001tak.3_Silent_p.A236A|MGAT4C_uc001tai.3_Silent_p.A236A|MGAT4C_uc001tah.3_Silent_p.A236A	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	236	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3														0.1875	6.314868	7.778561	3	13	KEEP	---	---	---	---	capture		Silent	SNP	86373796	86373796	9937	12	G	T	T	T	600	47	MGAT4C	2	2
PLXNC1	10154	broad.mit.edu	37	12	94613883	94613883	+	Missense_Mutation	SNP	A	G	G	rs114758530	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:94613883A>G	uc001tdc.2	+	c.1646A>G	c.(1645-1647)AAA>AGA	p.K549R		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	549	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3														0.21645	134.544983	151.662544	50	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94613883	94613883	12552	12	A	G	G	G	13	1	PLXNC1	4	4
PAN3	255967	broad.mit.edu	37	13	28830443	28830443	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:28830443G>A	uc001urz.2	+	c.577G>A	c.(577-579)GCT>ACT	p.A193T	PAN3_uc010tdo.1_Missense_Mutation_p.A339T|PAN3_uc001ury.2_Missense_Mutation_p.A27T|PAN3_uc001urx.2_Missense_Mutation_p.A139T	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	193	Interaction with polyadenylate-binding protein.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|protein phosphorylation	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)										0.096296	6.473665	28.53492	13	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28830443	28830443	11832	13	G	A	A	A	598	46	PAN3	2	2
C13orf26	122046	broad.mit.edu	37	13	31543068	31543068	+	Missense_Mutation	SNP	G	T	T	rs9533168	byFrequency	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31543068G>T	uc001uti.2	+	c.693G>T	c.(691-693)AAG>AAT	p.K231N		NM_152325	NP_689538	Q8N6G2	CM026_HUMAN	hypothetical protein LOC122046	231										ovary(2)	2		Lung SC(185;0.0281)		all cancers(112;0.0176)|Epithelial(112;0.0768)|OV - Ovarian serous cystadenocarcinoma(117;0.0852)										0.142857	20.909583	32.098235	13	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31543068	31543068	1769	13	G	T	T	T	425	33	C13orf26	2	2
HSPH1	10808	broad.mit.edu	37	13	31725284	31725284	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31725284G>C	uc001utl.2	-	c.714C>G	c.(712-714)TTC>TTG	p.F238L	HSPH1_uc001utj.2_Missense_Mutation_p.F236L|HSPH1_uc001utk.2_Missense_Mutation_p.F236L|HSPH1_uc010aaw.2_Missense_Mutation_p.F195L|HSPH1_uc010tds.1_Missense_Mutation_p.F160L|HSPH1_uc010tdt.1_Non-coding_Transcript	NM_006644	NP_006635	Q92598	HS105_HUMAN	heat shock 105kD	236					positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)										0.148148	8.382382	11.590374	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31725284	31725284	7731	13	G	C	C	C	477	37	HSPH1	3	3
NBEA	26960	broad.mit.edu	37	13	35733361	35733361	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:35733361A>T	uc001uvb.2	+	c.3053A>T	c.(3052-3054)TAC>TTC	p.Y1018F	NBEA_uc010abi.2_5'Flank	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	1018						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)										0.088889	1.442568	16.803332	8	82	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	35733361	35733361	10583	13	A	T	T	T	182	14	NBEA	3	3
DGKH	160851	broad.mit.edu	37	13	42761201	42761201	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:42761201G>A	uc001uyl.1	+	c.1555G>A	c.(1555-1557)GTA>ATA	p.V519I	DGKH_uc010tfh.1_Missense_Mutation_p.V519I|DGKH_uc001uym.1_Missense_Mutation_p.V519I|DGKH_uc010tfi.1_Missense_Mutation_p.V274I|DGKH_uc010tfj.1_Missense_Mutation_p.V374I|DGKH_uc001uyn.1_Non-coding_Transcript|DGKH_uc001uyo.1_Missense_Mutation_p.V374I|DGKH_uc001uyp.2_Non-coding_Transcript	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	519					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)										0.151786	27.695995	40.706008	17	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42761201	42761201	4649	13	G	A	A	A	624	48	DGKH	2	2
PCDH17	27253	broad.mit.edu	37	13	58208879	58208879	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:58208879G>T	uc001vhq.1	+	c.2199G>T	c.(2197-2199)GAG>GAT	p.E733D	PCDH17_uc010aec.1_Missense_Mutation_p.E733D	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	733	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(2)|pancreas(2)	4		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		Melanoma(72;952 1291 1619 12849 33676)								0.130435	7.519552	13.630949	6	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58208879	58208879	11932	13	G	T	T	T	425	33	PCDH17	2	2
FARP1	10160	broad.mit.edu	37	13	99061646	99061646	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:99061646G>T	uc001vnh.2	+	c.1469G>T	c.(1468-1470)GGA>GTA	p.G490V	FARP1_uc001vnj.2_Missense_Mutation_p.G490V	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	490					regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)											0.173913	7.089391	9.395495	4	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99061646	99061646	5912	13	G	T	T	T	533	41	FARP1	2	2
DLK1	8788	broad.mit.edu	37	14	101200981	101200981	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:101200981C>T	uc001yhs.3	+	c.900C>T	c.(898-900)ACC>ACT	p.T300T	DLK1_uc001yhu.3_Intron	NM_003836	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog precursor	300	Extracellular (Potential).				multicellular organismal development	extracellular space|integral to membrane|soluble fraction				ovary(2)	2		Melanoma(154;0.155)												0.119048	5.142714	11.139226	5	37	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	101200981	101200981	4744	14	C	T	T	T	288	23	DLK1	1	1
PARP2	10038	broad.mit.edu	37	14	20820502	20820502	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20820502C>G	uc001vxc.2	+	c.635C>G	c.(634-636)ACT>AGT	p.T212S	PARP2_uc001vxd.2_Missense_Mutation_p.T199S|PARP2_uc001vxb.1_Missense_Mutation_p.T212S|PARP2_uc010tle.1_5'Flank	NM_005484	NP_005475	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase family, member 2	212					protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity			ovary(1)|pancreas(1)	2	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)										0.134615	24.275629	37.741776	14	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20820502	20820502	11878	14	C	G	G	G	260	20	PARP2	3	3
OSGEP	55644	broad.mit.edu	37	14	20916076	20916076	+	Silent	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20916076C>A	uc001vxf.2	-	c.780G>T	c.(778-780)GTG>GTT	p.V260V		NM_017807	NP_060277	Q9NPF4	OSGEP_HUMAN	O-sialoglycoprotein endopeptidase	260					proteolysis|tRNA processing		metal ion binding|metalloendopeptidase activity|protein binding				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)										0.077193	-2.070484	49.976048	22	263	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	20916076	20916076	11698	14	C	A	A	A	262	21	OSGEP	2	2
HECTD1	25831	broad.mit.edu	37	14	31642585	31642585	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:31642585C>A	uc001wrc.1	-	c.933G>T	c.(931-933)CAG>CAT	p.Q311H		NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	311					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)	3	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)										0.181818	25.761751	32.037617	12	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31642585	31642585	7322	14	C	A	A	A	311	24	HECTD1	2	2
ARHGAP5	394	broad.mit.edu	37	14	32621650	32621650	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:32621650G>A	uc001wrl.2	+	c.4097G>A	c.(4096-4098)CGT>CAT	p.R1366H	ARHGAP5_uc001wrm.2_Missense_Mutation_p.R1365H|ARHGAP5_uc001wrn.2_Missense_Mutation_p.R1366H|ARHGAP5_uc001wro.2_Missense_Mutation_p.R105H|ARHGAP5_uc001wrp.2_Missense_Mutation_p.R101H	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	1366	Rho-GAP.				cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(3)|central_nervous_system(1)	4	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		NSCLC(9;77 350 3443 29227 41353)								0.128205	7.948609	13.20072	5	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32621650	32621650	900	14	G	A	A	A	520	40	ARHGAP5	1	1
AKAP6	9472	broad.mit.edu	37	14	33293523	33293523	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:33293523G>A	uc001wrq.2	+	c.6504G>A	c.(6502-6504)GAG>GAA	p.E2168E		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	2168					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|large_intestine(2)|lung(2)|pancreas(1)	16	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		Melanoma(49;821 1200 7288 13647 42351)				483				0.180328	21.986445	27.849568	11	50	KEEP	---	---	---	---	capture		Silent	SNP	33293523	33293523	458	14	G	A	A	A	438	34	AKAP6	2	2
KIAA0586	9786	broad.mit.edu	37	14	58955530	58955530	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:58955530T>C	uc001xdu.3	+	c.3674T>C	c.(3673-3675)TTA>TCA	p.L1225S	KIAA0586_uc010trr.1_Missense_Mutation_p.L1281S|KIAA0586_uc001xdt.3_Missense_Mutation_p.L1196S|KIAA0586_uc010trs.1_Missense_Mutation_p.L1155S|KIAA0586_uc001xdv.3_Missense_Mutation_p.L1164S|KIAA0586_uc010trt.1_Missense_Mutation_p.L1100S	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein	1164										ovary(1)	1														0.142857	14.695525	20.714127	7	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58955530	58955530	8493	14	T	C	C	C	793	61	KIAA0586	4	4
ZBTB25	7597	broad.mit.edu	37	14	64954703	64954703	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64954703C>T	uc001xhf.2	-	c.246G>A	c.(244-246)ACG>ACA	p.T82T	ZBTB25_uc001xhc.2_Intron|ZBTB25_uc001xhg.2_Silent_p.T82T	NM_006977	NP_008908	P24278	ZBT25_HUMAN	zinc finger protein 46	82	BTB.				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)										0.113636	5.143445	11.627307	5	39	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	64954703	64954703	18118	14	C	T	T	T	288	23	ZBTB25	1	1
PCNX	22990	broad.mit.edu	37	14	71575490	71575490	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:71575490G>A	uc001xmo.2	+	c.6471G>A	c.(6469-6471)TCG>TCA	p.S2157S	PCNX_uc010are.1_Silent_p.S2046S|PCNX_uc010arf.1_Silent_p.S945S|PCNX_uc001xmp.2_Silent_p.S241S	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	2157	Ser-rich.					integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)										0.122449	7.711514	14.467799	6	43	KEEP	---	---	---	---	capture		Silent	SNP	71575490	71575490	12011	14	G	A	A	A	483	38	PCNX	1	1
TSHR	7253	broad.mit.edu	37	14	81610007	81610007	+	Silent	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:81610007C>A	uc001xvd.1	+	c.1605C>A	c.(1603-1605)CTC>CTA	p.L535L		NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1	535	Cytoplasmic (Potential).				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)	298				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)					868				0.084211	-1.077891	15.609332	8	87	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	81610007	81610007	17173	14	C	A	A	A	366	29	TSHR	2	2
PSMC1	5700	broad.mit.edu	37	14	90725526	90725526	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:90725526A>G	uc001xyf.2	+	c.26A>G	c.(25-27)CAT>CGT	p.H9R	PSMC1_uc001xyg.2_5'UTR|PSMC1_uc001xyh.2_5'UTR|PSMC1_uc010twh.1_5'UTR	NM_002802	NP_002793	P62191	PRS4_HUMAN	proteasome 26S ATPase subunit 1	9					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)										0.238095	10.564323	11.880714	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90725526	90725526	13138	14	A	G	G	G	104	8	PSMC1	4	4
C15orf53	400359	broad.mit.edu	37	15	38988925	38988925	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:38988925G>T	uc001zkf.1	+	c.117G>T	c.(115-117)GCG>GCT	p.A39A		NM_207444	NP_997327	Q8NAA6	CO053_HUMAN	hypothetical protein LOC400359	39											0		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)										0.130435	9.43031	15.53299	6	40	KEEP	---	---	---	---	capture		Silent	SNP	38988925	38988925	1851	15	G	T	T	T	509	40	C15orf53	1	1
EPB42	2038	broad.mit.edu	37	15	43512963	43512963	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43512963C>G	uc001zrb.3	-	c.61G>C	c.(61-63)GCA>CCA	p.A21P	EPB42_uc001zra.3_Intron|EPB42_uc010udm.1_Intron	NM_000119	NP_000110	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2 isoform 1	Error:Variant_position_missing_in_P16452_after_alignment					erythrocyte maturation|peptide cross-linking|regulation of cell shape	cytoplasm|cytoskeleton|plasma membrane	ATP binding|protein binding|protein-glutamine gamma-glutamyltransferase activity|structural constituent of cytoskeleton			ovary(2)	2		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)										0.085714	0.906765	13.08338	6	64	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	43512963	43512963	5351	15	C	G	G	G	351	27	EPB42	3	3
CEP152	22995	broad.mit.edu	37	15	49034266	49034266	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:49034266C>T	uc001zwz.2	-	c.3867G>A	c.(3865-3867)AAG>AAA	p.K1289K	CEP152_uc001zwy.2_Silent_p.K1233K|CEP152_uc001zxa.1_Silent_p.K1196K	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	1233					G2/M transition of mitotic cell cycle	cytosol|microtubule organizing center				lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)										0.197183	32.710327	38.77358	14	57	KEEP	---	---	---	---	capture		Silent	SNP	49034266	49034266	3381	15	C	T	T	T	311	24	CEP152	2	2
ZNF280D	54816	broad.mit.edu	37	15	56970977	56970977	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:56970977C>G	uc002adu.2	-	c.1047G>C	c.(1045-1047)CAG>CAC	p.Q349H	ZNF280D_uc002adv.2_Missense_Mutation_p.Q336H|ZNF280D_uc010bfq.2_Missense_Mutation_p.Q349H|ZNF280D_uc002adw.1_Missense_Mutation_p.Q377H|ZNF280D_uc010bfr.1_Non-coding_Transcript|ZNF280D_uc010bfp.2_Non-coding_Transcript	NM_017661	NP_060131	Q6N043	Z280D_HUMAN	suppressor of hairy wing homolog 4 isoform 1	349					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)										0.109375	7.377436	17.04969	7	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56970977	56970977	18409	15	C	G	G	G	415	32	ZNF280D	3	3
RNF111	54778	broad.mit.edu	37	15	59377888	59377888	+	Silent	SNP	A	G	G	rs76979606	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:59377888A>G	uc002afw.2	+	c.2481A>G	c.(2479-2481)GCA>GCG	p.A827A	RNF111_uc002afs.2_Silent_p.A818A|RNF111_uc002aft.2_Silent_p.A827A|RNF111_uc002afu.2_Silent_p.A817A|RNF111_uc002afv.2_Silent_p.A818A|RNF111_uc002afx.2_Silent_p.A344A|RNF111_uc002afy.2_5'UTR	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	818					multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		NSCLC(72;983 1365 10746 34387 47081)								0.214286	11.927217	14.047983	6	22	KEEP	---	---	---	---	capture		Silent	SNP	59377888	59377888	13902	15	A	G	G	G	80	7	RNF111	4	4
CYP11A1	1583	broad.mit.edu	37	15	74635368	74635368	+	Missense_Mutation	SNP	C	T	T	rs6161	byFrequency	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:74635368C>T	uc002axt.2	-	c.940G>A	c.(940-942)GAG>AAG	p.E314K	CYP11A1_uc002axs.2_Missense_Mutation_p.E156K|CYP11A1_uc010bjm.1_Missense_Mutation_p.E156K|CYP11A1_uc010bjn.1_Intron|CYP11A1_uc010bjo.1_Missense_Mutation_p.E314K|CYP11A1_uc010bjp.1_Intron|CYP11A1_uc010ulj.1_Missense_Mutation_p.E94K	NM_000781	NP_000772	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A,	314					C21-steroid hormone biosynthetic process|cholesterol metabolic process|oxidation-reduction process|vitamin D metabolic process|xenobiotic metabolic process	mitochondrial matrix	cholesterol monooxygenase (side-chain-cleaving) activity|electron carrier activity|heme binding			ovary(2)	2					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Clotrimazole(DB00257)|Digitoxin(DB01396)|Digoxin(DB00390)|Medroxyprogesterone(DB00603)|Ouabain(DB01092)|Progesterone(DB00396)|Testosterone(DB00624)|Trilostane(DB01108)	Esophageal Squamous(87;818 1337 4093 9268 37314)								0.141176	19.946863	30.501982	12	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74635368	74635368	4309	15	C	T	T	T	403	31	CYP11A1	1	1
DNAJA4	55466	broad.mit.edu	37	15	78572750	78572750	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:78572750A>G	uc002bdi.2	+	c.1229A>G	c.(1228-1230)TAC>TGC	p.Y410C	DNAJA4_uc002bdj.1_Missense_Mutation_p.Y381C|DNAJA4_uc002bdk.2_Missense_Mutation_p.Y354C|DNAJA4_uc002bdm.1_Missense_Mutation_p.Y165C	NM_018602	NP_061072	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	381					protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding			skin(1)	1														0.166667	6.315183	8.210133	3	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78572750	78572750	4797	15	A	G	G	G	182	14	DNAJA4	4	4
AKAP13	11214	broad.mit.edu	37	15	86278796	86278796	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:86278796G>T	uc002blu.1	+	c.7459G>T	c.(7459-7461)GAG>TAG	p.E2487*	AKAP13_uc002blv.1_Nonsense_Mutation_p.E2483*|AKAP13_uc002blw.1_Nonsense_Mutation_p.E948*|AKAP13_uc002blx.1_Nonsense_Mutation_p.E728*	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	2483	Interaction with ESR1.				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)								0.142857	14.368277	21.245791	8	48	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	86278796	86278796	452	15	G	T	T	T	481	37	AKAP13	5	1
C15orf32	145858	broad.mit.edu	37	15	93015697	93015697	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:93015697C>G	uc002brc.1	+	c.319C>G	c.(319-321)CTC>GTC	p.L107V	C15orf32_uc010bod.1_Non-coding_Transcript	NM_153040	NP_694585	Q32M92	CO032_HUMAN	hypothetical protein LOC145858	107										ovary(1)	1	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0493)|OV - Ovarian serous cystadenocarcinoma(32;0.125)											0.092308	3.746289	14.582496	6	59	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	93015697	93015697	1840	15	C	G	G	G	364	28	C15orf32	3	3
ACSM2A	123876	broad.mit.edu	37	16	20480912	20480912	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20480912C>G	uc010bwe.2	+	c.467C>G	c.(466-468)GCT>GGT	p.A156G	ACSM2A_uc010bwd.1_Non-coding_Transcript|ACSM2A_uc010vax.1_Missense_Mutation_p.A77G|ACSM2A_uc002dhf.3_Missense_Mutation_p.A156G|ACSM2A_uc002dhg.3_Missense_Mutation_p.A156G|ACSM2A_uc010vay.1_Missense_Mutation_p.A77G	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	156					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			breast(1)	1														0.097561	14.373877	40.973778	16	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20480912	20480912	184	16	C	G	G	G	364	28	ACSM2A	3	3
DNAH3	55567	broad.mit.edu	37	16	20970576	20970576	+	Missense_Mutation	SNP	G	T	T	rs34121503	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20970576G>T	uc010vbe.1	-	c.10751C>A	c.(10750-10752)GCC>GAC	p.A3584D	DNAH3_uc010vbd.1_Missense_Mutation_p.A1019D	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3584	AAA 6 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(10)|large_intestine(2)|central_nervous_system(2)	14				GBM - Glioblastoma multiforme(48;0.207)										0.157895	26.665669	37.26683	15	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20970576	20970576	4786	16	G	T	T	T	546	42	DNAH3	2	2
HS3ST4	9951	broad.mit.edu	37	16	26147170	26147171	+	Missense_Mutation	DNP	CG	TT	TT	rs80278121	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:26147170_26147171CG>TT	uc002dof.2	+	c.972_973CG>TT	c.(970-975)ATCGAT>ATTTAT	p.D325Y		NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl	325	Lumenal (Potential).				heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)										0.096774	20.332411	70.830054	30	280	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	26147170	26147171	7661	16	CG	TT	TT	TT	395	31	HS3ST4	1	1
ZNF267	10308	broad.mit.edu	37	16	31926648	31926648	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31926648A>C	uc002ecs.3	+	c.1078A>C	c.(1078-1080)AAC>CAC	p.N360H		NM_003414	NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	360					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3														0.067227	-2.487611	20.586413	8	111	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	31926648	31926648	18398	16	A	C	C	C	169	13	ZNF267	4	4
OR1F1	4992	broad.mit.edu	37	16	3254810	3254810	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:3254810C>T	uc010uwu.1	+	c.564C>T	c.(562-564)TCC>TCT	p.S188S		NM_012360	NP_036492	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F,	188	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.088235	3.20834	14.853355	6	62	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	3254810	3254810	11362	16	C	T	T	T	301	24	OR1F1	2	2
ADCY9	115	broad.mit.edu	37	16	4016932	4016932	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:4016932C>T	uc002cvx.2	-	c.2906G>A	c.(2905-2907)CGT>CAT	p.R969H		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	969	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)	5														0.235294	9.693609	10.781535	4	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4016932	4016932	302	16	C	T	T	T	247	19	ADCY9	1	1
PRMT7	54496	broad.mit.edu	37	16	68381128	68381128	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68381128C>G	uc002evy.1	+	c.1206C>G	c.(1204-1206)GAC>GAG	p.D402E	PRMT7_uc002evx.1_Intron|PRMT7_uc010vlg.1_Missense_Mutation_p.D352E|PRMT7_uc002evz.1_Intron	NM_019023	NP_061896	Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	402					cell differentiation|DNA methylation involved in gamete generation|regulation of gene expression by genetic imprinting|regulation of protein binding|regulation of transcription, DNA-dependent|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	[myelin basic protein]-arginine N-methyltransferase activity|histone binding|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N monomethyltransferase activity|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)										0.428571	10.424217	10.455313	3	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68381128	68381128	12984	16	C	G	G	G	220	17	PRMT7	3	3
FTSJD1	55783	broad.mit.edu	37	16	71319487	71319487	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71319487G>A	uc010cga.2	-	c.337C>T	c.(337-339)CAA>TAA	p.Q113*	FTSJD1_uc002ezy.3_Nonsense_Mutation_p.Q113*|FTSJD1_uc002ezz.3_Nonsense_Mutation_p.Q113*	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	113						integral to membrane	methyltransferase activity|nucleic acid binding				0														0.111111	6.843396	17.615064	8	64	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	71319487	71319487	6341	16	G	A	A	A	585	45	FTSJD1	5	2
ZFHX3	463	broad.mit.edu	37	16	72827874	72827874	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:72827874T>C	uc002fck.2	-	c.8707A>G	c.(8707-8709)AGC>GGC	p.S2903G	ZFHX3_uc002fcl.2_Missense_Mutation_p.S1989G	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2903					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription repressor activity|transcription repressor activity|zinc ion binding			ovary(2)	2		Ovarian(137;0.13)												0.169231	25.787431	32.515715	11	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72827874	72827874	18222	16	T	C	C	C	689	53	ZFHX3	4	4
ZFHX3	463	broad.mit.edu	37	16	72830425	72830425	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:72830425C>T	uc002fck.2	-	c.6156G>A	c.(6154-6156)CCG>CCA	p.P2052P	ZFHX3_uc002fcl.2_Silent_p.P1138P	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2052	Poly-Pro.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription repressor activity|transcription repressor activity|zinc ion binding			ovary(2)	2		Ovarian(137;0.13)												0.257143	20.260784	22.132578	9	26	KEEP	---	---	---	---	capture		Silent	SNP	72830425	72830425	18222	16	C	T	T	T	288	23	ZFHX3	1	1
MBTPS1	8720	broad.mit.edu	37	16	84118642	84118642	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:84118642G>A	uc002fhi.2	-	c.1232C>T	c.(1231-1233)TCA>TTA	p.S411L		NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	411	Serine protease.|Lumenal (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2												OREG0023982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.12	10.332863	20.949095	9	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84118642	84118642	9750	16	G	A	A	A	585	45	MBTPS1	2	2
MBTPS1	8720	broad.mit.edu	37	16	84132690	84132690	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:84132690C>T	uc002fhi.2	-	c.389G>A	c.(388-390)CGA>CAA	p.R130Q		NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	130					cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2														0.223404	51.639903	58.241348	21	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84132690	84132690	9750	16	C	T	T	T	403	31	MBTPS1	1	1
HSDL1	83693	broad.mit.edu	37	16	84164008	84164008	+	Silent	SNP	G	A	A	rs34611937		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:84164008G>A	uc002fhk.2	-	c.249C>T	c.(247-249)TAC>TAT	p.Y83Y	HSDL1_uc010vnv.1_Silent_p.Y83Y	NM_031463	NP_113651	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1 isoform a	83					oxidation-reduction process	mitochondrion	oxidoreductase activity|protein binding				0														0.130435	12.447753	21.598045	9	60	KEEP	---	---	---	---	capture		Silent	SNP	84164008	84164008	7688	16	G	A	A	A	516	40	HSDL1	1	1
DNAH9	1770	broad.mit.edu	37	17	11795241	11795241	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11795241T>A	uc002gne.2	+	c.11260T>A	c.(11260-11262)TAC>AAC	p.Y3754N	DNAH9_uc010coo.2_Missense_Mutation_p.Y3048N|DNAH9_uc002gnf.2_Missense_Mutation_p.Y66N|DNAH9_uc010vvh.1_Missense_Mutation_p.Y107N	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3754					cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.110577	23.177922	54.376845	23	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11795241	11795241	4791	17	T	A	A	A	689	53	DNAH9	3	3
SLC47A1	55244	broad.mit.edu	37	17	19474875	19474875	+	Missense_Mutation	SNP	C	T	T	rs111653425	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:19474875C>T	uc002gvx.2	+	c.1394C>T	c.(1393-1395)GCC>GTC	p.A465V	SLC47A1_uc002gvy.1_Missense_Mutation_p.A465V|SLC47A1_uc010vyz.1_Intron|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Intron|SLC47A1_uc010vza.1_Missense_Mutation_p.A177V|SLC47A1_uc010vzb.1_Intron|SLC47A1_uc010vzc.1_Missense_Mutation_p.A137V	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1	465	Cytoplasmic (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)													0.14	10.838404	17.057081	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19474875	19474875	15144	17	C	T	T	T	338	26	SLC47A1	2	2
SGSM2	9905	broad.mit.edu	37	17	2246847	2246847	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:2246847A>G	uc002fum.3	+	c.66A>G	c.(64-66)CAA>CAG	p.Q22Q	SGSM2_uc010vqw.1_Silent_p.Q22Q|SGSM2_uc002fun.3_Silent_p.Q22Q	NM_014853	NP_055668	O43147	SGSM2_HUMAN	RUN and TBC1 domain containing 1 isoform 1	22						intracellular	Rab GTPase activator activity				0				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)										0.172414	12.458044	15.396746	5	24	KEEP	---	---	---	---	capture		Silent	SNP	2246847	2246847	14714	17	A	G	G	G	11	1	SGSM2	4	4
RHBDL3	162494	broad.mit.edu	37	17	30648080	30648080	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:30648080G>T	uc002hhe.1	+	c.1047G>T	c.(1045-1047)GTG>GTT	p.V349V	RHBDL3_uc010csw.1_Silent_p.V341V|RHBDL3_uc010csx.1_Missense_Mutation_p.G316W|RHBDL3_uc010csy.1_Silent_p.V251V|RHBDL3_uc002hhf.1_Silent_p.V251V	NM_138328	NP_612201	P58872	RHBL3_HUMAN	rhomboid protease 3	349	Helical; (Potential).					integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)												0.111111	4.174677	9.556665	4	32	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	30648080	30648080	13798	17	G	T	T	T	600	47	RHBDL3	2	2
SLFN11	91607	broad.mit.edu	37	17	33690266	33690266	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33690266C>T	uc010ctp.2	-	c.561G>A	c.(559-561)TCG>TCA	p.S187S	SLFN11_uc010ctq.2_Silent_p.S187S|SLFN11_uc002hjh.3_Silent_p.S187S|SLFN11_uc002hjg.3_Silent_p.S187S|SLFN11_uc010ctr.2_Silent_p.S187S	NM_001104588	NP_001098058	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	187						nucleus	ATP binding			large_intestine(1)|ovary(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.149606	37.542259	52.49293	19	108	KEEP	---	---	---	---	capture		Silent	SNP	33690266	33690266	15230	17	C	T	T	T	288	23	SLFN11	1	1
ERBB2	2064	broad.mit.edu	37	17	37868208	37868208	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37868208C>A	uc002hso.2	+	c.929C>A	c.(928-930)TCC>TAC	p.S310Y	ERBB2_uc002hsm.2_Missense_Mutation_p.S280Y|ERBB2_uc010cwa.2_Missense_Mutation_p.S295Y|ERBB2_uc002hsp.2_Missense_Mutation_p.S113Y|ERBB2_uc010cwb.2_Missense_Mutation_p.S310Y|ERBB2_uc010wek.1_Missense_Mutation_p.S34Y|ERBB2_uc002hsl.2_Missense_Mutation_p.S280Y|ERBB2_uc002hsn.1_Missense_Mutation_p.S310Y	NM_004448	NP_004439	P04626	ERBB2_HUMAN	erbB-2 isoform a	310	Extracellular (Potential).				cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.S310F(2)		lung(71)|central_nervous_system(16)|ovary(13)|stomach(12)|breast(5)|upper_aerodigestive_tract(4)|large_intestine(3)|liver(3)|endometrium(2)|pancreas(1)	130	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)			1	p.S310F(5637-Tumor)	271	TCGA GBM(5;<1E-8)			0.124031	15.557726	33.356653	16	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37868208	37868208	5399	17	C	A	A	A	390	30	ERBB2	2	2
KRT10	3858	broad.mit.edu	37	17	38978823	38978823	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38978823G>T	uc002hvi.2	-	c.15C>A	c.(13-15)TAC>TAA	p.Y5*	KRT10_uc010cxd.2_5'Flank|TMEM99_uc002hvj.1_Intron	NM_000421	NP_000412	P13645	K1C10_HUMAN	keratin 10	5	Head.				epidermis development		protein binding|structural constituent of epidermis				0		Breast(137;0.000301)												0.114286	4.884789	10.009454	4	31	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	38978823	38978823	8763	17	G	T	T	T	620	48	KRT10	5	2
COASY	80347	broad.mit.edu	37	17	40717048	40717048	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40717048C>T	uc010cyj.2	+	c.1372C>T	c.(1372-1374)CGG>TGG	p.R458W	COASY_uc002hzz.2_Missense_Mutation_p.R429W|COASY_uc002iab.2_Missense_Mutation_p.R134W|COASY_uc002iad.2_Missense_Mutation_p.R429W|COASY_uc002iac.2_Missense_Mutation_p.R429W|COASY_uc002iae.2_Missense_Mutation_p.R224W|MLX_uc002iaf.2_5'Flank|MLX_uc002iag.2_5'Flank|MLX_uc002iah.2_5'Flank	NM_001042532	NP_001035997	Q13057	COASY_HUMAN	coenzyme A synthase isoform c	429	DPCK.				coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)										0.166667	8.95844	12.117966	5	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40717048	40717048	3790	17	C	T	T	T	295	23	COASY	1	1
PSMC3IP	29893	broad.mit.edu	37	17	40726186	40726186	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40726186C>G	uc002iai.2	-	c.268G>C	c.(268-270)GAT>CAT	p.D90H	PSMC3IP_uc002iaj.2_Missense_Mutation_p.D27H|PSMC3IP_uc002iak.2_Missense_Mutation_p.D90H|PSMC3IP_uc010wgn.1_Missense_Mutation_p.D11H|PSMC3IP_uc010wgo.1_Intron|PSMC3IP_uc010wgp.1_Non-coding_Transcript	NM_016556	NP_057640	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein isoform 2	90					DNA recombination|meiosis	nucleus	DNA binding				0		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)										0.266667	11.693648	12.430994	4	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40726186	40726186	13141	17	C	G	G	G	416	32	PSMC3IP	3	3
MPP2	4355	broad.mit.edu	37	17	41958884	41958884	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41958884C>A	uc010wip.1	-	c.890G>T	c.(889-891)CGC>CTC	p.R297L	MPP2_uc002ien.1_Missense_Mutation_p.R269L|MPP2_uc010wim.1_Missense_Mutation_p.R241L|MPP2_uc002ieo.1_Missense_Mutation_p.R252L|MPP2_uc010win.1_Missense_Mutation_p.R113L|MPP2_uc010wio.1_Missense_Mutation_p.R241L	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	276	SH3.				signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)										0.125	11.06125	19.850296	8	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41958884	41958884	10126	17	C	A	A	A	351	27	MPP2	1	1
MTMR4	9110	broad.mit.edu	37	17	56573255	56573255	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56573255C>A	uc002iwj.2	-	c.2248G>T	c.(2248-2250)GAG>TAG	p.E750*		NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	750						cytoplasm|membrane	protein tyrosine phosphatase activity|zinc ion binding			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.07	-11.320623	26.781271	14	186	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	56573255	56573255	10339	17	C	A	A	A	390	30	MTMR4	5	2
HEATR6	63897	broad.mit.edu	37	17	58120943	58120943	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58120943G>A	uc002iyk.1	-	c.3527C>T	c.(3526-3528)CCA>CTA	p.P1176L	HEATR6_uc010ddk.1_Missense_Mutation_p.P715L|HEATR6_uc010wos.1_Missense_Mutation_p.P896L	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	1176							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)											0.14	8.991493	15.251379	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58120943	58120943	7316	17	G	A	A	A	611	47	HEATR6	2	2
ABCA8	10351	broad.mit.edu	37	17	66871443	66871443	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:66871443G>A	uc002jhq.2	-	c.4589C>T	c.(4588-4590)GCA>GTA	p.A1530V	ABCA8_uc002jhp.2_Missense_Mutation_p.A1490V|ABCA8_uc010wqq.1_Missense_Mutation_p.A1525V	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1490						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2	Breast(10;4.56e-13)													0.14	9.723158	15.955692	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66871443	66871443	39	17	G	A	A	A	598	46	ABCA8	2	2
ABCA9	10350	broad.mit.edu	37	17	67004355	67004355	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:67004355G>A	uc002jhu.2	-	c.3169C>T	c.(3169-3171)CGG>TGG	p.R1057W	ABCA9_uc010dez.2_Missense_Mutation_p.R1057W	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1057					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|central_nervous_system(1)	5	Breast(10;1.47e-12)													0.079646	-0.999847	19.366722	9	104	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	67004355	67004355	40	17	G	A	A	A	519	40	ABCA9	1	1
CD300E	342510	broad.mit.edu	37	17	72613315	72613315	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:72613315C>A	uc002jlb.1	-	c.330G>T	c.(328-330)TGG>TGT	p.W110C		NM_181449	NP_852114	Q496F6	CLM2_HUMAN	CD300e molecule precursor	110	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			large_intestine(1)|ovary(1)	2														0.070175	-10.274304	33.19529	16	212	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	72613315	72613315	3126	17	C	A	A	A	286	22	CD300E	2	2
CD300LF	146722	broad.mit.edu	37	17	72700795	72700795	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:72700795G>A	uc010wra.1	-	c.204C>T	c.(202-204)ACC>ACT	p.T68T	RAB37_uc002jlc.2_Intron|RAB37_uc010dfu.2_Intron|RAB37_uc002jld.2_Intron|CD300LF_uc002jlf.2_Silent_p.T71T|CD300LF_uc010dfw.2_Non-coding_Transcript|CD300LF_uc002jlg.2_Silent_p.T68T|CD300LF_uc002jlh.2_Silent_p.T68T|CD300LF_uc002jli.2_Silent_p.T71T|CD300LF_uc002jlj.1_Silent_p.T71T	NM_139018	NP_620587	Q8TDQ1	CLM1_HUMAN	NK inhibitory receptor precursor	68	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity				0														0.169231	64.962973	85.157738	33	162	KEEP	---	---	---	---	capture		Silent	SNP	72700795	72700795	3129	17	G	A	A	A	600	47	CD300LF	2	2
TP53	7157	broad.mit.edu	37	17	7579356	7579356	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7579356G>T	uc002gim.2	-	c.331C>A	c.(331-333)CTG>ATG	p.L111M	TP53_uc002gig.1_Missense_Mutation_p.L111M|TP53_uc002gih.2_Missense_Mutation_p.L111M|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Missense_Mutation_p.L111M|TP53_uc010cni.1_Missense_Mutation_p.L111M|TP53_uc002gij.2_Missense_Mutation_p.L111M|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Missense_Mutation_p.L72M|TP53_uc010cnk.1_Missense_Mutation_p.L126M	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	111	|Interaction with HIPK1 (By similarity).		L -> Q (in sporadic cancers; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).|L -> M (in a sporadic cancer; somatic mutation).|L -> R (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.0?(6)|p.G59fs*23(3)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y126fs*24(1)|p.Y107fs*44(1)|p.L111M(1)|p.L111fs*10(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.10628	16.503003	48.378746	22	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7579356	7579356	16923	17	G	T	T	T	425	33	TP53	2	2
DNAH17	8632	broad.mit.edu	37	17	76424765	76424765	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:76424765C>T	uc010dhp.1	-	c.3429G>A	c.(3427-3429)GAG>GAA	p.E1143E	DNAH17_uc002jvq.2_Silent_p.E428E|DNAH17_uc002jvs.2_Non-coding_Transcript	DNEL2				SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)											0.121212	5.575297	10.216475	4	29	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	76424765	76424765	4784	17	C	T	T	T	415	32	DNAH17	2	2
CHD3	1107	broad.mit.edu	37	17	7797875	7797875	+	Silent	SNP	T	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7797875T>G	uc002gjd.2	+	c.1395T>G	c.(1393-1395)CTT>CTG	p.L465L	CHD3_uc002gje.2_Silent_p.L406L|CHD3_uc002gjf.2_Silent_p.L406L|CHD3_uc002gjg.1_Silent_p.L234L	NM_001005271	NP_001005271	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	406	PHD-type 1.				chromatin assembly or disassembly|chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	chromatin|microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|chromatin binding|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)												0.253659	138.319162	149.694627	52	153	KEEP	---	---	---	---	capture		Silent	SNP	7797875	7797875	3460	17	T	G	G	G	808	63	CHD3	4	4
RNF213	57674	broad.mit.edu	37	17	78318746	78318746	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:78318746A>T	uc002jyh.1	+	c.830A>T	c.(829-831)CAC>CTC	p.H277L		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)											0.129032	6.279185	10.432746	4	27	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	78318746	78318746	13955	17	A	T	T	T	78	6	RNF213	3	3
RNF213	57674	broad.mit.edu	37	17	78319311	78319311	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:78319311G>A	uc002jyh.1	+	c.1395G>A	c.(1393-1395)ACG>ACA	p.T465T		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)											0.133333	5.28848	9.196183	4	26	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	78319311	78319311	13955	17	G	A	A	A	509	40	RNF213	1	1
ABR	29	broad.mit.edu	37	17	970440	970440	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:970440G>A	uc002fsd.2	-	c.1059C>T	c.(1057-1059)GCC>GCT	p.A353A	ABR_uc002fse.2_Silent_p.A307A|ABR_uc010vqg.1_Silent_p.A135A|ABR_uc002fsg.2_Silent_p.A316A|ABR_uc002fsh.1_Silent_p.A237A	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	353	PH.				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	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		Esophageal Squamous(197;2016 2115 4129 29033 46447)								0.238095	13.666447	14.980728	5	16	KEEP	---	---	---	---	capture		Silent	SNP	970440	970440	100	17	G	A	A	A	496	39	ABR	1	1
DSG3	1830	broad.mit.edu	37	18	29056118	29056118	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29056118G>A	uc002kws.2	+	c.2895G>A	c.(2893-2895)GTG>GTA	p.V965V	DSG3_uc002kwt.2_Silent_p.V247V	NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	965	Cytoplasmic (Potential).|Desmoglein repeat 2.				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.101449	10.652379	32.516418	14	124	KEEP	---	---	---	---	capture		Silent	SNP	29056118	29056118	4962	18	G	A	A	A	574	45	DSG3	2	2
CELF4	56853	broad.mit.edu	37	18	34855147	34855147	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:34855147G>A	uc002lae.2	-	c.508C>T	c.(508-510)CGC>TGC	p.R170C	CELF4_uc010dnd.1_Missense_Mutation_p.R169C|CELF4_uc002lag.2_Missense_Mutation_p.R160C|CELF4_uc002laf.2_Missense_Mutation_p.R165C|CELF4_uc002lai.2_Missense_Mutation_p.R155C|CELF4_uc002lah.1_5'Flank|CELF4_uc002laj.1_5'Flank	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1	170	Sufficient for RNA-binding and MSE- dependent splicing activity.|RRM 2.				embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2														0.232143	32.549441	36.226899	13	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34855147	34855147	3351	18	G	A	A	A	507	39	CELF4	1	1
RIT2	6014	broad.mit.edu	37	18	40503653	40503653	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:40503653G>T	uc002lav.2	-	c.310C>A	c.(310-312)CGT>AGT	p.R104S	RIT2_uc010dnf.2_Missense_Mutation_p.R104S	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	104					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1														0.069672	-10.614622	36.177518	17	227	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	40503653	40503653	13864	18	G	T	T	T	507	39	RIT2	1	1
KIAA1632	57724	broad.mit.edu	37	18	43440212	43440212	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43440212C>A	uc002lbm.2	-	c.6866G>T	c.(6865-6867)CGG>CTG	p.R2289L	KIAA1632_uc010xcq.1_Missense_Mutation_p.R843L|KIAA1632_uc010xcr.1_Non-coding_Transcript|KIAA1632_uc010xcs.1_Non-coding_Transcript|KIAA1632_uc002lbn.2_Missense_Mutation_p.R1164L	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	2289					autophagy						0														0.130435	14.633622	23.79451	9	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43440212	43440212	8558	18	C	A	A	A	299	23	KIAA1632	1	1
KIAA1632	57724	broad.mit.edu	37	18	43496539	43496539	+	Missense_Mutation	SNP	G	A	A	rs78339727	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43496539G>A	uc002lbm.2	-	c.3248C>T	c.(3247-3249)TCG>TTG	p.S1083L	KIAA1632_uc002lbo.1_Missense_Mutation_p.S1083L|KIAA1632_uc010xcq.1_5'UTR|KIAA1632_uc010xcr.1_Non-coding_Transcript|KIAA1632_uc010xcs.1_Non-coding_Transcript|KIAA1632_uc002lbn.2_5'UTR	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	1083					autophagy						0														0.205128	16.30798	19.43263	8	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43496539	43496539	8558	18	G	A	A	A	481	37	KIAA1632	1	1
ALPK2	115701	broad.mit.edu	37	18	56184260	56184260	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:56184260G>T	uc002lhj.3	-	c.5820C>A	c.(5818-5820)CAC>CAA	p.H1940Q		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1940	Alpha-type protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity	p.H1301H(1)		ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11										343				0.071429	-2.474278	18.708239	8	104	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	56184260	56184260	548	18	G	T	T	T	516	40	ALPK2	1	1
CCBE1	147372	broad.mit.edu	37	18	57106955	57106955	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:57106955G>A	uc002lib.2	-	c.869C>T	c.(868-870)CCA>CTA	p.P290L	CCBE1_uc010dpq.2_Intron|CCBE1_uc002lia.2_Missense_Mutation_p.P143L	NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	290	Collagen-like 1.				lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			ovary(1)	1		Colorectal(73;0.175)				NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)								0.134146	18.770985	29.413755	11	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57106955	57106955	2851	18	G	A	A	A	611	47	CCBE1	2	2
LAMA1	284217	broad.mit.edu	37	18	7014035	7014035	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:7014035G>C	uc002knm.2	-	c.3142C>G	c.(3142-3144)CTC>GTC	p.L1048V	LAMA1_uc010wzj.1_Missense_Mutation_p.L524V	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1048	Laminin EGF-like 12.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.26087	17.641233	18.830424	6	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7014035	7014035	8928	18	G	C	C	C	429	33	LAMA1	3	3
LAMA1	284217	broad.mit.edu	37	18	7015759	7015759	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:7015759C>A	uc002knm.2	-	c.3088G>T	c.(3088-3090)GAT>TAT	p.D1030Y	LAMA1_uc010wzj.1_Missense_Mutation_p.D506Y	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1030	Laminin EGF-like 11.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.083333	-0.564733	16.368261	8	88	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	7015759	7015759	8928	18	C	A	A	A	390	30	LAMA1	2	2
SLC44A2	57153	broad.mit.edu	37	19	10748382	10748382	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10748382G>C	uc002mpf.2	+	c.1654G>C	c.(1654-1656)GAG>CAG	p.E552Q	SLC44A2_uc002mpe.3_Missense_Mutation_p.E550Q|SLC44A2_uc002mpg.1_Missense_Mutation_p.E272Q|SLC44A2_uc002mph.2_Missense_Mutation_p.E101Q|SLC44A2_uc002mpi.2_5'Flank	NM_020428	NP_065161	Q8IWA5	CTL2_HUMAN	solute carrier family 44, member 2 isoform 1	552	Extracellular (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)									0.204545	23.550021	27.11356	9	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10748382	10748382	15133	19	G	C	C	C	533	41	SLC44A2	3	3
ZNF136	7695	broad.mit.edu	37	19	12297520	12297520	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12297520A>C	uc002mti.2	+	c.327A>C	c.(325-327)GAA>GAC	p.E109D	ZNF136_uc010xmh.1_Missense_Mutation_p.E43D	NM_003437	NP_003428	P52737	ZN136_HUMAN	zinc finger protein 136	109					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|protein binding|specific RNA polymerase II transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|pancreas(1)	2														0.162162	9.726315	13.743332	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12297520	12297520	18317	19	A	C	C	C	37	3	ZNF136	4	4
ZNF709	163051	broad.mit.edu	37	19	12575953	12575953	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12575953G>A	uc002mtv.3	-	c.783C>T	c.(781-783)TTC>TTT	p.F261F	ZNF709_uc002mtw.3_Silent_p.F229F|ZNF709_uc002mtx.3_Silent_p.F261F	NM_152601	NP_689814	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform a	261	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GBM(33;565 669 12371 29134 51667)								0.227273	11.862407	13.365145	5	17	KEEP	---	---	---	---	capture		Silent	SNP	12575953	12575953	18709	19	G	A	A	A	581	45	ZNF709	2	2
USHBP1	83878	broad.mit.edu	37	19	17367497	17367497	+	Missense_Mutation	SNP	G	C	C	rs112158497		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17367497G>C	uc002nfs.1	-	c.1253C>G	c.(1252-1254)CCA>CGA	p.P418R	USHBP1_uc002nfr.1_Missense_Mutation_p.P44R|USHBP1_uc002nft.1_Non-coding_Transcript|USHBP1_uc010xpk.1_Missense_Mutation_p.P354R	NM_031941	NP_114147	Q8N6Y0	USBP1_HUMAN	Usher syndrome 1C binding protein 1	418							PDZ domain binding			ovary(1)	1														0.166667	8.700939	11.827527	5	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17367497	17367497	17599	19	G	C	C	C	611	47	USHBP1	3	3
ZNF257	113835	broad.mit.edu	37	19	22271442	22271442	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22271442C>G	uc010ecx.2	+	c.890C>G	c.(889-891)TCC>TGC	p.S297C	ZNF257_uc010ecy.2_Missense_Mutation_p.S265C	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	297	C2H2-type 5; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.102564	5.07004	11.208448	4	35	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	22271442	22271442	18391	19	C	G	G	G	390	30	ZNF257	3	3
ZNF91	7644	broad.mit.edu	37	19	23545307	23545307	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:23545307T>C	uc002nre.2	-	c.474A>G	c.(472-474)AAA>AAG	p.K158K	ZNF91_uc010xrj.1_Silent_p.K126K	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	158	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)												0.18	21.846923	26.659511	9	41	KEEP	---	---	---	---	capture		Silent	SNP	23545307	23545307	18804	19	T	C	C	C	673	52	ZNF91	4	4
TSHZ3	57616	broad.mit.edu	37	19	31768675	31768675	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31768675C>T	uc002nsy.3	-	c.2024G>A	c.(2023-2025)CGG>CAG	p.R675Q		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	675					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.172414	9.662521	12.598797	5	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31768675	31768675	17176	19	C	T	T	T	299	23	TSHZ3	1	1
TSHZ3	57616	broad.mit.edu	37	19	31768683	31768683	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31768683G>C	uc002nsy.3	-	c.2016C>G	c.(2014-2016)AGC>AGG	p.S672R		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	672					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.166667	7.92338	10.42114	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31768683	31768683	17176	19	G	C	C	C	542	42	TSHZ3	3	3
KIAA0355	9710	broad.mit.edu	37	19	34843565	34843565	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:34843565A>G	uc002nvd.3	+	c.2918A>G	c.(2917-2919)AAA>AGA	p.K973R		NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	973										ovary(1)	1	Esophageal squamous(110;0.162)													0.106061	9.775999	19.94742	7	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34843565	34843565	8477	19	A	G	G	G	13	1	KIAA0355	4	4
HAUS5	23354	broad.mit.edu	37	19	36110349	36110349	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36110349C>T	uc002oam.1	+	c.1203C>T	c.(1201-1203)CGC>CGT	p.R401R		NM_015302	NP_056117	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5	401	Potential.				cell division|centrosome organization|mitosis|spindle assembly	HAUS complex|microtubule|microtubule organizing center|spindle					0														0.15625	7.455386	11.06602	5	27	KEEP	---	---	---	---	capture		Silent	SNP	36110349	36110349	7251	19	C	T	T	T	327	26	HAUS5	2	2
ARHGAP33	115703	broad.mit.edu	37	19	36273336	36273336	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36273336C>T	uc002obs.1	+	c.1147C>T	c.(1147-1149)CAC>TAC	p.H383Y	ARHGAP33_uc002obr.1_Missense_Mutation_p.H383Y|ARHGAP33_uc002obt.1_Missense_Mutation_p.H247Y|ARHGAP33_uc010eel.2_5'UTR|ARHGAP33_uc002obv.1_5'Flank	NM_052948	NP_443180	O14559	RHG33_HUMAN	sorting nexin 26	383	Rho-GAP.				cell communication|protein transport|signal transduction	intracellular	GTPase activator activity|phosphatidylinositol binding|protein binding			ovary(1)|pancreas(1)|skin(1)	3														0.126582	11.9922	22.747735	10	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36273336	36273336	894	19	C	T	T	T	273	21	ARHGAP33	2	2
APLP1	333	broad.mit.edu	37	19	36362814	36362814	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36362814C>T	uc002ocf.2	+	c.726C>T	c.(724-726)GAC>GAT	p.D242D	APLP1_uc010xsz.1_Silent_p.D203D|APLP1_uc002oce.2_Silent_p.D242D|APLP1_uc002ocg.2_Silent_p.D145D|APLP1_uc010xta.1_Silent_p.D236D	NM_001024807	NP_001019978	P51693	APLP1_HUMAN	amyloid precursor-like protein 1 isoform 1	242	Extracellular (Potential).|Poly-Glu.				apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.202381	67.38645	81.127778	34	134	KEEP	---	---	---	---	capture		Silent	SNP	36362814	36362814	789	19	C	T	T	T	246	19	APLP1	1	1
CLIP3	25999	broad.mit.edu	37	19	36508569	36508569	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36508569G>C	uc010eeq.1	-	c.1439C>G	c.(1438-1440)TCC>TGC	p.S480C	CLIP3_uc002ocz.1_Missense_Mutation_p.S480C	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	480					chaperone-mediated protein transport|fat cell differentiation|membrane biogenesis|negative regulation of microtubule polymerization|peptidyl-L-cysteine S-palmitoylation|positive regulation of apoptosis|positive regulation of endocytosis|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose transport|positive regulation of protein phosphorylation	early endosome membrane|Golgi stack|membrane raft|microsome|plasma membrane|recycling endosome membrane|trans-Golgi network membrane	ganglioside binding|microtubule binding			ovary(2)|pancreas(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)											0.109091	7.710304	16.033159	6	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36508569	36508569	3672	19	G	C	C	C	533	41	CLIP3	3	3
ZNF585A	199704	broad.mit.edu	37	19	37644311	37644311	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37644311C>A	uc002ofo.1	-	c.490G>T	c.(490-492)GGG>TGG	p.G164W	ZNF585A_uc002ofm.1_Missense_Mutation_p.G109W|ZNF585A_uc002ofn.1_Missense_Mutation_p.G109W	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	164	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.080537	1.38031	28.109206	12	137	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	37644311	37644311	18612	19	C	A	A	A	273	21	ZNF585A	2	2
ZNF585B	92285	broad.mit.edu	37	19	37677490	37677490	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37677490G>A	uc002ofq.2	-	c.949C>T	c.(949-951)CAA>TAA	p.Q317*	ZNF585B_uc002ofr.1_Nonsense_Mutation_p.Q131*	NM_152279	NP_689492	Q52M93	Z585B_HUMAN	zinc finger protein 585B	317	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			Melanoma(93;882 1454 18863 28917 48427)								0.067114	-8.577167	20.358875	10	139	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	37677490	37677490	18613	19	G	A	A	A	585	45	ZNF585B	5	2
ZNF780A	284323	broad.mit.edu	37	19	40581044	40581044	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40581044A>T	uc010xvh.1	-	c.1308T>A	c.(1306-1308)CAT>CAA	p.H436Q	ZNF780A_uc002omw.3_Intron|ZNF780A_uc002omy.2_Missense_Mutation_p.H435Q|ZNF780A_uc002omz.2_Missense_Mutation_p.H435Q	NM_001142577	NP_001136049	O75290	Z780A_HUMAN	zinc finger protein 780A isoform a	435	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)													0.075472	-4.960134	34.215796	16	196	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	40581044	40581044	18750	19	A	T	T	T	154	12	ZNF780A	3	3
CYP2A6	1548	broad.mit.edu	37	19	41352810	41352810	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:41352810G>T	uc002opl.3	-	c.801C>A	c.(799-801)TTC>TTA	p.F267L	CYP2A6_uc010ehe.1_Missense_Mutation_p.F63L|CYP2A6_uc010ehf.1_Non-coding_Transcript	NM_000762	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A,	267					coumarin catabolic process|exogenous drug catabolic process|oxidation-reduction process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|enzyme binding|heme binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Chlorzoxazone(DB00356)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Formoterol(DB00983)|Halothane(DB01159)|Letrozole(DB01006)|Methoxsalen(DB00553)|Metyrapone(DB01011)|Nicotine(DB00184)|Pilocarpine(DB01085)|Tolbutamide(DB01124)|Tranylcypromine(DB00752)									0.136364	13.026768	21.482488	9	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41352810	41352810	4327	19	G	T	T	T	581	45	CYP2A6	2	2
CREB3L3	84699	broad.mit.edu	37	19	4157105	4157105	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4157105C>G	uc002lzl.2	+	c.270C>G	c.(268-270)TCC>TCG	p.S90S	CREB3L3_uc002lzm.2_Silent_p.S80S|CREB3L3_uc010xib.1_Silent_p.S81S|CREB3L3_uc010xic.1_Silent_p.S81S	NM_032607	NP_115996	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like	90	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)										0.235294	7.943457	9.086533	4	13	KEEP	---	---	---	---	capture		Silent	SNP	4157105	4157105	3997	19	C	G	G	G	288	23	CREB3L3	3	3
PSG5	5673	broad.mit.edu	37	19	43690508	43690508	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43690508C>T	uc002ovv.2	-	c.50G>A	c.(49-51)GGG>GAG	p.G17E	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_5'Flank|PSG5_uc002ovu.2_Missense_Mutation_p.G17E|PSG5_uc002ovx.2_Missense_Mutation_p.G17E|PSG5_uc002ovw.2_Missense_Mutation_p.G17E	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	17					female pregnancy	extracellular region					0		Prostate(69;0.00899)												0.088	5.847208	27.284449	11	114	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	43690508	43690508	13111	19	C	T	T	T	286	22	PSG5	2	2
ZNF155	7711	broad.mit.edu	37	19	44501276	44501276	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44501276A>C	uc010xwt.1	+	c.1300A>C	c.(1300-1302)AGT>CGT	p.S434R	ZNF155_uc002oxy.1_Missense_Mutation_p.S423R|ZNF155_uc002oxz.1_Missense_Mutation_p.S423R	NM_198089	NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	423					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Prostate(69;0.0352)				NSCLC(61;554 1277 20909 42067 42312)								0.073826	-5.291451	22.520732	11	138	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	44501276	44501276	18327	19	A	C	C	C	91	7	ZNF155	4	4
PLIN4	729359	broad.mit.edu	37	19	4512578	4512578	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4512578G>C	uc002mar.1	-	c.1352C>G	c.(1351-1353)ACC>AGC	p.T451S	PLIN4_uc010dub.1_5'Flank	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	451	11.|27 X 33 AA approximate tandem repeat.					lipid particle|plasma membrane					0														0.135135	8.853865	13.623736	5	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4512578	4512578	12518	19	G	C	C	C	572	44	PLIN4	3	3
TRAPPC6A	79090	broad.mit.edu	37	19	45668167	45668167	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45668167C>G	uc002pav.2	-	c.256G>C	c.(256-258)GAC>CAC	p.D86H	TRAPPC6A_uc002paw.2_Missense_Mutation_p.D72H	NM_024108	NP_077013	O75865	TPC6A_HUMAN	trafficking protein particle complex 6A	72					vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)										0.102041	5.138315	12.87496	5	44	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	45668167	45668167	17007	19	C	G	G	G	416	32	TRAPPC6A	3	3
FGF21	26291	broad.mit.edu	37	19	49261199	49261199	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49261199C>T	uc002pkn.1	+	c.352C>T	c.(352-354)CCT>TCT	p.P118S	FUT1_uc002pkk.2_5'Flank|FUT1_uc002pkm.1_5'Flank|FGF21_uc002pko.1_Missense_Mutation_p.P118S	NM_019113	NP_061986	Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21 precursor	118					cell-cell signaling|positive regulation of ERK1 and ERK2 cascade|positive regulation of glucose import	extracellular region|soluble fraction	growth factor activity				0		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)										0.163399	46.886458	63.35618	25	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49261199	49261199	6087	19	C	T	T	T	286	22	FGF21	2	2
GYS1	2997	broad.mit.edu	37	19	49486081	49486081	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49486081G>A	uc002plp.2	-	c.837C>T	c.(835-837)CCC>CCT	p.P279P	GYS1_uc010xzy.1_Intron|GYS1_uc010emm.2_Silent_p.P215P|GYS1_uc010xzz.1_Silent_p.P199P|GYS1_uc010yaa.1_Intron	NM_002103	NP_002094	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle) isoform 1	279					glucose metabolic process|glycogen biosynthetic process	cytosol	glycogen (starch) synthase activity|protein binding			ovary(2)	2		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)										0.07619	-1.346201	17.949589	8	97	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	49486081	49486081	7192	19	G	A	A	A	600	47	GYS1	2	2
TSKS	60385	broad.mit.edu	37	19	50265430	50265430	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50265430G>A	uc002ppm.2	-	c.230C>T	c.(229-231)TCG>TTG	p.S77L		NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate	77							protein binding			large_intestine(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)										0.25	18.613462	20.202825	7	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50265430	50265430	17177	19	G	A	A	A	481	37	TSKS	1	1
KLK15	55554	broad.mit.edu	37	19	51330971	51330971	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51330971G>T	uc002ptl.2	-	c.144C>A	c.(142-144)GGC>GGA	p.G48G	KLK15_uc002ptm.2_Silent_p.G48G|KLK15_uc002ptn.2_Silent_p.G48G|KLK15_uc002pto.2_Silent_p.G47G|KLK15_uc010ych.1_Non-coding_Transcript|KLK15_uc010yci.1_Silent_p.G47G|KLK15_uc010eod.2_Non-coding_Transcript	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	48	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)		Pancreas(140;10 2513 7143 9246)								0.263158	27.335698	29.261573	10	28	KEEP	---	---	---	---	capture		Silent	SNP	51330971	51330971	8717	19	G	T	T	T	483	38	KLK15	1	1
ZNF578	147660	broad.mit.edu	37	19	53005109	53005109	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53005109A>T	uc002pzp.3	+	c.11A>T	c.(10-12)GAG>GTG	p.E4V		NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578	Error:Variant_position_missing_in_Q96N58_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)										0.170543	41.370005	54.614507	22	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53005109	53005109	18605	19	A	T	T	T	143	11	ZNF578	3	3
ZNF665	79788	broad.mit.edu	37	19	53668524	53668524	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53668524A>G	uc010eqm.1	-	c.1219T>C	c.(1219-1221)TGC>CGC	p.C407R		NM_024733	NP_079009	Q9H7R5	ZN665_HUMAN	zinc finger protein 665	342	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0196)										0.155556	11.795111	16.895555	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53668524	53668524	18668	19	A	G	G	G	104	8	ZNF665	4	4
VN1R4	317703	broad.mit.edu	37	19	53770098	53770098	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53770098C>A	uc010ydu.1	-	c.821G>T	c.(820-822)AGT>ATT	p.S274I		NM_173857	NP_776256	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	274	Helical; Name=7; (Potential).				response to pheromone	actin cytoskeleton|cytoplasm|integral to membrane|plasma membrane	pheromone receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.00294)										0.142857	11.890481	17.914436	7	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53770098	53770098	17747	19	C	A	A	A	260	20	VN1R4	2	2
CACNG7	59284	broad.mit.edu	37	19	54444851	54444851	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54444851C>T	uc002qcr.1	+	c.552C>T	c.(550-552)TCC>TCT	p.S184S	CACNG7_uc010era.1_Silent_p.S184S	NM_031896	NP_114102	P62955	CCG7_HUMAN	voltage-dependent calcium channel gamma-7	184	Helical; (Potential).				regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)										0.189655	25.79031	31.014869	11	47	KEEP	---	---	---	---	capture		Silent	SNP	54444851	54444851	2678	19	C	T	T	T	301	24	CACNG7	2	2
LILRA3	11026	broad.mit.edu	37	19	54802136	54802136	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54802136C>A	uc002qfd.2	-	c.1052G>T	c.(1051-1053)GGG>GTG	p.G351V	LILRA6_uc002qew.1_Intron|LILRA3_uc010erk.2_Missense_Mutation_p.G287V	NM_006865	NP_006856	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor,	351	Ig-like C2-type 4.				defense response	extracellular region|plasma membrane	antigen binding|receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.161616	24.084972	34.839762	16	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54802136	54802136	9112	19	C	A	A	A	286	22	LILRA3	2	2
LAIR1	3903	broad.mit.edu	37	19	54868141	54868141	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54868141A>T	uc002qfk.1	-	c.542T>A	c.(541-543)CTG>CAG	p.L181Q	LAIR1_uc002qfl.1_Missense_Mutation_p.L164Q|LAIR1_uc002qfm.1_Missense_Mutation_p.L180Q|LAIR1_uc002qfn.1_Missense_Mutation_p.L163Q|LAIR1_uc010yex.1_Missense_Mutation_p.L174Q|LAIR1_uc002qfo.2_Missense_Mutation_p.L163Q	NM_002287	NP_002278	Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like	181	Helical; (Potential).					integral to membrane|plasma membrane	protein binding|receptor activity			ovary(4)	4	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)										0.225	22.754738	25.533198	9	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54868141	54868141	8925	19	A	T	T	T	91	7	LAIR1	3	3
ZNF460	10794	broad.mit.edu	37	19	57802180	57802180	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57802180G>T	uc002qog.2	+	c.271G>T	c.(271-273)GGG>TGG	p.G91W	ZNF460_uc010ygv.1_Missense_Mutation_p.G50W	NM_006635	NP_006626	Q14592	ZN460_HUMAN	zinc finger protein 460	91	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)										0.181818	15.381088	19.561657	8	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57802180	57802180	18517	19	G	T	T	T	559	43	ZNF460	2	2
MUC16	94025	broad.mit.edu	37	19	9019331	9019331	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9019331G>T	uc002mkp.2	-	c.37556C>A	c.(37555-37557)ACC>AAC	p.T12519N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12521	Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.075188	-2.74788	21.873989	10	123	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	9019331	9019331	10367	19	G	T	T	T	572	44	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9061146	9061146	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9061146G>T	uc002mkp.2	-	c.26300C>A	c.(26299-26301)ACG>AAG	p.T8767K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8769	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.081871	2.220713	32.662493	14	157	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	9061146	9061146	10367	19	G	T	T	T	520	40	MUC16	1	1
MUC16	94025	broad.mit.edu	37	19	9061229	9061229	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9061229C>T	uc002mkp.2	-	c.26217G>A	c.(26215-26217)AAG>AAA	p.K8739K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8741	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.103774	9.029893	25.648862	11	95	KEEP	---	---	---	---	capture		Silent	SNP	9061229	9061229	10367	19	C	T	T	T	311	24	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9061841	9061841	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9061841C>G	uc002mkp.2	-	c.25605G>C	c.(25603-25605)GAG>GAC	p.E8535D		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8537	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.07767	2.316642	21.10597	8	95	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	9061841	9061841	10367	19	C	G	G	G	415	32	MUC16	3	3
MUC16	94025	broad.mit.edu	37	19	9067106	9067106	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9067106G>T	uc002mkp.2	-	c.20340C>A	c.(20338-20340)GTC>GTA	p.V6780V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6782	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.09375	14.028827	72.417173	33	319	KEEP	---	---	---	---	capture		Silent	SNP	9067106	9067106	10367	19	G	T	T	T	574	45	MUC16	2	2
PALMD	54873	broad.mit.edu	37	1	100133241	100133241	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:100133241G>T	uc001dsf.2	+	c.170G>T	c.(169-171)AGC>ATC	p.S57I	PALMD_uc001dsg.2_Missense_Mutation_p.S57I	NM_017734	NP_060204	Q9NP74	PALMD_HUMAN	palmdelphin	57	Potential.				regulation of cell shape	cytoplasm|membrane				ovary(1)|pancreas(1)	2		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)										0.108974	12.05865	35.70192	17	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100133241	100133241	11828	1	G	T	T	T	442	34	PALMD	2	2
AMY2B	280	broad.mit.edu	37	1	104116920	104116920	+	Silent	SNP	C	T	T	rs12131520		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:104116920C>T	uc001duq.2	+	c.783C>T	c.(781-783)GAC>GAT	p.D261D	AMY2B_uc010ouo.1_Non-coding_Transcript|LOC648740_uc001dur.2_Silent_p.D261D|AMY2B_uc001dus.1_5'Flank	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	261					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)										0.127778	32.595194	56.909234	23	157	KEEP	---	---	---	---	capture		Silent	SNP	104116920	104116920	598	1	C	T	T	T	259	20	AMY2B	2	2
EPS8L3	79574	broad.mit.edu	37	1	110294292	110294292	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110294292C>T	uc001dyq.1	-	c.1550G>A	c.(1549-1551)GGC>GAC	p.G517D	EPS8L3_uc001dys.1_Missense_Mutation_p.G486D|EPS8L3_uc001dyr.1_Missense_Mutation_p.G516D|EPS8L3_uc009wfm.1_Missense_Mutation_p.G453D|EPS8L3_uc009wfn.1_Missense_Mutation_p.G461D	NM_139053	NP_620641	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway	516						cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)										0.119048	5.751516	11.731136	5	37	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	110294292	110294292	5390	1	C	T	T	T	338	26	EPS8L3	2	2
VANGL1	81839	broad.mit.edu	37	1	116206407	116206407	+	Silent	SNP	C	T	T	rs41275546		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:116206407C>T	uc001efv.1	+	c.330C>T	c.(328-330)TAC>TAT	p.Y110Y	VANGL1_uc009wgy.1_Silent_p.Y108Y|VANGL1_uc001efw.1_Silent_p.Y110Y	NM_138959	NP_620409	Q8TAA9	VANG1_HUMAN	vang-like 1	110	Cytoplasmic (Potential).				multicellular organismal development	integral to membrane	protein binding			central_nervous_system(1)	1	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)										0.121212	4.380334	9.018412	4	29	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	116206407	116206407	17684	1	C	T	T	T	233	18	VANGL1	2	2
GJA5	2702	broad.mit.edu	37	1	147231026	147231026	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:147231026C>G	uc001eps.1	-	c.321G>C	c.(319-321)AAG>AAC	p.K107N	GJA5_uc001ept.1_Missense_Mutation_p.K107N	NM_181703	NP_859054	P36382	CXA5_HUMAN	connexin 40	107	Cytoplasmic (Potential).				angiogenesis|cell-cell junction assembly|muscle contraction	integral to membrane				ovary(1)	1	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)											0.115385	14.019672	29.183552	12	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147231026	147231026	6672	1	C	G	G	G	363	28	GJA5	3	3
HIST2H2AC	8338	broad.mit.edu	37	1	149858798	149858798	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:149858798G>A	uc001etd.2	+	c.274G>A	c.(274-276)GAG>AAG	p.E92K	HIST2H2BE_uc001etc.2_5'Flank	NM_003517	NP_003508	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	92					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)	1	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)											0.113744	24.193547	55.214826	24	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149858798	149858798	7465	1	G	A	A	A	481	37	HIST2H2AC	1	1
VPS45	11311	broad.mit.edu	37	1	150082663	150082663	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:150082663C>T	uc001etp.2	+	c.1546C>T	c.(1546-1548)CTA>TTA	p.L516L	VPS45_uc010pbp.1_Non-coding_Transcript|VPS45_uc010pbq.1_Silent_p.L480L|VPS45_uc010pbs.1_Silent_p.L411L|VPS45_uc001etq.2_Silent_p.L336L	NM_007259	NP_009190	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45A	516					blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)	1	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.128205	7.84742	13.100607	5	34	KEEP	---	---	---	---	capture		Silent	SNP	150082663	150082663	17778	1	C	T	T	T	415	32	VPS45	2	2
LINGO4	339398	broad.mit.edu	37	1	151773964	151773964	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151773964C>G	uc001ezf.1	-	c.1217G>C	c.(1216-1218)GGG>GCG	p.G406A		NM_001004432	NP_001004432	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	406	Extracellular (Potential).|LRRCT.					integral to membrane				large_intestine(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)											0.112676	8.754904	19.267338	8	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151773964	151773964	9144	1	C	G	G	G	286	22	LINGO4	3	3
FLG	2312	broad.mit.edu	37	1	152275372	152275372	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152275372C>T	uc001ezu.1	-	c.11990G>A	c.(11989-11991)GGA>GAA	p.G3997E		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3997					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)											0.1	4.669098	15.861656	7	63	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	152275372	152275372	6160	1	C	T	T	T	390	30	FLG	2	2
FLG2	388698	broad.mit.edu	37	1	152329506	152329506	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152329506G>T	uc001ezw.3	-	c.756C>A	c.(754-756)AAC>AAA	p.N252K		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	252	Ser-rich.|Filaggrin 1.						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)											0.113043	13.914215	30.890486	13	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152329506	152329506	6161	1	G	T	T	T	464	36	FLG2	2	2
KPRP	448834	broad.mit.edu	37	1	152732787	152732787	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152732787G>A	uc001fal.1	+	c.723G>A	c.(721-723)GGG>GGA	p.G241G		NM_001025231	NP_001020402	Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	241						cytoplasm				ovary(4)|pancreas(1)	5	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.087302	3.628352	25.345427	11	115	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	152732787	152732787	8751	1	G	A	A	A	522	41	KPRP	2	2
S100A3	6274	broad.mit.edu	37	1	153520845	153520845	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153520845C>T	uc001fca.1	-	c.117G>A	c.(115-117)CAG>CAA	p.Q39Q	S100A4_uc001fby.2_5'Flank|S100A4_uc001fbz.2_5'Flank	NM_002960	NP_002951	P33764	S10A3_HUMAN	S100 calcium binding protein A3	39	EF-hand 1.						calcium ion binding|protein binding				0	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.092308	6.396876	28.152153	12	118	KEEP	---	---	---	---	capture		Silent	SNP	153520845	153520845	14259	1	C	T	T	T	415	32	S100A3	2	2
GATAD2B	57459	broad.mit.edu	37	1	153788945	153788945	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153788945G>A	uc001fdb.3	-	c.1020C>T	c.(1018-1020)AGC>AGT	p.S340S		NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	340	CR2.				regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)											0.183673	15.145786	19.751923	9	40	KEEP	---	---	---	---	capture		Silent	SNP	153788945	153788945	6525	1	G	A	A	A	490	38	GATAD2B	1	1
UBAP2L	9898	broad.mit.edu	37	1	154213988	154213988	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154213988G>A	uc001fep.3	+	c.704_splice	c.e9-1	p.S235_splice	UBAP2L_uc009wot.2_Splice_Site_SNP_p.S235_splice|UBAP2L_uc010pek.1_Splice_Site_SNP_p.S227_splice|UBAP2L_uc010pel.1_Splice_Site_SNP_p.S245_splice|UBAP2L_uc010pen.1_Splice_Site_SNP_p.S149_splice	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)											0.104478	7.773981	18.199896	7	60	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	154213988	154213988	17395	1	G	A	A	A	455	35	UBAP2L	5	2
ZBTB7B	51043	broad.mit.edu	37	1	154988743	154988743	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154988743C>G	uc001fgj.3	+	c.1304C>G	c.(1303-1305)CCC>CGC	p.P435R	ZBTB7B_uc001fgk.3_Missense_Mutation_p.P401R|ZBTB7B_uc009wpa.2_Missense_Mutation_p.P401R|ZBTB7B_uc010peq.1_Missense_Mutation_p.P435R|ZBTB7B_uc001fgl.3_Missense_Mutation_p.P401R	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	401					cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|specific RNA polymerase II transcription factor activity|zinc ion binding				0	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)											0.076923	-7.457013	16.407902	10	120	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	154988743	154988743	18141	1	C	G	G	G	286	22	ZBTB7B	3	3
THBS3	7059	broad.mit.edu	37	1	155167915	155167915	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155167915G>A	uc001fix.2	-	c.2171C>T	c.(2170-2172)ACG>ATG	p.T724M	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Missense_Mutation_p.T715M|THBS3_uc001fiz.2_Missense_Mutation_p.T687M|THBS3_uc001fiy.2_Missense_Mutation_p.T253M|THBS3_uc010pfu.1_Missense_Mutation_p.T604M|THBS3_uc010pfv.1_Non-coding_Transcript	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	724					cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		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)							217				0.220588	35.295457	40.178112	15	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155167915	155167915	16383	1	G	A	A	A	520	40	THBS3	1	1
GBA	2629	broad.mit.edu	37	1	155209714	155209714	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155209714C>G	uc001fjh.2	-	c.270G>C	c.(268-270)CTG>CTC	p.L90L	RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Intron|GBA_uc010pfx.1_Silent_p.L90L|GBA_uc001fji.2_Silent_p.L90L|GBA_uc001fjj.2_Silent_p.L90L|GBA_uc001fjk.2_Silent_p.L90L|GBA_uc001fjl.2_Silent_p.L90L|GBA_uc010pfy.1_Silent_p.L3L|GBA_uc009wqk.1_Silent_p.L3L	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor	90					carbohydrate metabolic process|cell death|lysosome organization|sphingolipid metabolic process	lysosomal membrane	cation binding|glucosylceramidase activity|protein binding			ovary(1)	1	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)		Alglucerase(DB00088)|Imiglucerase(DB00053)									0.111111	9.882634	19.297887	7	56	KEEP	---	---	---	---	capture		Silent	SNP	155209714	155209714	6532	1	C	G	G	G	366	29	GBA	3	3
RUSC1	23623	broad.mit.edu	37	1	155291648	155291648	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155291648C>T	uc001fkj.2	+	c.84C>T	c.(82-84)CGC>CGT	p.R28R	RAG1AP1_uc010pey.1_Intron|C1orf104_uc001fkh.1_5'Flank|C1orf104_uc001fki.2_Intron|RUSC1_uc001fkk.2_Silent_p.R28R|RUSC1_uc009wqn.1_Non-coding_Transcript|RUSC1_uc009wqo.1_5'Flank|RUSC1_uc001fkl.2_5'Flank|RUSC1_uc001fkp.2_5'Flank|RUSC1_uc001fkq.2_5'Flank|RUSC1_uc010pgb.1_5'Flank|RUSC1_uc009wqp.1_5'Flank|RUSC1_uc001fkn.2_5'Flank|RUSC1_uc001fko.2_5'Flank|RUSC1_uc001fkr.2_5'Flank	NM_001105203	NP_001098673	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1 isoform a	28						cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)											0.207407	58.464696	69.150557	28	107	KEEP	---	---	---	---	capture		Silent	SNP	155291648	155291648	14230	1	C	T	T	T	327	26	RUSC1	2	2
BCAN	63827	broad.mit.edu	37	1	156622617	156622617	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156622617G>T	uc001fpp.2	+	c.1875G>T	c.(1873-1875)GTG>GTT	p.V625V	BCAN_uc001fpo.2_Silent_p.V625V	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	625					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.103896	6.886454	18.872212	8	69	KEEP	---	---	---	---	capture		Silent	SNP	156622617	156622617	1366	1	G	T	T	T	587	46	BCAN	2	2
NES	10763	broad.mit.edu	37	1	156640981	156640981	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156640981A>T	uc001fpq.2	-	c.2999T>A	c.(2998-3000)CTG>CAG	p.L1000Q		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	1000	Tail.				brain development|embryonic camera-type eye development|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.07173	-3.796471	40.957679	17	220	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	156640981	156640981	10736	1	A	T	T	T	91	7	NES	3	3
SPTA1	6708	broad.mit.edu	37	1	158622358	158622358	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158622358C>G	uc001fst.1	-	c.3274G>C	c.(3274-3276)GGA>CGA	p.G1092R		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1092	Spectrin 11.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.111111	7.50952	15.584088	6	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158622358	158622358	15630	1	C	G	G	G	312	24	SPTA1	3	3
SPTA1	6708	broad.mit.edu	37	1	158627405	158627405	+	Silent	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158627405A>T	uc001fst.1	-	c.2667T>A	c.(2665-2667)GCT>GCA	p.A889A		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	889	Spectrin 9.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.155039	35.936905	50.586897	20	109	KEEP	---	---	---	---	capture		Silent	SNP	158627405	158627405	15630	1	A	T	T	T	184	15	SPTA1	3	3
OR6K2	81448	broad.mit.edu	37	1	158669912	158669912	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158669912G>A	uc001fsu.1	-	c.531C>T	c.(529-531)TTC>TTT	p.F177F		NM_001005279	NP_001005279	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)													0.078014	-0.98765	24.685591	11	130	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	158669912	158669912	11612	1	G	A	A	A	425	33	OR6K2	2	2
OR6N2	81442	broad.mit.edu	37	1	158746557	158746557	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158746557T>A	uc010pir.1	-	c.869A>T	c.(868-870)TAC>TTC	p.Y290F		NM_001005278	NP_001005278	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N,	290	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_hematologic(112;0.0378)													0.137584	66.687036	104.537982	41	257	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158746557	158746557	11617	1	T	A	A	A	741	57	OR6N2	3	3
VANGL2	57216	broad.mit.edu	37	1	160394996	160394996	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160394996A>C	uc001fwb.1	+	c.1394A>C	c.(1393-1395)GAG>GCG	p.E465A	VANGL2_uc001fwc.1_Missense_Mutation_p.E465A	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	465	Cytoplasmic (Potential).				apical protein localization|heart looping|sensory cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.125	7.447331	18.620609	10	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160394996	160394996	17685	1	A	C	C	C	143	11	VANGL2	4	4
ARHGAP30	257106	broad.mit.edu	37	1	161029432	161029432	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161029432C>A	uc001fxl.2	-	c.172G>T	c.(172-174)GGG>TGG	p.G58W	ARHGAP30_uc001fxk.2_Missense_Mutation_p.G58W|ARHGAP30_uc001fxm.2_De_novo_Start_InFrame|ARHGAP30_uc009wtx.2_De_novo_Start_InFrame|ARHGAP30_uc001fxn.1_De_novo_Start_InFrame	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	58	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)	2	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)											0.112903	7.079326	16.25104	7	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161029432	161029432	891	1	C	A	A	A	312	24	ARHGAP30	2	2
SPEN	23013	broad.mit.edu	37	1	16261546	16261546	+	Silent	SNP	C	T	T	rs111293962		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:16261546C>T	uc001axk.1	+	c.8811C>T	c.(8809-8811)AAC>AAT	p.N2937N	SPEN_uc010obp.1_Silent_p.N2896N	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	2937					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	14		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)					p.N2937N(LCLC103H-Tumor)|p.N2937N(MHHCALL3-Tumor)|p.N2937N(RT112-Tumor)|p.N2937N(RT11284-Tumor)	551				0.105263	3.710264	12.539548	6	51	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	16261546	16261546	15550	1	C	T	T	T	220	17	SPEN	2	2
PBX1	5087	broad.mit.edu	37	1	164815883	164815883	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:164815883T>C	uc001gct.2	+	c.1263T>C	c.(1261-1263)CCT>CCC	p.P421P	PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Silent_p.P338P|PBX1_uc001gcs.2_3'UTR|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	421					negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulator activity		EWSR1/PBX1(3)	soft_tissue(3)	3										361				0.137255	45.751759	78.243726	35	220	KEEP	---	---	---	---	capture		Silent	SNP	164815883	164815883	11912	1	T	C	C	C	704	55	PBX1	4	4
ILDR2	387597	broad.mit.edu	37	1	166896326	166896326	+	Silent	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:166896326T>A	uc001gdx.1	-	c.972A>T	c.(970-972)CCA>CCT	p.P324P		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	324	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1														0.146667	20.874319	29.87189	11	64	KEEP	---	---	---	---	capture		Silent	SNP	166896326	166896326	8011	1	T	A	A	A	704	55	ILDR2	3	3
DCAF6	55827	broad.mit.edu	37	1	168014232	168014232	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:168014232A>G	uc001gex.2	+	c.2025A>G	c.(2023-2025)GAA>GAG	p.E675E	DCAF6_uc001gev.2_Silent_p.E618E|DCAF6_uc001gew.2_Silent_p.E598E|DCAF6_uc010plk.1_Silent_p.E644E|DCAF6_uc001gey.2_Silent_p.E471E|DCAF6_uc001gez.2_5'UTR	NM_018442	NP_060912	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform a	603					positive regulation of transcription from RNA polymerase II promoter|protein ubiquitination	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)	2														0.147541	34.477007	49.026007	18	104	KEEP	---	---	---	---	capture		Silent	SNP	168014232	168014232	4445	1	A	G	G	G	50	4	DCAF6	4	4
PIGC	5279	broad.mit.edu	37	1	172411045	172411045	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:172411045C>G	uc001gil.2	-	c.718G>C	c.(718-720)GTG>CTG	p.V240L	PIGC_uc001gii.1_Intron|PIGC_uc001gij.1_Intron|C1orf105_uc001gik.2_Intron|PIGC_uc001gin.2_Missense_Mutation_p.V240L|PIGC_uc001gio.2_Missense_Mutation_p.V240L	NM_153747	NP_714969	Q92535	PIGC_HUMAN	phosphatidylinositol glycan, class C	240	Helical; (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			lung(1)	1														0.111111	10.48721	19.898158	7	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172411045	172411045	12310	1	C	G	G	G	247	19	PIGC	3	3
ASTN1	460	broad.mit.edu	37	1	176863786	176863786	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176863786C>A	uc001glc.2	-	c.2852G>T	c.(2851-2853)AGC>ATC	p.S951I	ASTN1_uc001glb.1_Missense_Mutation_p.S951I|ASTN1_uc001gld.1_Missense_Mutation_p.S951I	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	959					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	11										849				0.152381	27.239702	39.377649	16	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176863786	176863786	1083	1	C	A	A	A	364	28	ASTN1	2	2
C1orf25	81627	broad.mit.edu	37	1	185125793	185125793	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:185125793C>A	uc001grf.3	-	c.52G>T	c.(52-54)GAG>TAG	p.E18*	C1orf26_uc001grg.3_5'Flank|C1orf26_uc001grh.3_5'Flank|C1orf25_uc010pon.1_Intron	NM_030934	NP_112196	Q7Z2T5	TRM1L_HUMAN	N2,N2-dimethylguanosine tRNA	18						intracellular	RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding				0														0.208333	10.36041	12.252527	5	19	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	185125793	185125793	2108	1	C	A	A	A	390	30	C1orf25	5	2
HMCN1	83872	broad.mit.edu	37	1	185951496	185951496	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:185951496G>T	uc001grq.1	+	c.2765G>T	c.(2764-2766)CGT>CTT	p.R922L	HMCN1_uc001grr.1_Missense_Mutation_p.R263L	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	922	Ig-like C2-type 6.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.133333	13.058234	20.887237	8	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185951496	185951496	7511	1	G	T	T	T	520	40	HMCN1	1	1
FAM5C	339479	broad.mit.edu	37	1	190067563	190067563	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:190067563A>C	uc001gse.1	-	c.1886T>G	c.(1885-1887)CTG>CGG	p.L629R	FAM5C_uc010pot.1_Missense_Mutation_p.L527R	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	629						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.140411	68.974706	105.654234	41	251	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190067563	190067563	5817	1	A	C	C	C	91	7	FAM5C	4	4
RNPEP	6051	broad.mit.edu	37	1	201958634	201958634	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201958634C>T	uc001gxd.2	+	c.712C>T	c.(712-714)CTG>TTG	p.L238L	RNPEP_uc001gxe.2_Intron|RNPEP_uc001gxf.2_Silent_p.L107L	NM_020216	NP_064601	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase	238					leukotriene biosynthetic process|proteolysis		epoxide hydrolase activity|zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		GBM(19;39 479 7473 13131 19462)								0.130435	13.624514	22.793561	9	60	KEEP	---	---	---	---	capture		Silent	SNP	201958634	201958634	13988	1	C	T	T	T	415	32	RNPEP	2	2
PROX1	5629	broad.mit.edu	37	1	214171034	214171034	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:214171034C>T	uc001hkh.2	+	c.1156C>T	c.(1156-1158)CTC>TTC	p.L386F	PROX1_uc001hkg.1_Missense_Mutation_p.L386F	NM_002763	NP_002754	Q92786	PROX1_HUMAN	prospero homeobox 1	386					aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of gene-specific transcription|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of gene-specific transcription|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulator activity			ovary(3)|lung(1)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)										0.085714	3.222461	27.556012	12	128	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	214171034	214171034	13003	1	C	T	T	T	416	32	PROX1	2	2
HHIPL2	79802	broad.mit.edu	37	1	222717463	222717463	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222717463C>G	uc001hnh.1	-	c.390G>C	c.(388-390)CCG>CCC	p.P130P		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	130					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)										0.179775	31.767216	40.340367	16	73	KEEP	---	---	---	---	capture		Silent	SNP	222717463	222717463	7378	1	C	G	G	G	288	23	HHIPL2	3	3
CDC42BPA	8476	broad.mit.edu	37	1	227333373	227333373	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:227333373C>T	uc001hqr.2	-	c.960G>A	c.(958-960)AGG>AGA	p.R320R	CDC42BPA_uc001hqs.2_Silent_p.R320R|CDC42BPA_uc009xes.2_Silent_p.R320R|CDC42BPA_uc010pvs.1_Silent_p.R320R	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	320	Protein kinase.				actin cytoskeleton reorganization|intracellular signal transduction|protein phosphorylation	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|ovary(1)|pancreas(1)	10		all_cancers(173;0.156)|Prostate(94;0.0792)								1574				0.102564	5.440393	17.721389	8	70	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	227333373	227333373	3200	1	C	T	T	T	337	26	CDC42BPA	2	2
URB2	9816	broad.mit.edu	37	1	229771573	229771573	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229771573A>G	uc001hts.1	+	c.1213A>G	c.(1213-1215)ATA>GTA	p.I405V	URB2_uc009xfd.1_Missense_Mutation_p.I405V	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	405						nucleolus				central_nervous_system(2)|ovary(1)	3										340				0.173913	16.173359	20.789165	8	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229771573	229771573	17587	1	A	G	G	G	104	8	URB2	4	4
TTC13	79573	broad.mit.edu	37	1	231052000	231052000	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:231052000G>A	uc001huf.3	-	c.2032C>T	c.(2032-2034)CCC>TCC	p.P678S	TTC13_uc009xfi.2_Missense_Mutation_p.P625S|TTC13_uc009xfj.2_Non-coding_Transcript|TTC13_uc001hug.3_Missense_Mutation_p.P624S|TTC13_uc009xfk.1_Missense_Mutation_p.P567S	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	678							binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)										0.152027	78.018518	112.304412	45	251	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231052000	231052000	17234	1	G	A	A	A	533	41	TTC13	2	2
SIPA1L2	57568	broad.mit.edu	37	1	232607217	232607217	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:232607217C>T	uc001hvg.2	-	c.2143G>A	c.(2143-2145)GGG>AGG	p.G715R		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	715	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.09	3.496596	20.461563	9	91	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	232607217	232607217	14825	1	C	T	T	T	273	21	SIPA1L2	2	2
NID1	4811	broad.mit.edu	37	1	236142361	236142361	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236142361C>T	uc001hxo.2	-	c.3556G>A	c.(3556-3558)GCT>ACT	p.A1186T	NID1_uc009xgd.2_Missense_Mutation_p.A1053T|NID1_uc009xgc.2_Missense_Mutation_p.A267T	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	1186					bioluminescence|cell-matrix adhesion|protein-chromophore linkage	basement membrane|membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)									0.112903	6.578543	15.751481	7	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	236142361	236142361	10815	1	C	T	T	T	325	25	NID1	2	2
GPR137B	7107	broad.mit.edu	37	1	236341783	236341783	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236341783G>T	uc001hxq.2	+	c.534G>T	c.(532-534)GTG>GTT	p.V178V	GPR137B_uc001hxr.1_5'UTR|GPR137B_uc009xge.2_Non-coding_Transcript	NM_003272	NP_003263	O60478	G137B_HUMAN	G protein-coupled receptor 137B	178	Helical; (Potential).			V -> M (in Ref. 4; BAD97352).		integral to plasma membrane|membrane fraction					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)											0.159292	31.471523	43.974971	18	95	KEEP	---	---	---	---	capture		Silent	SNP	236341783	236341783	6920	1	G	T	T	T	587	46	GPR137B	2	2
RYR2	6262	broad.mit.edu	37	1	237756780	237756780	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237756780A>C	uc001hyl.1	+	c.4280A>C	c.(4279-4281)TAT>TCT	p.Y1427S		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1427	Cytoplasmic (By similarity).|B30.2/SPRY 3.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.088889	3.127873	18.517354	8	82	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	237756780	237756780	14249	1	A	C	C	C	208	16	RYR2	4	4
RYR2	6262	broad.mit.edu	37	1	237886504	237886504	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237886504C>G	uc001hyl.1	+	c.10631C>G	c.(10630-10632)CCA>CGA	p.P3544R	RYR2_uc010pxz.1_Missense_Mutation_p.P499R	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3544					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.137097	26.593229	42.397324	17	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237886504	237886504	14249	1	C	G	G	G	273	21	RYR2	3	3
ID3	3399	broad.mit.edu	37	1	23885479	23885479	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23885479G>C	uc001bhh.3	-	c.332C>G	c.(331-333)TCC>TGC	p.S111C	ID3_uc001bhg.1_Missense_Mutation_p.P147A	NM_002167	NP_002158	Q02535	ID3_HUMAN	inhibitor of DNA binding 3	111					negative regulation of sequence-specific DNA binding transcription factor activity	nucleus	transcription corepressor activity|transcription repressor activity			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00314)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;8.83e-25)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;6.5e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)										0.153846	8.382794	11.361402	4	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23885479	23885479	7791	1	G	C	C	C	533	41	ID3	3	3
OPN3	23596	broad.mit.edu	37	1	241757786	241757786	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241757786C>T	uc001hza.2	-	c.1153G>A	c.(1153-1155)GAC>AAC	p.D385N	KMO_uc009xgp.2_3'UTR|OPN3_uc001hzb.2_Non-coding_Transcript|OPN3_uc001hzc.2_Non-coding_Transcript	NM_014322	NP_055137	Q9H1Y3	OPN3_HUMAN	opsin 3	385	Cytoplasmic (Potential).				phototransduction|protein-chromophore linkage|regulation of circadian rhythm|visual perception	integral to plasma membrane	G-protein coupled photoreceptor activity				0	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)											0.159091	25.588843	35.345934	14	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241757786	241757786	11287	1	C	T	T	T	403	31	OPN3	1	1
ZNF669	79862	broad.mit.edu	37	1	247264334	247264334	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247264334C>A	uc001ice.2	-	c.737G>T	c.(736-738)GGA>GTA	p.G246V	ZNF669_uc001icf.2_Missense_Mutation_p.G160V	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	246					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)											0.116279	4.240347	10.478719	5	38	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	247264334	247264334	18671	1	C	A	A	A	390	30	ZNF669	2	2
NLRP3	114548	broad.mit.edu	37	1	247587649	247587649	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247587649G>T	uc001icr.2	+	c.904G>T	c.(904-906)GAC>TAC	p.D302Y	NLRP3_uc001ics.2_Missense_Mutation_p.D302Y|NLRP3_uc001icu.2_Missense_Mutation_p.D302Y|NLRP3_uc001icw.2_Missense_Mutation_p.D302Y|NLRP3_uc001icv.2_Missense_Mutation_p.D302Y|NLRP3_uc010pyw.1_Missense_Mutation_p.D300Y|NLRP3_uc001ict.1_Missense_Mutation_p.D300Y	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	302	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			ovary(5)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	11	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)							412				0.089744	2.068851	15.317538	7	71	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	247587649	247587649	10881	1	G	T	T	T	533	41	NLRP3	2	2
TRIM63	84676	broad.mit.edu	37	1	26384907	26384907	+	Missense_Mutation	SNP	C	T	T	rs61749355		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26384907C>T	uc001bli.1	-	c.805G>A	c.(805-807)GAG>AAG	p.E269K		NM_032588	NP_115977	Q969Q1	TRI63_HUMAN	muscle specific ring finger protein 1	269	COS.|Potential.					cytoplasm|microtubule|nucleus	ligase activity|signal transducer activity|titin binding|zinc ion binding			kidney(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)										0.243243	23.060142	25.281075	9	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26384907	26384907	17084	1	C	T	T	T	403	31	TRIM63	1	1
USP24	23358	broad.mit.edu	37	1	55600058	55600058	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:55600058G>A	uc001cyg.3	-	c.2750C>T	c.(2749-2751)GCT>GTT	p.A917V		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	1077					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13														0.125	7.348366	12.842415	5	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55600058	55600058	17618	1	G	A	A	A	442	34	USP24	2	2
LRRC7	57554	broad.mit.edu	37	1	70484411	70484411	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70484411C>A	uc001dep.2	+	c.1216C>A	c.(1216-1218)CTT>ATT	p.L406I	LRRC7_uc009wbg.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	406	LRR 17.					centrosome|focal adhesion|nucleolus	protein binding			ovary(8)|breast(2)|central_nervous_system(2)|liver(1)	13										783				0.084746	0.753522	11.056163	5	54	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	70484411	70484411	9396	1	C	A	A	A	312	24	LRRC7	2	2
LRRC7	57554	broad.mit.edu	37	1	70505059	70505059	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70505059C>T	uc001dep.2	+	c.3438C>T	c.(3436-3438)CCC>CCT	p.P1146P	LRRC7_uc009wbg.2_Silent_p.P430P|LRRC7_uc001deq.2_Silent_p.P387P	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1146						centrosome|focal adhesion|nucleolus	protein binding			ovary(8)|breast(2)|central_nervous_system(2)|liver(1)	13									p.P1146P(CHAGOK1-Tumor)	783				0.192982	21.729494	26.726997	11	46	KEEP	---	---	---	---	capture		Silent	SNP	70505059	70505059	9396	1	C	T	T	T	275	22	LRRC7	2	2
LRRIQ3	127255	broad.mit.edu	37	1	74507233	74507233	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:74507233A>C	uc001dfy.3	-	c.1382T>G	c.(1381-1383)TTG>TGG	p.L461W	LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	461										ovary(2)	2										2				0.12	32.249997	57.041084	21	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74507233	74507233	9406	1	A	C	C	C	65	5	LRRIQ3	4	4
CLCA1	1179	broad.mit.edu	37	1	86959934	86959934	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86959934G>T	uc001dlt.2	+	c.1745G>T	c.(1744-1746)CGT>CTT	p.R582L	CLCA1_uc001dls.1_Missense_Mutation_p.R521L	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor	582					calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)										0.085714	0.901046	13.081549	6	64	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	86959934	86959934	3593	1	G	T	T	T	520	40	CLCA1	1	1
ZNF644	84146	broad.mit.edu	37	1	91405078	91405078	+	Silent	SNP	T	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:91405078T>G	uc001dnw.2	-	c.1833A>C	c.(1831-1833)TCA>TCC	p.S611S	ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron|ZNF644_uc001dny.1_Silent_p.S611S	NM_201269	NP_958357	Q9H582	ZN644_HUMAN	zinc finger protein 644 isoform 1	611					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)										0.134831	23.039894	34.542101	12	77	KEEP	---	---	---	---	capture		Silent	SNP	91405078	91405078	18655	1	T	G	G	G	652	51	ZNF644	4	4
SPTLC3	55304	broad.mit.edu	37	20	13098266	13098266	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:13098266G>A	uc002wod.1	+	c.1046G>A	c.(1045-1047)CGG>CAG	p.R349Q		NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base	349					sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)									0.153285	34.883801	50.668598	21	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13098266	13098266	15639	20	G	A	A	A	507	39	SPTLC3	1	1
ZNF133	7692	broad.mit.edu	37	20	18296557	18296557	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:18296557C>T	uc010zrv.1	+	c.1071C>T	c.(1069-1071)ATC>ATT	p.I357I	ZNF133_uc010gcq.2_Silent_p.I354I|ZNF133_uc010zrw.1_Silent_p.I291I|ZNF133_uc010gcr.2_Silent_p.I354I|ZNF133_uc010zrx.1_Silent_p.I259I|ZNF133_uc002wql.3_Silent_p.I353I|ZNF133_uc010gcs.2_Silent_p.I353I|ZNF133_uc010zry.1_Silent_p.I259I|ZNF133_uc002wqm.2_Silent_p.I354I	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	354	C2H2-type 6.				regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2														0.153846	22.076203	30.990626	12	66	KEEP	---	---	---	---	capture		Silent	SNP	18296557	18296557	18314	20	C	T	T	T	395	31	ZNF133	1	1
CD93	22918	broad.mit.edu	37	20	23065996	23065996	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23065996C>G	uc002wsv.2	-	c.834G>C	c.(832-834)GGG>GGC	p.G278G		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	278	EGF-like 1.|Extracellular (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	integral to membrane|plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)													0.212121	14.004484	16.535343	7	26	KEEP	---	---	---	---	capture		Silent	SNP	23065996	23065996	3175	20	C	G	G	G	275	22	CD93	3	3
TGM3	7053	broad.mit.edu	37	20	2320589	2320589	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2320589G>T	uc002wfx.3	+	c.1890G>T	c.(1888-1890)CTG>CTT	p.L630L		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	630					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)	8					L-Glutamine(DB00130)									0.272727	7.419661	7.932142	3	8	KEEP	---	---	---	---	capture		Silent	SNP	2320589	2320589	16359	20	G	T	T	T	574	45	TGM3	2	2
CEP250	11190	broad.mit.edu	37	20	34091163	34091163	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34091163A>T	uc002xcm.2	+	c.4966A>T	c.(4966-4968)AGA>TGA	p.R1656*	CEP250_uc010zve.1_Nonsense_Mutation_p.R1024*	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	1656	Gln/Glu-rich.|Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)											0.081761	-3.235036	25.092339	13	146	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	34091163	34091163	3385	20	A	T	T	T	140	11	CEP250	5	3
DLGAP4	22839	broad.mit.edu	37	20	35061024	35061024	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:35061024G>A	uc002xff.2	+	c.904G>A	c.(904-906)GCC>ACC	p.A302T	DLGAP4_uc010zvp.1_Missense_Mutation_p.A302T	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a	302					cell-cell signaling	membrane	protein binding			ovary(1)|skin(1)	2	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)												0.214286	7.121181	8.173681	3	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35061024	35061024	4742	20	G	A	A	A	494	38	DLGAP4	1	1
LBP	3929	broad.mit.edu	37	20	36997785	36997785	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:36997785G>A	uc002xic.1	+	c.1128G>A	c.(1126-1128)GAG>GAA	p.E376E		NM_004139	NP_004130	P18428	LBP_HUMAN	lipopolysaccharide-binding protein precursor	376					acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)												0.232877	39.061355	43.814546	17	56	KEEP	---	---	---	---	capture		Silent	SNP	36997785	36997785	8974	20	G	A	A	A	438	34	LBP	2	2
FAM65C	140876	broad.mit.edu	37	20	49212036	49212036	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49212036C>T	uc010zyt.1	-	c.1920G>A	c.(1918-1920)CTG>CTA	p.L640L	FAM65C_uc010zyu.1_Intron|FAM65C_uc002xvm.2_Silent_p.L636L	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	636										ovary(2)	2														0.181818	15.972506	20.158882	8	36	KEEP	---	---	---	---	capture		Silent	SNP	49212036	49212036	5824	20	C	T	T	T	262	21	FAM65C	2	2
ATP9A	10079	broad.mit.edu	37	20	50273602	50273602	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:50273602T>A	uc002xwg.1	-	c.1381A>T	c.(1381-1383)AAG>TAG	p.K461*	ATP9A_uc010gih.1_Nonsense_Mutation_p.K325*|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	461	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4														0.193548	9.927611	12.65222	6	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	50273602	50273602	1217	20	T	A	A	A	806	62	ATP9A	5	3
CTSZ	1522	broad.mit.edu	37	20	57572776	57572776	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:57572776T>C	uc002yai.2	-	c.520A>G	c.(520-522)AAT>GAT	p.N174D	CTSZ_uc002yaj.3_Missense_Mutation_p.N174D|CTSZ_uc010gjt.1_Non-coding_Transcript	NM_001336	NP_001327	Q9UBR2	CATZ_HUMAN	cathepsin Z preproprotein	174					proteolysis	endoplasmic reticulum|extracellular space|lysosome	cysteine-type endopeptidase activity			kidney(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)											0.170213	16.079095	20.908765	8	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57572776	57572776	4202	20	T	C	C	C	819	63	CTSZ	4	4
TMPRSS15	5651	broad.mit.edu	37	21	19687506	19687506	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:19687506G>A	uc002ykw.2	-	c.1989C>T	c.(1987-1989)GAC>GAT	p.D663D		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	663	Extracellular (Potential).|LDL-receptor class A 2.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|breast(1)	6														0.116667	16.575031	33.914054	14	106	KEEP	---	---	---	---	capture		Silent	SNP	19687506	19687506	16787	21	G	A	A	A	516	40	TMPRSS15	1	1
TRPM2	7226	broad.mit.edu	37	21	45860714	45860714	+	Missense_Mutation	SNP	G	T	T	rs45578242		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45860714G>T	uc010gpt.1	+	c.4462G>T	c.(4462-4464)GCC>TCC	p.A1488S	TRPM2_uc002zet.1_Missense_Mutation_p.A1438S|TRPM2_uc002zeu.1_Missense_Mutation_p.A1438S|TRPM2_uc002zew.1_Missense_Mutation_p.A1438S|TRPM2_uc002zex.1_Missense_Mutation_p.A1224S|TRPM2_uc002zey.1_Missense_Mutation_p.A917S|TRPM2_uc011aff.1_Missense_Mutation_p.A119S	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	1438	Nudix hydrolase.|Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.205128	18.57995	21.724063	8	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45860714	45860714	17137	21	G	T	T	T	598	46	TRPM2	2	2
PCNT	5116	broad.mit.edu	37	21	47831327	47831327	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47831327C>T	uc002zji.3	+	c.5340C>T	c.(5338-5340)GCC>GCT	p.A1780A	PCNT_uc002zjj.2_Silent_p.A1662A	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	1780	Potential.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)													0.129032	5.816595	9.938833	4	27	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	47831327	47831327	12010	21	C	T	T	T	288	23	PCNT	1	1
XKR3	150165	broad.mit.edu	37	22	17280787	17280787	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:17280787C>G	uc002zlv.2	-	c.463G>C	c.(463-465)GAT>CAT	p.D155H	XKR3_uc011agf.1_Missense_Mutation_p.D155H	NM_175878	NP_787074	Q5GH77	XKR3_HUMAN	X Kell blood group precursor-related family,	155						integral to membrane|plasma membrane				large_intestine(1)|ovary(1)	2	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)												0.078212	3.565498	36.060725	14	165	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	17280787	17280787	18013	22	C	G	G	G	390	30	XKR3	3	3
CLTCL1	8218	broad.mit.edu	37	22	19207455	19207455	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:19207455G>C	uc002zpb.2	-	c.2858C>G	c.(2857-2859)CCG>CGG	p.P953R	CLTCL1_uc011agv.1_Missense_Mutation_p.P953R|CLTCL1_uc011agw.1_Missense_Mutation_p.P953R	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	953	Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)									1206				0.09589	2.996944	14.933167	7	66	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	19207455	19207455	3705	22	G	C	C	C	507	39	CLTCL1	3	3
TBX1	6899	broad.mit.edu	37	22	19751721	19751721	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:19751721G>C	uc002zqa.1	+	c.556G>C	c.(556-558)GAC>CAC	p.D186H	TBX1_uc002zqb.2_Missense_Mutation_p.D186H|TBX1_uc002zqc.2_Missense_Mutation_p.D186H	NM_080647	NP_542378	O43435	TBX1_HUMAN	T-box 1 isoform C	186	T-box.				embryonic viscerocranium morphogenesis|heart development|parathyroid gland development|pharyngeal system development|regulation of transcription from RNA polymerase II promoter|soft palate development|thymus development	nucleus	protein homodimerization activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)	2	Colorectal(54;0.0993)	all_lung(157;3.05e-06)												0.333333	8.123437	8.344125	3	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19751721	19751721	16176	22	G	C	C	C	481	37	TBX1	3	3
SCARF2	91179	broad.mit.edu	37	22	20781765	20781765	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:20781765G>A	uc002zsj.1	-	c.1628C>T	c.(1627-1629)TCA>TTA	p.S543L	SCARF2_uc002zsk.1_Missense_Mutation_p.S538L	NM_153334	NP_699165	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2 isoform 1	538	Cytoplasmic (Potential).				cell adhesion	integral to membrane	protein binding|receptor activity			breast(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)											0.116279	4.241032	10.477276	5	38	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	20781765	20781765	14365	22	G	A	A	A	585	45	SCARF2	2	2
MYO18B	84700	broad.mit.edu	37	22	26422651	26422651	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26422651G>A	uc003abz.1	+	c.6711G>A	c.(6709-6711)CCG>CCA	p.P2237P	MYO18B_uc003aca.1_Silent_p.P2118P|MYO18B_uc010guy.1_Silent_p.P2119P|MYO18B_uc010guz.1_Silent_p.P2117P|MYO18B_uc011aka.1_Silent_p.P1391P|MYO18B_uc011akb.1_Silent_p.P1750P|MYO18B_uc010gva.1_Silent_p.P220P|MYO18B_uc010gvb.1_Non-coding_Transcript	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2237						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12									p.P2237P(GCT-Tumor)|p.P2237P(NCIH69-Tumor)|p.P2237P(HS229.T-Tumor)	968				0.25	15.716162	17.304669	7	21	KEEP	---	---	---	---	capture		Silent	SNP	26422651	26422651	10461	22	G	A	A	A	483	38	MYO18B	1	1
C22orf31	25770	broad.mit.edu	37	22	29454777	29454777	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:29454777C>G	uc003aej.1	-	c.826G>C	c.(826-828)GAG>CAG	p.E276Q		NM_015370	NP_056185	O95567	CV031_HUMAN	hypothetical protein LOC25770	276											0														0.195122	20.485606	24.031713	8	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29454777	29454777	2224	22	C	G	G	G	403	31	C22orf31	3	3
NEFH	4744	broad.mit.edu	37	22	29885403	29885403	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:29885403G>T	uc003afo.2	+	c.1774G>T	c.(1774-1776)GCA>TCA	p.A592S	NEFH_uc003afp.2_Intron	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	592	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				cell death|nervous system development	neurofilament					0														0.136842	18.513063	30.640001	13	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29885403	29885403	10713	22	G	T	T	T	546	42	NEFH	2	2
THOC5	8563	broad.mit.edu	37	22	29915087	29915087	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:29915087G>A	uc003afr.2	-	c.1397C>T	c.(1396-1398)TCG>TTG	p.S466L	THOC5_uc003afq.2_Missense_Mutation_p.S127L|THOC5_uc003afs.2_Missense_Mutation_p.S466L|THOC5_uc003aft.2_Missense_Mutation_p.S466L|THOC5_uc003afu.2_Missense_Mutation_p.S466L|THOC5_uc010gvo.2_Missense_Mutation_p.S210L	NM_001002878	NP_001002878	Q13769	THOC5_HUMAN	THO complex 5	466					intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding			breast(2)	2														0.15	25.260263	37.007501	15	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29915087	29915087	16396	22	G	A	A	A	481	37	THOC5	1	1
BPIL2	254240	broad.mit.edu	37	22	32843317	32843317	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32843317T>C	uc003amn.2	-	c.256A>G	c.(256-258)AGT>GGT	p.S86G	BPIL2_uc010gwo.2_5'UTR|BPIL2_uc011amb.1_5'UTR	NM_174932	NP_777592	Q8NFQ6	BPIL2_HUMAN	bactericidal/permeability-increasing	86						extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)	1														0.111111	5.308787	13.388301	6	48	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	32843317	32843317	1520	22	T	C	C	C	715	55	BPIL2	4	4
TNRC6B	23112	broad.mit.edu	37	22	40660763	40660763	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40660763A>G	uc011aor.1	+	c.529A>G	c.(529-531)AAC>GAC	p.N177D	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Missense_Mutation_p.N177D|TNRC6B_uc003ayo.2_5'UTR	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	177					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0										794				0.173333	19.635766	27.208093	13	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40660763	40660763	16882	22	A	G	G	G	65	5	TNRC6B	4	4
TNRC6B	23112	broad.mit.edu	37	22	40662984	40662984	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40662984G>C	uc011aor.1	+	c.2750G>C	c.(2749-2751)GGC>GCC	p.G917A	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Missense_Mutation_p.G917A|TNRC6B_uc003ayo.2_Missense_Mutation_p.G721A	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	917					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0										794				0.116279	7.444453	13.674417	5	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40662984	40662984	16882	22	G	C	C	C	546	42	TNRC6B	3	3
RABL2B	11158	broad.mit.edu	37	22	51208446	51208446	+	Splice_Site_SNP	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:51208446T>C	uc003bnm.1	-	c.298_splice	c.e7-1	p.V100_splice	RPL23AP82_uc011asd.1_Intron|RPL23AP82_uc003bni.2_Intron|RABL2B_uc011ase.1_Intron|RABL2B_uc011asf.1_Splice_Site_SNP_p.V100_splice|RABL2B_uc003bnn.1_Splice_Site_SNP_p.V100_splice|RABL2B_uc003bnk.1_Splice_Site_SNP_p.V100_splice|RABL2B_uc003bno.1_Splice_Site_SNP_p.V100_splice|RABL2B_uc011asg.1_Splice_Site_SNP_p.V100_splice|RABL2B_uc003bnl.1_Splice_Site_SNP_p.V100_splice|RABL2B_uc011ash.1_Intron	NM_001130923	NP_001124395			RAB, member of RAS oncogene family-like 2B						small GTPase mediated signal transduction		GTP binding|GTPase activity				0		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.0539)|LUAD - Lung adenocarcinoma(64;0.247)		GBM(148;358 1894 4987 13698 40400)								0.090909	0.900115	12.037919	6	60	FSTAR-RETAIN	---	---	---	---	capture		Splice_Site_SNP	SNP	51208446	51208446	13430	22	T	C	C	C	715	55	RABL2B	5	4
SULT1C2	6819	broad.mit.edu	37	2	108922030	108922030	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:108922030A>G	uc010ywq.1	+	c.799A>G	c.(799-801)ATT>GTT	p.I267V	SULT1C2_uc010ywp.1_Missense_Mutation_p.I168V|SULT1C2_uc002tdx.2_Missense_Mutation_p.I264V|SULT1C2_uc002tdy.2_Missense_Mutation_p.I253V	NM_176825	NP_001047	O00338	ST1C2_HUMAN	sulfotransferase family, cytosolic, 1C, member 1	253					3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine metabolic process|sulfation|xenobiotic metabolic process	cytosol|microtubule cytoskeleton	sulfotransferase activity			ovary(1)	1														0.073394	-1.386887	19.008154	8	101	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	108922030	108922030	15897	2	A	G	G	G	52	4	SULT1C2	4	4
GREB1	9687	broad.mit.edu	37	2	11770205	11770205	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:11770205G>A	uc002rbk.1	+	c.4581G>A	c.(4579-4581)GAG>GAA	p.E1527E	GREB1_uc002rbp.1_Silent_p.E525E	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1527						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		Ovarian(39;850 945 2785 23371 33093)								0.184615	26.363691	32.425585	12	53	KEEP	---	---	---	---	capture		Silent	SNP	11770205	11770205	7037	2	G	A	A	A	425	33	GREB1	2	2
CCDC93	54520	broad.mit.edu	37	2	118698860	118698860	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:118698860C>T	uc002tlj.2	-	c.1427G>A	c.(1426-1428)CGA>CAA	p.R476Q	CCDC93_uc010fld.1_Missense_Mutation_p.R476Q	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	476										large_intestine(1)|ovary(1)	2														0.12844	18.611761	33.243882	14	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118698860	118698860	2997	2	C	T	T	T	403	31	CCDC93	1	1
MYO7B	4648	broad.mit.edu	37	2	128366421	128366421	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128366421G>A	uc002top.2	+	c.2782G>A	c.(2782-2784)GGC>AGC	p.G928S		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	928						apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)										0.230769	7.080103	7.901335	3	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128366421	128366421	10478	2	G	A	A	A	559	43	MYO7B	2	2
HNMT	3176	broad.mit.edu	37	2	138762712	138762712	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:138762712A>G	uc002tvc.2	+	c.440A>G	c.(439-441)TAT>TGT	p.Y147C	HNMT_uc002tvf.2_Missense_Mutation_p.Y147C	NM_006895	NP_008826	P50135	HNMT_HUMAN	histamine N-methyltransferase isoform 1	147					respiratory gaseous exchange	cytoplasm	histamine N-methyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)									0.113208	17.629438	33.271043	12	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138762712	138762712	7547	2	A	G	G	G	208	16	HNMT	4	4
LRP1B	53353	broad.mit.edu	37	2	141116420	141116420	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141116420C>T	uc002tvj.1	-	c.11227G>A	c.(11227-11229)GGT>AGT	p.G3743S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3743	Extracellular (Potential).|LDL-receptor class A 31.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.129032	24.014534	40.63527	16	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141116420	141116420	9328	2	C	T	T	T	299	23	LRP1B	1	1
UPP2	151531	broad.mit.edu	37	2	158991312	158991312	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:158991312C>A	uc002tzo.2	+	c.1035C>A	c.(1033-1035)AAC>AAA	p.N345K	UPP2_uc002tzp.2_Missense_Mutation_p.N288K	NM_001135098	NP_001128570	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform b	288					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0														0.081967	-0.467155	21.322341	10	112	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	158991312	158991312	17574	2	C	A	A	A	259	20	UPP2	2	2
UPP2	151531	broad.mit.edu	37	2	158991346	158991346	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:158991346C>T	uc002tzo.2	+	c.1069C>T	c.(1069-1071)CGG>TGG	p.R357W	UPP2_uc002tzp.2_Missense_Mutation_p.R300W	NM_001135098	NP_001128570	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform b	300					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0														0.214765	74.04044	85.217486	32	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158991346	158991346	17574	2	C	T	T	T	243	19	UPP2	1	1
SLC4A10	57282	broad.mit.edu	37	2	162751233	162751233	+	Silent	SNP	G	A	A	rs61748241		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:162751233G>A	uc002ubx.3	+	c.1239G>A	c.(1237-1239)TTG>TTA	p.L413L	SLC4A10_uc010fpa.1_Silent_p.L425L|SLC4A10_uc010zcr.1_Non-coding_Transcript|SLC4A10_uc002uby.3_Silent_p.L383L|SLC4A10_uc010zcs.1_Silent_p.L394L	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	413	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5														0.147826	25.591476	39.296376	17	98	KEEP	---	---	---	---	capture		Silent	SNP	162751233	162751233	15148	2	G	A	A	A	607	47	SLC4A10	2	2
COBLL1	22837	broad.mit.edu	37	2	165551184	165551184	+	Silent	SNP	C	T	T	rs76695941	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165551184C>T	uc010zcw.1	-	c.3033G>A	c.(3031-3033)AGG>AGA	p.R1011R	COBLL1_uc002ucp.2_Silent_p.R944R|COBLL1_uc002ucq.2_Silent_p.R906R|COBLL1_uc010zcx.1_Silent_p.R952R|COBLL1_uc002ucn.2_Silent_p.R372R|COBLL1_uc002uco.2_Silent_p.R675R	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	982										ovary(2)|pancreas(1)	3														0.135135	6.868014	11.629281	5	32	KEEP	---	---	---	---	capture		Silent	SNP	165551184	165551184	3792	2	C	T	T	T	285	22	COBLL1	2	2
ABCB11	8647	broad.mit.edu	37	2	169787351	169787351	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:169787351C>G	uc002ueo.1	-	c.3235G>C	c.(3235-3237)GAT>CAT	p.D1079H	ABCB11_uc010zda.1_Missense_Mutation_p.D521H|ABCB11_uc010zdb.1_Missense_Mutation_p.D555H	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1079	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)									0.114286	5.67485	10.80772	4	31	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	169787351	169787351	43	2	C	G	G	G	377	29	ABCB11	3	3
UBR3	130507	broad.mit.edu	37	2	170938271	170938271	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170938271A>T	uc010zdi.1	+	c.5585A>T	c.(5584-5586)TAC>TTC	p.Y1862F	UBR3_uc002ufr.3_Non-coding_Transcript|UBR3_uc010fqa.2_Missense_Mutation_p.Y683F|UBR3_uc002uft.3_Missense_Mutation_p.Y719F|UBR3_uc010zdj.1_Missense_Mutation_p.Y553F|UBR3_uc002ufu.3_Missense_Mutation_p.Y368F	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1862					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0														0.129032	12.358439	20.665376	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170938271	170938271	17461	2	A	T	T	T	182	14	UBR3	3	3
MYO3B	140469	broad.mit.edu	37	2	171248951	171248951	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:171248951A>G	uc002ufy.2	+	c.1737A>G	c.(1735-1737)AGA>AGG	p.R579R	MYO3B_uc002ufv.2_Silent_p.R566R|MYO3B_uc010fqb.1_Silent_p.R566R|MYO3B_uc002ufz.2_Silent_p.R579R|MYO3B_uc002ufw.2_Non-coding_Transcript|MYO3B_uc002ufx.2_Non-coding_Transcript|MYO3B_uc002ugb.2_Non-coding_Transcript	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	579	Myosin head-like.				protein phosphorylation|response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(5)|skin(2)|central_nervous_system(1)	16										1118				0.123596	16.45628	28.805395	11	78	KEEP	---	---	---	---	capture		Silent	SNP	171248951	171248951	10472	2	A	G	G	G	115	9	MYO3B	4	4
RAD51AP2	729475	broad.mit.edu	37	2	17699262	17699262	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:17699262C>T	uc002rcl.1	-	c.421G>A	c.(421-423)GAG>AAG	p.E141K	RAD51AP2_uc010exn.1_Missense_Mutation_p.E132K	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	141										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)													0.114286	9.046607	19.316868	8	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17699262	17699262	13447	2	C	T	T	T	416	32	RAD51AP2	2	2
TTN	7273	broad.mit.edu	37	2	179421791	179421791	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179421791C>T	uc010zfg.1	-	c.80386G>A	c.(80386-80388)GGT>AGT	p.G26796S	TTN_uc010zfh.1_Missense_Mutation_p.G20491S|TTN_uc010zfi.1_Missense_Mutation_p.G20424S|TTN_uc010zfj.1_Missense_Mutation_p.G20299S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3187										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.128205	8.647268	13.900241	5	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179421791	179421791	17290	2	C	T	T	T	312	24	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179599524	179599524	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179599524C>T	uc010zfg.1	-	c.11395G>A	c.(11395-11397)GAT>AAT	p.D3799N	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.D460N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3569										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.102804	9.652178	26.463797	11	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179599524	179599524	17290	2	C	T	T	T	390	30	TTN	2	2
MYT1L	23040	broad.mit.edu	37	2	1893099	1893099	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1893099C>A	uc002qxe.2	-	c.2434G>T	c.(2434-2436)GGC>TGC	p.G812C	MYT1L_uc002qxd.2_Missense_Mutation_p.G810C|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	812					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)										0.089286	0.631324	10.173697	5	51	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	1893099	1893099	10502	2	C	A	A	A	286	22	MYT1L	2	2
ANKAR	150709	broad.mit.edu	37	2	190584478	190584478	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:190584478G>C	uc002uqw.1	+	c.2192G>C	c.(2191-2193)CGC>CCC	p.R731P	ANKAR_uc002uqu.2_Non-coding_Transcript|ANKAR_uc002uqx.1_Non-coding_Transcript	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	802	ARM 2.					integral to membrane	binding			ovary(2)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)											0.129032	7.680259	11.832279	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190584478	190584478	626	2	G	C	C	C	494	38	ANKAR	3	3
CPS1	1373	broad.mit.edu	37	2	211441119	211441119	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:211441119A>G	uc010fur.2	+	c.304A>G	c.(304-306)ATG>GTG	p.M102V	CPS1_uc002vee.3_Missense_Mutation_p.M96V	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a	96	Anthranilate phosphoribosyltransferase homolog.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)	12				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)										0.08046	2.822334	34.039304	14	160	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	211441119	211441119	3961	2	A	G	G	G	52	4	CPS1	4	4
APOB	338	broad.mit.edu	37	2	21228305	21228305	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21228305T>A	uc002red.2	-	c.11435A>T	c.(11434-11436)GAG>GTG	p.E3812V		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3812					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.110236	12.057502	31.151532	14	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21228305	21228305	796	2	T	A	A	A	702	54	APOB	3	3
FN1	2335	broad.mit.edu	37	2	216232721	216232721	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:216232721C>T	uc002vfa.2	-	c.6883G>A	c.(6883-6885)GAC>AAC	p.D2295N	FN1_uc002vfb.2_Missense_Mutation_p.D2083N|FN1_uc002vfc.2_Missense_Mutation_p.D2058N|FN1_uc002vfd.2_Missense_Mutation_p.D2239N|FN1_uc002vfe.2_Missense_Mutation_p.D2173N|FN1_uc002vff.2_Missense_Mutation_p.D2148N|FN1_uc002vfg.2_Missense_Mutation_p.D2114N|FN1_uc002vfh.2_Missense_Mutation_p.D1994N|FN1_uc002vfi.2_Missense_Mutation_p.D2264N|FN1_uc002vfj.2_Missense_Mutation_p.D2085N|FN1_uc002vez.2_Missense_Mutation_p.D458N|FN1_uc010zjp.1_Missense_Mutation_p.D832N|FN1_uc002vfk.1_Intron|FN1_uc010fva.1_Non-coding_Transcript|FN1_uc010fvb.1_Non-coding_Transcript	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	2204	Fibronectin type-I 10.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1374				0.103448	2.80092	11.897138	6	52	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	216232721	216232721	6204	2	C	T	T	T	377	29	FN1	2	2
VIL1	7429	broad.mit.edu	37	2	219294119	219294119	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219294119A>C	uc002via.2	+	c.679A>C	c.(679-681)AAC>CAC	p.N227H	VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Missense_Mutation_p.N227H|VIL1_uc002vic.1_Missense_Mutation_p.N227H	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1	227	Core.				actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.190476	17.480088	21.241647	8	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	219294119	219294119	17731	2	A	C	C	C	117	9	VIL1	4	4
SLC23A3	151295	broad.mit.edu	37	2	220026772	220026772	+	Silent	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220026772G>C	uc010zkr.1	-	c.1716C>G	c.(1714-1716)CTC>CTG	p.L572L	NHEJ1_uc002vjp.3_5'Flank|NHEJ1_uc002vjq.3_Intron|SLC23A3_uc010zks.1_Silent_p.L564L|SLC23A3_uc010fwb.2_Silent_p.L447L	NM_001144890	NP_001138362	Q6PIS1	S23A3_HUMAN	solute carrier family 23 (nucleobase	564	Cytoplasmic (Potential).				transmembrane transport	integral to membrane	protein binding|transporter activity				0		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.128205	9.509038	14.709446	5	34	KEEP	---	---	---	---	capture		Silent	SNP	220026772	220026772	14961	2	G	C	C	C	522	41	SLC23A3	3	3
C2orf24	27013	broad.mit.edu	37	2	220040963	220040963	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220040963G>A	uc002vju.3	-	c.160C>T	c.(160-162)CTC>TTC	p.L54F	C2orf24_uc002vjv.2_Missense_Mutation_p.L54F|FAM134A_uc002vjw.3_5'Flank|FAM134A_uc010fwc.2_5'Flank	NM_015680	NP_056495	Q9BV87	CNPD1_HUMAN	hypothetical protein LOC27013	54						integral to membrane					0		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.296296	18.882643	19.889295	8	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220040963	220040963	2245	2	G	A	A	A	442	34	C2orf24	2	2
OBSL1	23363	broad.mit.edu	37	2	220427250	220427250	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220427250C>A	uc010fwk.2	-	c.2827G>T	c.(2827-2829)GCG>TCG	p.A943S	OBSL1_uc010zli.1_5'UTR|OBSL1_uc010fwl.1_Missense_Mutation_p.A418S|OBSL1_uc002vmi.2_Missense_Mutation_p.A943S|OBSL1_uc002vmj.2_Missense_Mutation_p.A530S	NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1	943	Ig-like 7.				cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)										0.166667	6.115676	8.010469	3	15	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	220427250	220427250	11218	2	C	A	A	A	351	27	OBSL1	1	1
TRIP12	9320	broad.mit.edu	37	2	230724018	230724018	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:230724018G>A	uc002vpx.1	-	c.497C>T	c.(496-498)TCT>TTT	p.S166F	TRIP12_uc002vpw.1_Missense_Mutation_p.S124F|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_Non-coding_Transcript|TRIP12_uc010fxh.1_Missense_Mutation_p.S124F	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	124					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|breast(1)|central_nervous_system(1)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)										0.111765	19.892561	45.222334	19	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	230724018	230724018	17106	2	G	A	A	A	429	33	TRIP12	2	2
SP110	3431	broad.mit.edu	37	2	231067349	231067349	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231067349C>G	uc002vqg.3	-	c.994G>C	c.(994-996)GAG>CAG	p.E332Q	SP110_uc002vqh.3_Missense_Mutation_p.E332Q|SP110_uc002vqi.3_Missense_Mutation_p.E332Q|SP110_uc010fxk.2_Missense_Mutation_p.E330Q|SP110_uc010fxj.2_Intron	NM_080424	NP_536349	Q9HB58	SP110_HUMAN	SP110 nuclear body protein isoform c	332					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)						445				0.1	7.570962	18.759145	7	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231067349	231067349	15461	2	C	G	G	G	416	32	SP110	3	3
AGAP1	116987	broad.mit.edu	37	2	236649636	236649636	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:236649636G>A	uc002vvs.2	+	c.340G>A	c.(340-342)GAT>AAT	p.D114N	AGAP1_uc002vvt.2_Missense_Mutation_p.D114N	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	114	Small GTPase-like.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)	2														0.096154	3.53405	12.0393	5	47	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	236649636	236649636	368	2	G	A	A	A	585	45	AGAP1	2	2
SLC4A1AP	22950	broad.mit.edu	37	2	27887160	27887160	+	Missense_Mutation	SNP	C	T	T	rs9679004	byFrequency;by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27887160C>T	uc002rlk.3	+	c.541C>T	c.(541-543)CGT>TGT	p.R181C	SUPT7L_uc002rlh.1_5'Flank|SUPT7L_uc002rli.1_5'Flank|SUPT7L_uc010ymf.1_5'Flank|SUPT7L_uc002rlj.1_5'Flank|SUPT7L_uc010ezh.1_5'Flank	NM_018158	NP_060628	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger),	181						cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)													0.235294	20.484729	22.66204	8	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27887160	27887160	15150	2	C	T	T	T	299	23	SLC4A1AP	1	1
EHD3	30845	broad.mit.edu	37	2	31484432	31484432	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:31484432C>T	uc002rnu.2	+	c.933C>T	c.(931-933)ATC>ATT	p.I311I	EHD3_uc010ymt.1_Intron	NM_014600	NP_055415	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	311					blood coagulation|endocytic recycling|protein homooligomerization	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)													0.119048	8.261282	20.309999	10	74	KEEP	---	---	---	---	capture		Silent	SNP	31484432	31484432	5168	2	C	T	T	T	369	29	EHD3	2	2
ALLC	55821	broad.mit.edu	37	2	3745030	3745030	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:3745030C>G	uc010ewt.2	+	c.834C>G	c.(832-834)GAC>GAG	p.D278E	ALLC_uc002qyf.2_Missense_Mutation_p.D49E	NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a	297							allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)										0.322581	29.238373	30.105241	10	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3745030	3745030	537	2	C	G	G	G	220	17	ALLC	3	3
CDKL4	344387	broad.mit.edu	37	2	39406387	39406387	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:39406387G>C	uc010fal.1	-	c.868C>G	c.(868-870)CAA>GAA	p.Q290E	CDKL4_uc002rrm.2_Missense_Mutation_p.Q290E	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	290					protein phosphorylation	cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)								219				0.130435	16.825544	25.992258	9	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39406387	39406387	3285	2	G	C	C	C	585	45	CDKL4	3	3
TTC7A	57217	broad.mit.edu	37	2	47273468	47273468	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:47273468A>G	uc010fbb.2	+	c.1817A>G	c.(1816-1818)AAG>AGG	p.K606R	TTC7A_uc002rvm.2_Missense_Mutation_p.K572R|TTC7A_uc002rvn.1_Intron|TTC7A_uc002rvo.2_Missense_Mutation_p.K606R|TTC7A_uc010fbc.2_Missense_Mutation_p.K252R|TTC7A_uc002rvp.2_Missense_Mutation_p.K487R|TTC7A_uc002rvq.2_Missense_Mutation_p.K346R|TTC7A_uc002rvr.2_Missense_Mutation_p.K55R	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	606							binding			breast(1)	1		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)											0.176471	21.044314	26.074077	9	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47273468	47273468	17267	2	A	G	G	G	39	3	TTC7A	4	4
TSPYL6	388951	broad.mit.edu	37	2	54483229	54483229	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:54483229C>T	uc002rxr.2	-	c.60G>A	c.(58-60)CCG>CCA	p.P20P	ACYP2_uc002rxq.3_Intron	NM_001003937	NP_001003937	Q8N831	TSYL6_HUMAN	TSPY-like 6	20					nucleosome assembly	nucleus					0														0.149254	15.174686	23.028709	10	57	KEEP	---	---	---	---	capture		Silent	SNP	54483229	54483229	17216	2	C	T	T	T	340	27	TSPYL6	1	1
PNPT1	87178	broad.mit.edu	37	2	55873404	55873404	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:55873404T>C	uc002rzf.2	-	c.1728A>G	c.(1726-1728)CAA>CAG	p.Q576Q	PNPT1_uc002rzg.2_Non-coding_Transcript	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	576					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)											0.117647	6.676769	11.56102	4	30	KEEP	---	---	---	---	capture		Silent	SNP	55873404	55873404	12600	2	T	C	C	C	777	60	PNPT1	4	4
EHBP1	23301	broad.mit.edu	37	2	63175761	63175761	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63175761C>A	uc002sby.2	+	c.1885C>A	c.(1885-1887)CAA>AAA	p.Q629K	EHBP1_uc010fcp.2_Missense_Mutation_p.Q594K|EHBP1_uc002sbz.2_Missense_Mutation_p.Q594K|EHBP1_uc002scb.2_Missense_Mutation_p.Q594K	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1	629						cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)							379				0.096154	2.434296	10.940993	5	47	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	63175761	63175761	5164	2	C	A	A	A	377	29	EHBP1	2	2
CEP68	23177	broad.mit.edu	37	2	65296693	65296693	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:65296693G>C	uc002sdl.3	+	c.115G>C	c.(115-117)GGG>CGG	p.G39R	CEP68_uc002sdj.2_Missense_Mutation_p.G39R|CEP68_uc010yqb.1_Missense_Mutation_p.G39R|CEP68_uc002sdk.3_Missense_Mutation_p.G39R|CEP68_uc010yqc.1_Missense_Mutation_p.G39R|CEP68_uc010yqd.1_Missense_Mutation_p.G39R	NM_015147	NP_055962	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	39					centrosome organization	centrosome					0														0.263158	9.82723	10.826328	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65296693	65296693	3391	2	G	C	C	C	611	47	CEP68	3	3
ETAA1	54465	broad.mit.edu	37	2	67629997	67629997	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:67629997G>T	uc002sdz.1	+	c.433G>T	c.(433-435)GAA>TAA	p.E145*		NM_019002	NP_061875	Q9NY74	ETAA1_HUMAN	ETAA16 protein	145						cytoplasm|nucleus				ovary(3)|large_intestine(1)	4														0.103448	5.805257	14.887363	6	52	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	67629997	67629997	5460	2	G	T	T	T	585	45	ETAA1	5	2
PROKR1	10887	broad.mit.edu	37	2	68873421	68873421	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:68873421G>T	uc010yqj.1	+	c.468G>T	c.(466-468)CTG>CTT	p.L156L	PROKR1_uc002ses.2_Non-coding_Transcript	NM_138964	NP_620414	Q8TCW9	PKR1_HUMAN	G protein-coupled receptor 73	156	Helical; Name=3; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(1)	1														0.12766	8.015492	14.36974	6	41	KEEP	---	---	---	---	capture		Silent	SNP	68873421	68873421	12995	2	G	T	T	T	600	47	PROKR1	2	2
GKN1	56287	broad.mit.edu	37	2	69204787	69204787	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:69204787G>T	uc002sfc.2	+	c.127G>T	c.(127-129)GAC>TAC	p.D43Y		NM_019617	NP_062563	Q9NS71	GKN1_HUMAN	18 kDa antrum mucosa protein precursor	43					digestion|positive regulation of cell division	extracellular region				breast(1)	1														0.109589	6.842271	17.86683	8	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69204787	69204787	6692	2	G	T	T	T	585	45	GKN1	2	2
ALMS1	7840	broad.mit.edu	37	2	73677116	73677116	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:73677116C>T	uc002sje.1	+	c.3465C>T	c.(3463-3465)TTC>TTT	p.F1155F	ALMS1_uc002sjf.1_Silent_p.F1111F|ALMS1_uc002sjg.2_Silent_p.F541F|ALMS1_uc002sjh.1_Silent_p.F541F	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1153	34 X 47 AA approximate tandem repeat.|13.				G2/M transition of mitotic cell cycle|visual perception	centrosome|cilium|cytosol|microtubule basal body|spindle pole				ovary(2)|breast(2)|lung(1)|pancreas(1)	6														0.068966	-10.794829	33.785234	16	216	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	73677116	73677116	538	2	C	T	T	T	389	30	ALMS1	2	2
TGOLN2	10618	broad.mit.edu	37	2	85554057	85554057	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85554057G>T	uc010fgd.1	-	c.798C>A	c.(796-798)ATC>ATA	p.I266I	TGOLN2_uc002soz.2_Silent_p.I266I|TGOLN2_uc002spa.2_Intron|TGOLN2_uc002spb.2_Intron|TGOLN2_uc002spc.1_Silent_p.I266I	NM_006464	NP_006455	O43493	TGON2_HUMAN	trans-golgi network protein 2	266	Extracellular (Potential).					integral to membrane|nucleus|plasma membrane|trans-Golgi network|transport vesicle	protein binding				0														0.087719	0.729058	10.532744	5	52	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	85554057	85554057	16364	2	G	T	T	T	421	33	TGOLN2	2	2
KDM3A	55818	broad.mit.edu	37	2	86697482	86697482	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:86697482G>A	uc002sri.3	+	c.1675G>A	c.(1675-1677)GAG>AAG	p.E559K	KDM3A_uc010ytj.1_Missense_Mutation_p.E559K|KDM3A_uc010ytk.1_Missense_Mutation_p.E507K	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	559					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|oxidation-reduction process|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)	4						NSCLC(96;1150 1523 6936 46253 49736)								0.080808	0.317601	18.052481	8	91	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	86697482	86697482	8432	2	G	A	A	A	533	41	KDM3A	2	2
TRIM43	129868	broad.mit.edu	37	2	96261982	96261982	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:96261982G>C	uc002suv.2	+	c.540G>C	c.(538-540)AGG>AGC	p.R180S		NM_138800	NP_620155	Q96BQ3	TRI43_HUMAN	tripartite motif-containing 43	180						intracellular	zinc ion binding			ovary(1)	1														0.104167	4.744508	12.224694	5	43	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	96261982	96261982	17062	2	G	C	C	C	529	41	TRIM43	3	3
ABI3BP	25890	broad.mit.edu	37	3	100605006	100605006	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:100605006T>C	uc003dun.2	-	c.644A>G	c.(643-645)AAT>AGT	p.N215S	ABI3BP_uc003duo.2_Missense_Mutation_p.N208S|ABI3BP_uc003dup.3_Missense_Mutation_p.N208S	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein	215	Fibronectin type-III 1.					extracellular space				ovary(2)|large_intestine(1)	3														0.176471	21.544369	26.573983	9	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100605006	100605006	92	3	T	C	C	C	676	52	ABI3BP	4	4
MYH15	22989	broad.mit.edu	37	3	108158716	108158716	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108158716G>A	uc003dxa.1	-	c.3003C>T	c.(3001-3003)ATC>ATT	p.I1001I		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1001	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7														0.099099	7.939189	25.780329	11	100	KEEP	---	---	---	---	capture		Silent	SNP	108158716	108158716	10429	3	G	A	A	A	577	45	MYH15	2	2
PLCXD2	257068	broad.mit.edu	37	3	111427038	111427038	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:111427038G>T	uc003dyb.2	+	c.429G>T	c.(427-429)CTG>CTT	p.L143L	PLCXD2_uc003dya.2_Silent_p.L143L|PLCXD2_uc003dxz.2_Silent_p.L143L	NM_001134478	NP_001127950	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X	143	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity				0														0.088	1.421878	22.89157	11	114	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	111427038	111427038	12468	3	G	T	T	T	574	45	PLCXD2	2	2
CD80	941	broad.mit.edu	37	3	119276545	119276545	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:119276545G>T	uc003ecq.2	-	c.31C>A	c.(31-33)CCA>ACA	p.P11T	CD80_uc010hqt.1_Missense_Mutation_p.P11T|CD80_uc010hqu.1_Missense_Mutation_p.P11T|CD80_uc003ecr.1_Missense_Mutation_p.P11T	NM_005191	NP_005182	P33681	CD80_HUMAN	CD80 antigen precursor	11					cell-cell signaling|interspecies interaction between organisms|intracellular signal transduction|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of signal transduction|positive regulation of T-helper 1 cell differentiation|positive regulation of transcription, DNA-dependent|T cell activation|T cell costimulation	integral to membrane	coreceptor activity|protein binding|transcription activator activity			ovary(1)	1					Abatacept(DB01281)	Melanoma(132;135 1764 1806 5833 14593)								0.153846	6.905003	9.866546	4	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119276545	119276545	3166	3	G	T	T	T	572	44	CD80	2	2
GTF2E1	2960	broad.mit.edu	37	3	120469649	120469649	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:120469649G>T	uc003edz.3	+	c.250G>T	c.(250-252)GGG>TGG	p.G84W	GTF2E1_uc003edy.2_Missense_Mutation_p.G84W	NM_005513	NP_005504	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1,	84	HTH TFE/IIEalpha-type.				interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|RNA polymerase II transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)										0.096774	10.158191	30.314341	12	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120469649	120469649	7136	3	G	T	T	T	507	39	GTF2E1	1	1
PARP9	83666	broad.mit.edu	37	3	122255087	122255087	+	Nonsense_Mutation	SNP	G	A	A	rs77625852	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122255087G>A	uc010hri.2	-	c.2113C>T	c.(2113-2115)CAG>TAG	p.Q705*	PARP9_uc003eff.3_Nonsense_Mutation_p.Q670*|PARP9_uc011bjs.1_Nonsense_Mutation_p.Q670*|PARP9_uc003efg.2_Nonsense_Mutation_p.Q250*|PARP9_uc003efi.2_Nonsense_Mutation_p.Q670*|PARP9_uc003efh.2_Nonsense_Mutation_p.Q705*|PARP9_uc003efj.2_Nonsense_Mutation_p.Q670*	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	705	PARP catalytic.				cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(114;0.0519)						175				0.120459	67.536746	141.196206	63	460	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	122255087	122255087	11883	3	G	A	A	A	585	45	PARP9	5	2
MRPL3	11222	broad.mit.edu	37	3	131190061	131190061	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:131190061T>C	uc011blp.1	-	c.773A>G	c.(772-774)CAT>CGT	p.H258R	MRPL3_uc011blo.1_Missense_Mutation_p.H126R|MRPL3_uc003eoh.2_Missense_Mutation_p.H231R	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	231					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0														0.144828	32.273579	49.88776	21	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131190061	131190061	10186	3	T	C	C	C	663	51	MRPL3	4	4
NCK1	4690	broad.mit.edu	37	3	136664801	136664801	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:136664801C>G	uc003erh.2	+	c.603C>G	c.(601-603)TTC>TTG	p.F201L	NCK1_uc011bme.1_Missense_Mutation_p.F137L	NM_006153	NP_006144	P16333	NCK1_HUMAN	NCK adaptor protein 1	201	SH3 3.				axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1														0.086331	7.68936	31.783769	12	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136664801	136664801	10618	3	C	G	G	G	376	29	NCK1	3	3
DZIP1L	199221	broad.mit.edu	37	3	137802955	137802955	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:137802955C>A	uc003erq.2	-	c.1203G>T	c.(1201-1203)ATG>ATT	p.M401I	DZIP1L_uc003err.1_Missense_Mutation_p.M401I	NM_173543	NP_775814	Q8IYY4	DZI1L_HUMAN	DAZ interacting protein 1-like	401	Potential.					intracellular	zinc ion binding			ovary(1)|pancreas(1)	2														0.142857	24.093657	36.967729	15	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137802955	137802955	5050	3	C	A	A	A	273	21	DZIP1L	2	2
ACPL2	92370	broad.mit.edu	37	3	141011429	141011429	+	Silent	SNP	C	T	T	rs116687012	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:141011429C>T	uc003etu.2	+	c.825C>T	c.(823-825)TAC>TAT	p.Y275Y	ACPL2_uc003etv.2_Silent_p.Y275Y|ACPL2_uc011bna.1_Silent_p.Y237Y|ACPL2_uc011bnb.1_Silent_p.Y258Y	NM_152282	NP_689495	Q8TE99	ACPL2_HUMAN	acid phosphatase-like 2 precursor	275						extracellular region	acid phosphatase activity				0														0.182692	36.063331	45.898087	19	85	KEEP	---	---	---	---	capture		Silent	SNP	141011429	141011429	167	3	C	T	T	T	246	19	ACPL2	1	1
FAM194A	131831	broad.mit.edu	37	3	150398256	150398256	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:150398256A>T	uc003eyg.2	-	c.1110T>A	c.(1108-1110)GAT>GAA	p.D370E	FAM194A_uc003eyh.2_Missense_Mutation_p.D224E	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	370										ovary(1)|skin(1)	2														0.15873	21.11116	28.10151	10	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150398256	150398256	5737	3	A	T	T	T	102	8	FAM194A	3	3
CAPN7	23473	broad.mit.edu	37	3	15265058	15265058	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:15265058A>T	uc003bzn.2	+	c.715A>T	c.(715-717)ATG>TTG	p.M239L		NM_014296	NP_055111	Q9Y6W3	CAN7_HUMAN	calpain 7	239	Calpain catalytic.				proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1														0.166667	6.213394	8.109827	3	15	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	15265058	15265058	2749	3	A	T	T	T	52	4	CAPN7	3	3
SHOX2	6474	broad.mit.edu	37	3	157815867	157815867	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:157815867G>A	uc003fbs.2	-	c.1017C>T	c.(1015-1017)ATC>ATT	p.I339I	SHOX2_uc010hvw.2_Silent_p.I303I|SHOX2_uc003fbr.2_Silent_p.I315I	NM_003030	NP_003021	O60902	SHOX2_HUMAN	short stature homeobox 2 isoform b	315	OAR.				nervous system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)											0.159236	46.931319	64.253936	25	132	KEEP	---	---	---	---	capture		Silent	SNP	157815867	157815867	14784	3	G	A	A	A	473	37	SHOX2	1	1
SI	6476	broad.mit.edu	37	3	164710118	164710118	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164710118T>G	uc003fei.2	-	c.4909A>C	c.(4909-4911)ACC>CCC	p.T1637P		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1637	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.125	14.732665	24.616486	9	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	164710118	164710118	14792	3	T	G	G	G	741	57	SI	4	4
BCHE	590	broad.mit.edu	37	3	165547912	165547912	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:165547912C>T	uc003fem.3	-	c.910G>A	c.(910-912)GAA>AAA	p.E304K	BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	304					acetylcholine catabolic process|choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)									0.192308	21.917677	26.516957	10	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165547912	165547912	1379	3	C	T	T	T	377	29	BCHE	2	2
GHSR	2693	broad.mit.edu	37	3	172165646	172165646	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:172165646G>T	uc003fib.1	-	c.558C>A	c.(556-558)CAC>CAA	p.H186Q	GHSR_uc011bpv.1_Missense_Mutation_p.H186Q	NM_198407	NP_940799	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor isoform 1a	186	Extracellular (Potential).				actin polymerization or depolymerization|adult feeding behavior|decidualization|growth hormone secretion|hormone-mediated signaling pathway|negative regulation of inflammatory response|negative regulation of interleukin-1 beta production|negative regulation of interleukin-6 biosynthetic process|negative regulation of tumor necrosis factor biosynthetic process|positive regulation of appetite|positive regulation of multicellular organism growth	cell surface|integral to membrane|membrane raft|neuron projection|plasma membrane	growth hormone secretagogue receptor activity|growth hormone-releasing hormone receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			Esophageal Squamous(93;641 1401 20883 29581 34638)								0.294118	28.640099	29.92789	10	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172165646	172165646	6643	3	G	T	T	T	516	40	GHSR	1	1
PEX5L	51555	broad.mit.edu	37	3	179592167	179592167	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:179592167C>T	uc003fki.1	-	c.674G>A	c.(673-675)AGC>AAC	p.S225N	PEX5L_uc011bqd.1_Missense_Mutation_p.S182N|PEX5L_uc011bqe.1_Missense_Mutation_p.S33N|PEX5L_uc011bqf.1_Missense_Mutation_p.S117N|PEX5L_uc003fkj.1_Missense_Mutation_p.S190N|PEX5L_uc010hxd.1_Missense_Mutation_p.S223N|PEX5L_uc011bqg.1_Missense_Mutation_p.S201N|PEX5L_uc011bqh.1_Missense_Mutation_p.S166N	NM_016559	NP_057643	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	225					protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)							648				0.15942	16.025829	23.786669	11	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179592167	179592167	12171	3	C	T	T	T	364	28	PEX5L	2	2
C3orf59	151963	broad.mit.edu	37	3	192635598	192635598	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:192635598G>A	uc011bsp.1	-	c.32C>T	c.(31-33)GCA>GTA	p.A11V		NM_178496	NP_848591	Q8IYB1	M21D2_HUMAN	hypothetical protein LOC151963	11											0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)										0.294118	11.667312	12.312979	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	192635598	192635598	2330	3	G	A	A	A	598	46	C3orf59	2	2
AZI2	64343	broad.mit.edu	37	3	28382010	28382010	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:28382010T>C	uc003ceb.2	-	c.99A>G	c.(97-99)GAA>GAG	p.E33E	AZI2_uc003cec.2_5'UTR|AZI2_uc003ced.2_Silent_p.E33E|AZI2_uc003cee.3_Silent_p.E33E|AZI2_uc003ceg.2_Silent_p.E33E|AZI2_uc011axd.1_Silent_p.E33E|AZI2_uc003cef.2_Silent_p.E33E	NM_022461	NP_071906	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2 isoform a	33						mitochondrion|plasma membrane				ovary(2)	2														0.131579	9.448823	14.460583	5	33	KEEP	---	---	---	---	capture		Silent	SNP	28382010	28382010	1262	3	T	C	C	C	673	52	AZI2	4	4
DLEC1	9940	broad.mit.edu	37	3	38158308	38158308	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38158308C>T	uc003chp.1	+	c.4107C>T	c.(4105-4107)CTC>CTT	p.L1369L	DLEC1_uc003cho.1_Silent_p.L1369L|DLEC1_uc010hgv.1_Silent_p.L1372L|DLEC1_uc003chr.1_Silent_p.L440L|DLEC1_uc010hgx.1_Non-coding_Transcript|DLEC1_uc003chs.1_5'Flank	NM_007337	NP_031363	Q9Y238	DLEC1_HUMAN	deleted in lung and esophageal cancer 1 isoform	1369					negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|breast(1)|skin(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)										0.134146	12.681387	23.32422	11	71	KEEP	---	---	---	---	capture		Silent	SNP	38158308	38158308	4732	3	C	T	T	T	366	29	DLEC1	2	2
CYP8B1	1582	broad.mit.edu	37	3	42916001	42916001	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:42916001G>T	uc003cmh.2	-	c.1308C>A	c.(1306-1308)GGC>GGA	p.G436G	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CYP8B1_uc010hif.2_Silent_p.G436G	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,	436					bile acid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)										0.193548	41.632587	49.755779	18	75	KEEP	---	---	---	---	capture		Silent	SNP	42916001	42916001	4363	3	G	T	T	T	483	38	CYP8B1	1	1
C3orf75	54859	broad.mit.edu	37	3	47539870	47539870	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47539870T>C	uc003crk.2	-	c.578A>G	c.(577-579)AAT>AGT	p.N193S	C3orf75_uc003crj.2_Missense_Mutation_p.N120S|C3orf75_uc011bba.1_Missense_Mutation_p.N144S|C3orf75_uc003crl.1_Missense_Mutation_p.N193S	NM_001031703	NP_001026873	Q0PNE2	CC075_HUMAN	transmembrane protein 103	193											0														0.152174	12.300426	17.62396	7	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47539870	47539870	2338	3	T	C	C	C	676	52	C3orf75	4	4
P4HTM	54681	broad.mit.edu	37	3	49039984	49039984	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49039984A>G	uc003cvh.2	+	c.679A>G	c.(679-681)ATT>GTT	p.I227V	P4HTM_uc003cvg.2_Missense_Mutation_p.I227V|P4HTM_uc010hkm.1_Missense_Mutation_p.I113V	NM_177938	NP_808807	Q9NXG6	P4HTM_HUMAN	hypoxia-inducible factor prolyl 4-hydroxylase	227	Lumenal (Potential).|EF-hand 2.				oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)									0.263158	27.134156	29.061058	10	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49039984	49039984	11773	3	A	G	G	G	104	8	P4HTM	4	4
USP19	10869	broad.mit.edu	37	3	49151713	49151713	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49151713G>C	uc011bch.1	-	c.2291C>G	c.(2290-2292)TCC>TGC	p.S764C	USP19_uc003cwa.2_Missense_Mutation_p.S471C|USP19_uc003cvz.3_Missense_Mutation_p.S766C|USP19_uc011bcg.1_Missense_Mutation_p.S754C|USP19_uc003cwb.2_Intron|USP19_uc003cwc.1_Missense_Mutation_p.S421C|USP19_uc003cwd.1_Missense_Mutation_p.S663C	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	663	Cytoplasmic (Potential).				proteasomal ubiquitin-dependent protein catabolic process	endoplasmic reticulum membrane|integral to membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(4)	4				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.176471	14.530755	17.882852	6	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49151713	49151713	17613	3	G	C	C	C	533	41	USP19	3	3
TRAIP	10293	broad.mit.edu	37	3	49881339	49881339	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49881339C>T	uc003cxs.1	-	c.303G>A	c.(301-303)CAG>CAA	p.Q101Q	TRAIP_uc010hla.1_Silent_p.Q101Q|TRAIP_uc011bcx.1_Silent_p.Q101Q	NM_005879	NP_005870	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	101	Potential.				cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding			lung(3)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.162162	10.817528	14.851176	6	31	KEEP	---	---	---	---	capture		Silent	SNP	49881339	49881339	16992	3	C	T	T	T	311	24	TRAIP	2	2
RBM6	10180	broad.mit.edu	37	3	50009498	50009498	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:50009498G>A	uc003cyc.2	+	c.1330G>A	c.(1330-1332)GAT>AAT	p.D444N	RBM6_uc011bdh.1_Non-coding_Transcript|RBM6_uc010hlc.1_5'UTR|RBM6_uc003cyd.2_5'UTR|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Non-coding_Transcript|RBM6_uc010hle.1_Non-coding_Transcript|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	444					RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)										0.089744	3.062205	16.316752	7	71	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	50009498	50009498	13606	3	G	A	A	A	429	33	RBM6	2	2
PBRM1	55193	broad.mit.edu	37	3	52682408	52682408	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52682408G>A	uc003des.2	-	c.765C>T	c.(763-765)CTC>CTT	p.L255L	PBRM1_uc003dex.2_Non-coding_Transcript|PBRM1_uc003deq.2_Silent_p.L255L|PBRM1_uc003der.2_Silent_p.L255L|PBRM1_uc003det.2_Silent_p.L255L|PBRM1_uc003deu.2_Silent_p.L255L|PBRM1_uc003dev.2_Non-coding_Transcript|PBRM1_uc003dew.2_Silent_p.L255L|PBRM1_uc010hmk.1_Silent_p.L255L|PBRM1_uc003dey.2_Silent_p.L255L|PBRM1_uc003dez.1_Silent_p.L255L|PBRM1_uc003dfb.1_Silent_p.L153L	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	255	Bromo 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)										0.108696	4.483614	11.42674	5	41	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	52682408	52682408	11911	3	G	A	A	A	470	37	PBRM1	1	1
ITIH1	3697	broad.mit.edu	37	3	52812964	52812964	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52812964A>G	uc003dfs.2	+	c.312A>G	c.(310-312)GCA>GCG	p.A104A	ITIH1_uc010hmn.1_Non-coding_Transcript	NM_002215	NP_002206	P19827	ITIH1_HUMAN	inter-alpha (globulin) inhibitor H1	104	VIT.				hyaluronan metabolic process|leukocyte activation	extracellular region	calcium ion binding|serine-type endopeptidase inhibitor activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)										0.130435	7.516769	13.631679	6	40	KEEP	---	---	---	---	capture		Silent	SNP	52812964	52812964	8207	3	A	G	G	G	80	7	ITIH1	4	4
DCP1A	55802	broad.mit.edu	37	3	53326488	53326488	+	Missense_Mutation	SNP	G	T	T	rs34229192		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:53326488G>T	uc003dgs.3	-	c.994C>A	c.(994-996)CCC>ACC	p.P332T	DCP1A_uc003dgt.3_Non-coding_Transcript	NM_018403	NP_060873	Q9NPI6	DCP1A_HUMAN	DCP1 decapping enzyme homolog A	332					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)										0.16129	7.970737	11.343074	5	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53326488	53326488	4469	3	G	T	T	T	533	41	DCP1A	2	2
DCP1A	55802	broad.mit.edu	37	3	53326592	53326592	+	Missense_Mutation	SNP	G	C	C	rs35988197		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:53326592G>C	uc003dgs.3	-	c.890C>G	c.(889-891)GCC>GGC	p.A297G	DCP1A_uc003dgt.3_Non-coding_Transcript	NM_018403	NP_060873	Q9NPI6	DCP1A_HUMAN	DCP1 decapping enzyme homolog A	297					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)										0.227273	11.859141	13.36611	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53326592	53326592	4469	3	G	C	C	C	546	42	DCP1A	3	3
MINA	84864	broad.mit.edu	37	3	97686208	97686208	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97686208T>C	uc003drz.1	-	c.230A>G	c.(229-231)TAT>TGT	p.Y77C	MINA_uc003dsa.1_Missense_Mutation_p.Y77C|MINA_uc003dsb.1_Missense_Mutation_p.Y77C|MINA_uc003dsc.1_Missense_Mutation_p.Y77C|MINA_uc010hpa.1_Non-coding_Transcript|MINA_uc010hpb.1_Intron	NM_001042533	NP_001035998	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a	77					ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1														0.143498	60.553865	87.866672	32	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97686208	97686208	9976	3	T	C	C	C	637	49	MINA	4	4
ADH4	127	broad.mit.edu	37	4	100052703	100052703	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:100052703C>G	uc003hun.2	-	c.795G>C	c.(793-795)AAG>AAC	p.K265N	ADH4_uc011ced.1_Missense_Mutation_p.K284N	NM_000670	NP_000661	P08319	ADH4_HUMAN	class II alcohol dehydrogenase, pi subunit	265					alcohol catabolic process|cellular aldehyde metabolic process|ethanol oxidation|quinone cofactor metabolic process|retinol metabolic process|xenobiotic metabolic process	cytosol|microtubule cytoskeleton	alcohol dehydrogenase activity, zinc-dependent|all-trans retinal binding|benzaldehyde dehydrogenase activity|NAD binding|NADPH:quinone reductase activity|retinol binding|retinol dehydrogenase activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)	NADH(DB00157)									0.116279	6.042169	12.275917	5	38	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	100052703	100052703	311	4	C	G	G	G	311	24	ADH4	3	3
ZNF518B	85460	broad.mit.edu	37	4	10447910	10447910	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:10447910C>T	uc003gmn.2	-	c.43G>A	c.(43-45)GGC>AGC	p.G15S		NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	15					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3														0.192308	32.492802	39.380502	15	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10447910	10447910	18557	4	C	T	T	T	299	23	ZNF518B	1	1
FAT4	79633	broad.mit.edu	37	4	126370186	126370186	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126370186A>T	uc003ifj.3	+	c.8015A>T	c.(8014-8016)GAC>GTC	p.D2672V	FAT4_uc011cgp.1_Missense_Mutation_p.D970V|FAT4_uc003ifi.1_Missense_Mutation_p.D150V	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	2672	Cadherin 26.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.121212	10.156387	19.434527	8	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126370186	126370186	5928	4	A	T	T	T	130	10	FAT4	3	3
PHF17	79960	broad.mit.edu	37	4	129793163	129793163	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:129793163C>T	uc003igk.2	+	c.2275C>T	c.(2275-2277)CGG>TGG	p.R759W	PHF17_uc003igl.2_Missense_Mutation_p.R747W|PHF17_uc011cgy.1_Missense_Mutation_p.R759W	NM_199320	NP_955352	Q6IE81	JADE1_HUMAN	PHD finger protein 17 long isoform	759					apoptosis|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell growth|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	histone acetyltransferase complex|mitochondrion	protein binding|zinc ion binding				0														0.171429	11.331616	14.901242	6	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129793163	129793163	12251	4	C	T	T	T	243	19	PHF17	1	1
MAML3	55534	broad.mit.edu	37	4	140810914	140810914	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:140810914T>A	uc003ihz.1	-	c.1664A>T	c.(1663-1665)AAC>ATC	p.N555I	MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3	555	Asn-rich.|Gln-rich.				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)									182				0.059084	-58.333179	79.465404	40	637	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	140810914	140810914	9590	4	T	A	A	A	780	60	MAML3	3	3
TBC1D9	23158	broad.mit.edu	37	4	141583238	141583238	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:141583238G>A	uc010ioj.2	-	c.1612C>T	c.(1612-1614)CAT>TAT	p.H538Y		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	538	Rab-GAP TBC.					intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)												0.155556	35.483738	50.785605	21	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141583238	141583238	16153	4	G	A	A	A	624	48	TBC1D9	2	2
TIGD4	201798	broad.mit.edu	37	4	153691222	153691222	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:153691222G>A	uc003imy.2	-	c.935C>T	c.(934-936)TCT>TTT	p.S312F		NM_145720	NP_663772	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	312	DDE.					chromosome, centromeric region|nucleus	chromatin binding|DNA binding			ovary(1)	1	all_hematologic(180;0.093)													0.150943	14.061291	20.254049	8	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153691222	153691222	16427	4	G	A	A	A	429	33	TIGD4	2	2
RNF175	285533	broad.mit.edu	37	4	154641373	154641373	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:154641373G>C	uc003int.2	-	c.593C>G	c.(592-594)GCC>GGC	p.A198G	RNF175_uc003inu.1_Missense_Mutation_p.A70G	NM_173662	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	198	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)												0.144928	19.903791	28.272973	10	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154641373	154641373	13940	4	G	C	C	C	546	42	RNF175	3	3
CPE	1363	broad.mit.edu	37	4	166416828	166416828	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:166416828G>T	uc003irg.3	+	c.1331G>T	c.(1330-1332)GGG>GTG	p.G444V		NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein	444					cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.138889	8.150879	12.687494	5	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166416828	166416828	3937	4	G	T	T	T	559	43	CPE	2	2
DDX60	55601	broad.mit.edu	37	4	169212925	169212925	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:169212925C>T	uc003irp.2	-	c.1015G>A	c.(1015-1017)GAG>AAG	p.E339K		NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	339							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)										0.090909	2.796825	13.934206	6	60	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	169212925	169212925	4549	4	C	T	T	T	377	29	DDX60	2	2
CCDC111	201973	broad.mit.edu	37	4	185615780	185615780	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:185615780T>G	uc003iwk.2	+	c.1530T>G	c.(1528-1530)GAT>GAG	p.D510E	CCDC111_uc003iwj.2_Missense_Mutation_p.D509E|CCDC111_uc003iwl.2_Missense_Mutation_p.D510E|CCDC111_uc003iwm.2_Missense_Mutation_p.D381E|CCDC111_uc003iwn.2_Missense_Mutation_p.D250E|MLF1IP_uc003iwp.2_Non-coding_Transcript|MLF1IP_uc003iwq.2_3'UTR	NM_152683	NP_689896	Q96LW4	CC111_HUMAN	coiled-coil domain containing 111	510					DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)										0.190476	20.776274	24.536525	8	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185615780	185615780	2868	4	T	G	G	G	660	51	CCDC111	4	4
MTNR1A	4543	broad.mit.edu	37	4	187455099	187455099	+	Missense_Mutation	SNP	G	T	T	rs28383652	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187455099G>T	uc003izd.1	-	c.797C>A	c.(796-798)GCC>GAC	p.A266D		NM_005958	NP_005949	P48039	MTR1A_HUMAN	melatonin receptor 1A	266	Extracellular (Potential).				circadian rhythm|G-protein signaling, coupled to cyclic nucleotide second messenger|mating behavior	integral to plasma membrane	melatonin receptor activity			ovary(1)	1		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Melatonin(DB01065)|Ramelteon(DB00980)									0.18	16.801997	21.574147	9	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187455099	187455099	10344	4	G	T	T	T	546	42	MTNR1A	2	2
GABRA2	2555	broad.mit.edu	37	4	46390697	46390697	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46390697G>A	uc003gxc.3	-	c.27C>T	c.(25-27)AAC>AAT	p.N9N	GABRA2_uc010igc.2_Silent_p.N9N|GABRA2_uc011bzc.1_5'UTR|GABRA2_uc003gxe.2_Silent_p.N9N|GABRA2_uc010igd.1_Silent_p.N9N	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	9					gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.22069	67.863467	78.252172	32	113	KEEP	---	---	---	---	capture		Silent	SNP	46390697	46390697	6412	4	G	A	A	A	620	48	GABRA2	2	2
CWH43	80157	broad.mit.edu	37	4	49052794	49052794	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:49052794C>T	uc003gyv.2	+	c.1949C>T	c.(1948-1950)ACT>ATT	p.T650I	CWH43_uc011bzl.1_Missense_Mutation_p.T623I	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog	650					GPI anchor biosynthetic process	integral to membrane				ovary(1)	1														0.097826	5.500887	20.406309	9	83	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	49052794	49052794	4233	4	C	T	T	T	260	20	CWH43	2	2
TMPRSS11D	9407	broad.mit.edu	37	4	68691516	68691516	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:68691516A>T	uc003hdq.2	-	c.1029T>A	c.(1027-1029)TAT>TAA	p.Y343*	LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc003hdp.2_Nonsense_Mutation_p.Y124*|TMPRSS11D_uc011caj.1_Nonsense_Mutation_p.Y226*	NM_004262	NP_004253	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	343	Peptidase S1.|Extracellular (Potential).				proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1														0.134328	14.132655	22.817797	9	58	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	68691516	68691516	16782	4	A	T	T	T	206	16	TMPRSS11D	5	3
PPEF2	5470	broad.mit.edu	37	4	76809396	76809396	+	Missense_Mutation	SNP	G	A	A	rs61756411		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:76809396G>A	uc003hix.2	-	c.503C>T	c.(502-504)ACC>ATC	p.T168I	PPEF2_uc003hiy.2_Non-coding_Transcript|PPEF2_uc003hiz.1_Missense_Mutation_p.T168I	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	168	Catalytic.				detection of stimulus involved in sensory perception|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			NSCLC(105;1359 1603 15961 44567 47947)								0.125984	20.218741	37.557043	16	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76809396	76809396	12738	4	G	A	A	A	572	44	PPEF2	2	2
CCNI	10983	broad.mit.edu	37	4	77976472	77976472	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:77976472G>C	uc003hkm.2	-	c.521C>G	c.(520-522)CCA>CGA	p.P174R	CCNI_uc011ccb.1_Missense_Mutation_p.P160R	NM_006835	NP_006826	Q14094	CCNI_HUMAN	cyclin I	174					spermatogenesis					ovary(1)	1														0.119048	4.443081	10.432136	5	37	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	77976472	77976472	3053	4	G	C	C	C	611	47	CCNI	3	3
SCD5	79966	broad.mit.edu	37	4	83601861	83601861	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:83601861T>C	uc003hna.2	-	c.568A>G	c.(568-570)AAG>GAG	p.K190E	SCD5_uc003hnb.3_Missense_Mutation_p.N190D	NM_001037582	NP_001032671	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5 isoform a	190					fatty acid biosynthetic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)								68				0.090909	3.733147	13.011038	5	50	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	83601861	83601861	14368	4	T	C	C	C	832	64	SCD5	4	4
DRD5	1816	broad.mit.edu	37	4	9784055	9784055	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:9784055C>T	uc003gmb.3	+	c.402C>T	c.(400-402)ATC>ATT	p.I134I		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	134	Helical; Name=3; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane					0					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)									0.105263	3.171915	9.05794	4	34	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	9784055	9784055	4944	4	C	T	T	T	369	29	DRD5	2	2
MARCH6	10299	broad.mit.edu	37	5	10417436	10417436	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:10417436C>T	uc003jet.1	+	c.2203C>T	c.(2203-2205)CTG>TTG	p.L735L	MARCH6_uc011cmu.1_Silent_p.L687L|MARCH6_uc003jeu.1_Silent_p.L433L|MARCH6_uc011cmv.1_Silent_p.L630L	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	735	Helical; (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding				0														0.086957	2.028107	17.921723	8	84	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	10417436	10417436	9688	5	C	T	T	T	415	32	MARCH6	2	2
APC	324	broad.mit.edu	37	5	112175508	112175508	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112175508A>G	uc010jby.2	+	c.4217A>G	c.(4216-4218)CAG>CGG	p.Q1406R	APC_uc011cvt.1_Missense_Mutation_p.Q1388R|APC_uc003kpz.3_Missense_Mutation_p.Q1406R|APC_uc003kpy.3_Missense_Mutation_p.Q1406R|APC_uc010jbz.2_Missense_Mutation_p.Q1123R|APC_uc010jca.2_Missense_Mutation_p.Q706R	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1406	Ser-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of protein catabolic process|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.Q1406*(1)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)		large_intestine(2012)|stomach(123)|soft_tissue(55)|small_intestine(34)|pancreas(25)|breast(23)|urinary_tract(20)|lung(18)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|upper_aerodigestive_tract(6)|adrenal_gland(6)|NS(5)|bone(5)|skin(4)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2396		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		12		629	TSP Lung(16;0.13)			0.116279	10.68697	23.156462	10	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112175508	112175508	773	5	A	G	G	G	91	7	APC	4	4
ZNF608	57507	broad.mit.edu	37	5	123985341	123985341	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:123985341G>A	uc003ktq.1	-	c.1212C>T	c.(1210-1212)ACC>ACT	p.T404T	ZNF608_uc003ktr.1_Non-coding_Transcript|ZNF608_uc003kts.1_Silent_p.T404T|ZNF608_uc003ktt.1_Silent_p.T404T	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	404						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)					p.T404T(NCIH23-Tumor)|p.T404T(NAMALWA-Tumor)	447				0.185185	31.377868	38.906604	15	66	KEEP	---	---	---	---	capture		Silent	SNP	123985341	123985341	18629	5	G	A	A	A	548	43	ZNF608	2	2
FBN2	2201	broad.mit.edu	37	5	127697462	127697462	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127697462C>T	uc003kuu.2	-	c.2508G>A	c.(2506-2508)ACG>ACA	p.T836T	FBN2_uc003kuv.2_Silent_p.T803T	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	836	EGF-like 12; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.173913	30.27712	39.486119	16	76	KEEP	---	---	---	---	capture		Silent	SNP	127697462	127697462	5939	5	C	T	T	T	236	19	FBN2	1	1
SHROOM1	134549	broad.mit.edu	37	5	132159971	132159971	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:132159971A>G	uc003kxx.2	-	c.1382T>C	c.(1381-1383)GTA>GCA	p.V461A	SHROOM1_uc003kxy.1_Missense_Mutation_p.V461A	NM_133456	NP_597713	Q2M3G4	SHRM1_HUMAN	shroom family member 1	461					actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding			pancreas(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)											0.214286	7.718092	8.772746	3	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132159971	132159971	14788	5	A	G	G	G	182	14	SHROOM1	4	4
KIF20A	10112	broad.mit.edu	37	5	137519240	137519240	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137519240G>C	uc003lcj.2	+	c.1109G>C	c.(1108-1110)AGC>ACC	p.S370T	KIF20A_uc011cyo.1_Missense_Mutation_p.S352T	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	370	Kinesin-motor.				cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)											0.117647	6.111571	13.360808	6	45	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	137519240	137519240	8597	5	G	C	C	C	442	34	KIF20A	3	3
CDC23	8697	broad.mit.edu	37	5	137524733	137524733	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137524733T>C	uc003lcl.2	-	c.1728A>G	c.(1726-1728)TCA>TCG	p.S576S		NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	cell division cycle protein 23	576					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)											0.150943	9.090613	15.441163	8	45	KEEP	---	---	---	---	capture		Silent	SNP	137524733	137524733	3189	5	T	C	C	C	756	59	CDC23	4	4
DNAH5	1767	broad.mit.edu	37	5	13867953	13867953	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:13867953T>A	uc003jfd.2	-	c.3983A>T	c.(3982-3984)AAG>ATG	p.K1328M		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1328	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.134021	19.806584	32.410796	13	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13867953	13867953	4787	5	T	A	A	A	728	56	DNAH5	3	3
PCDHA7	56141	broad.mit.edu	37	5	140215307	140215307	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140215307G>A	uc003lhq.2	+	c.1339G>A	c.(1339-1341)GAC>AAC	p.D447N	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.D447N	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	447	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			NSCLC(160;258 2013 5070 22440 28951)								0.125	7.821905	14.412467	6	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140215307	140215307	11949	5	G	A	A	A	481	37	PCDHA7	1	1
PCDHGB4	8641	broad.mit.edu	37	5	140768876	140768876	+	Silent	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140768876T>A	uc003lkc.1	+	c.1425T>A	c.(1423-1425)TCT>TCA	p.S475S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc011dav.1_Silent_p.S475S	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	475	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.122449	8.81739	15.653277	6	43	KEEP	---	---	---	---	capture		Silent	SNP	140768876	140768876	11985	5	T	A	A	A	704	55	PCDHGB4	3	3
PCDHGA8	9708	broad.mit.edu	37	5	140772822	140772822	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140772822C>G	uc003lkd.1	+	c.442C>G	c.(442-444)CCT>GCT	p.P148A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.3_Missense_Mutation_p.P148A	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	148	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.225	24.354615	27.13304	9	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140772822	140772822	11980	5	C	G	G	G	390	30	PCDHGA8	3	3
PCDH12	51294	broad.mit.edu	37	5	141325298	141325298	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:141325298T>C	uc003llx.2	-	c.3203A>G	c.(3202-3204)AAC>AGC	p.N1068S		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	1068	Cytoplasmic (Potential).				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.263158	27.228693	29.160067	10	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141325298	141325298	11930	5	T	C	C	C	780	60	PCDH12	4	4
IL17B	27190	broad.mit.edu	37	5	148756389	148756389	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:148756389C>A	uc003lqo.2	-	c.221G>T	c.(220-222)AGG>ATG	p.R74M		NM_014443	NP_055258	Q9UHF5	IL17B_HUMAN	interleukin 17B precursor	74					cell-cell signaling|immune response|inflammatory response	extracellular space	cytokine activity|signal transducer activity			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.096154	2.738938	11.241039	5	47	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	148756389	148756389	7936	5	C	A	A	A	312	24	IL17B	2	2
SYNPO	11346	broad.mit.edu	37	5	150028398	150028398	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150028398C>T	uc003lsn.2	+	c.1293C>T	c.(1291-1293)TTC>TTT	p.F431F	SYNPO_uc003lso.3_Silent_p.F187F|SYNPO_uc003lsp.2_Silent_p.F187F	NM_001109974	NP_001103444	Q8N3V7	SYNPO_HUMAN	synaptopodin isoform B	431					positive regulation of actin filament bundle assembly|regulation of stress fiber assembly	actin cytoskeleton|cytoplasm|dendritic spine|perikaryon|postsynaptic density|postsynaptic membrane|tight junction	actin binding|protein binding			large_intestine(1)	1		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.078522	-6.555608	72.02125	34	399	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	150028398	150028398	15977	5	C	T	T	T	376	29	SYNPO	2	2
ZNF300	91975	broad.mit.edu	37	5	150276377	150276377	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150276377C>G	uc003lsy.1	-	c.424G>C	c.(424-426)GAC>CAC	p.D142H	IRGM_uc011dcl.1_Intron	NM_052860	NP_443092	Q96RE9	ZN300_HUMAN	zinc finger protein 300	142					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.074074	-2.663992	22.513979	10	125	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	150276377	150276377	18423	5	C	G	G	G	416	32	ZNF300	3	3
KIF4B	285643	broad.mit.edu	37	5	154394493	154394493	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:154394493A>G	uc010jih.1	+	c.1074A>G	c.(1072-1074)GTA>GTG	p.V358V		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	358	Potential.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)											0.094203	5.268041	28.137339	13	125	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	154394493	154394493	8615	5	A	G	G	G	171	14	KIF4B	4	4
HAVCR1	26762	broad.mit.edu	37	5	156456833	156456833	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156456833G>A	uc010jij.1	-	c.1006C>T	c.(1006-1008)CAA>TAA	p.Q336*	HAVCR1_uc011ddl.1_Silent_p.F155F|HAVCR1_uc003lwi.2_Nonsense_Mutation_p.Q336*	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	331	Cytoplasmic (Potential).				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.214286	7.316847	8.372464	3	11	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	156456833	156456833	7255	5	G	A	A	A	585	45	HAVCR1	5	2
ADRA1B	147	broad.mit.edu	37	5	159343983	159343983	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:159343983A>C	uc003lxt.1	+	c.71A>C	c.(70-72)AAC>ACC	p.N24T		NM_000679	NP_000670	P35368	ADA1B_HUMAN	alpha-1B-adrenergic receptor	24	Extracellular (By similarity).				cell proliferation|cell-cell signaling|G-protein signaling, coupled to cAMP nucleotide second messenger|intracellular protein kinase cascade	integral to plasma membrane	alpha1-adrenergic receptor activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alfuzosin(DB00346)|Bethanidine(DB00217)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Guanfacine(DB01018)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Modafinil(DB00745)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Olanzapine(DB00334)|Phendimetrazine(DB01579)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Trazodone(DB00656)									0.236842	21.555875	23.961707	9	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159343983	159343983	336	5	A	C	C	C	26	2	ADRA1B	4	4
GABRG2	2566	broad.mit.edu	37	5	161580356	161580356	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:161580356C>G	uc010jjc.2	+	c.1530C>G	c.(1528-1530)GTC>GTG	p.V510V	GABRG2_uc003lyy.3_Silent_p.V470V|GABRG2_uc003lyz.3_Silent_p.V462V|GABRG2_uc011dej.1_Silent_p.V367V	NM_198903	NP_944493	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	462	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)	4	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)										0.111111	18.422848	38.610397	15	120	KEEP	---	---	---	---	capture		Silent	SNP	161580356	161580356	6423	5	C	G	G	G	405	32	GABRG2	3	3
ODZ2	57451	broad.mit.edu	37	5	167630824	167630824	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:167630824C>T	uc010jjd.2	+	c.3534C>T	c.(3532-3534)CTC>CTT	p.L1178L	ODZ2_uc003lzr.3_Silent_p.L955L|ODZ2_uc003lzt.3_Silent_p.L551L|ODZ2_uc010jje.2_Silent_p.L449L	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)										0.069343	-13.003426	39.511426	19	255	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	167630824	167630824	11240	5	C	T	T	T	366	29	ODZ2	2	2
CLK4	57396	broad.mit.edu	37	5	178050348	178050348	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178050348G>A	uc003mjf.1	-	c.70C>T	c.(70-72)CGT>TGT	p.R24C	CLK4_uc003mjg.1_5'UTR|CLK4_uc010jku.1_5'UTR|CLK4_uc003mjh.1_5'UTR|CLK4_uc010jkv.1_Non-coding_Transcript|CLK4_uc011dgg.1_Missense_Mutation_p.R24C|CLK4_uc011dgh.1_5'UTR|CLK4_uc011dgi.1_Missense_Mutation_p.R24C|CLK4_uc011dgj.1_Missense_Mutation_p.R24C|CLK4_uc003mji.2_Missense_Mutation_p.R24C|CLK4_uc010jkw.1_Missense_Mutation_p.R24C	NM_020666	NP_065717	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	24						nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(1)	1	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)					p.R24S(EN-Tumor)	146				0.135135	7.851246	12.623716	5	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178050348	178050348	3677	5	G	A	A	A	481	37	CLK4	1	1
GRM6	2916	broad.mit.edu	37	5	178408747	178408747	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178408747G>A	uc003mjr.2	-	c.2545C>T	c.(2545-2547)CAG>TAG	p.Q849*	GRM6_uc003mjq.2_Nonsense_Mutation_p.Q252*	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor	849	Cytoplasmic (Potential).				detection of visible light|visual perception	integral to plasma membrane				ovary(2)|breast(1)|pancreas(1)	4	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)										0.138889	6.348286	10.889211	5	31	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	178408747	178408747	7080	5	G	A	A	A	598	46	GRM6	5	2
CDH18	1016	broad.mit.edu	37	5	19503202	19503202	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:19503202C>A	uc003jgc.2	-	c.1529G>T	c.(1528-1530)AGT>ATT	p.S510I	CDH18_uc003jgd.2_Missense_Mutation_p.S510I|CDH18_uc011cnm.1_Missense_Mutation_p.S510I	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	510	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.096774	4.200275	14.304929	6	56	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	19503202	19503202	3232	5	C	A	A	A	260	20	CDH18	2	2
CDH12	1010	broad.mit.edu	37	5	21975242	21975242	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:21975242C>G	uc010iuc.2	-	c.484G>C	c.(484-486)GAT>CAT	p.D162H	CDH12_uc011cno.1_Missense_Mutation_p.D162H|CDH12_uc003jgk.2_Missense_Mutation_p.D162H	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	162	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2														0.126667	34.518281	54.914015	19	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21975242	21975242	3227	5	C	G	G	G	390	30	CDH12	3	3
CDH9	1007	broad.mit.edu	37	5	26915831	26915831	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:26915831C>T	uc003jgs.1	-	c.430G>A	c.(430-432)GAA>AAA	p.E144K	CDH9_uc010iug.2_Missense_Mutation_p.E144K	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	144	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.076471	-5.266269	26.005209	13	157	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	26915831	26915831	3246	5	C	T	T	T	390	30	CDH9	2	2
PDZD2	23037	broad.mit.edu	37	5	32088391	32088391	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32088391A>G	uc003jhl.2	+	c.4837A>G	c.(4837-4839)AGT>GGT	p.S1613G	PDZD2_uc003jhm.2_Missense_Mutation_p.S1613G	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1613					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|large_intestine(1)	7														0.148936	27.301288	38.404264	14	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32088391	32088391	12122	5	A	G	G	G	143	11	PDZD2	4	4
C1QTNF3	114899	broad.mit.edu	37	5	34028882	34028882	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:34028882C>A	uc003jio.2	-	c.677G>T	c.(676-678)GGT>GTT	p.G226V	C1QTNF3_uc003jim.2_Missense_Mutation_p.G33V|C1QTNF3_uc003jin.2_Missense_Mutation_p.G153V	NM_181435	NP_852100	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3	153	C1q.					collagen					0	all_lung(31;0.0207)													0.121951	5.1439	10.888177	5	36	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	34028882	34028882	2031	5	C	A	A	A	234	18	C1QTNF3	2	2
C5orf33	133686	broad.mit.edu	37	5	36225683	36225683	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:36225683C>A	uc003jkf.3	-	c.521G>T	c.(520-522)AGA>ATA	p.R174I	C5orf33_uc010iux.2_Missense_Mutation_p.R11I|C5orf33_uc003jkg.3_Missense_Mutation_p.R11I|C5orf33_uc011cov.1_Missense_Mutation_p.R11I	NM_001085411	NP_001078880	Q4G0N4	CE033_HUMAN	hypothetical protein LOC133686 isoform 1	174							NAD+ kinase activity			ovary(2)	2	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.103896	9.989203	34.040081	16	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36225683	36225683	2390	5	C	A	A	A	416	32	C5orf33	2	2
WDR70	55100	broad.mit.edu	37	5	37392168	37392168	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:37392168A>T	uc003jkv.2	+	c.242A>T	c.(241-243)GAG>GTG	p.E81V	WDR70_uc010iva.1_Missense_Mutation_p.E81V	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70	81										ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.097222	4.47134	16.171766	7	65	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	37392168	37392168	17894	5	A	T	T	T	143	11	WDR70	3	3
RICTOR	253260	broad.mit.edu	37	5	38959337	38959337	+	Missense_Mutation	SNP	G	C	C	rs61753520		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:38959337G>C	uc003jlo.2	-	c.2138C>G	c.(2137-2139)GCT>GGT	p.A713G	RICTOR_uc003jlp.2_Missense_Mutation_p.A713G|RICTOR_uc010ivf.2_Missense_Mutation_p.A428G	NM_152756	NP_689969	Q6R327	RICTR_HUMAN	rapamycin-insensitive companion of mTOR	713					actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7	all_lung(31;0.000396)									698				0.2	7.517152	8.772042	3	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38959337	38959337	13833	5	G	C	C	C	442	34	RICTOR	3	3
ADCY2	108	broad.mit.edu	37	5	7709395	7709395	+	Silent	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:7709395G>C	uc003jdz.1	+	c.1473G>C	c.(1471-1473)TCG>TCC	p.S491S	ADCY2_uc011cmo.1_Silent_p.S311S	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	491	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)	6														0.111111	5.180199	11.876559	5	40	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	7709395	7709395	295	5	G	C	C	C	496	39	ADCY2	3	3
RASA1	5921	broad.mit.edu	37	5	86672799	86672799	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:86672799C>T	uc003kiw.2	+	c.2286C>T	c.(2284-2286)CAC>CAT	p.H762H	RASA1_uc010jav.2_Non-coding_Transcript|RASA1_uc003kix.2_Silent_p.H585H|RASA1_uc011ctv.1_Silent_p.H595H|RASA1_uc011ctw.1_Silent_p.H596H|RASA1_uc010jaw.2_Silent_p.H584H	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	762	Ras-GAP.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)					p.H762H(GDM1-Tumor)	386				0.230769	29.977096	33.42822	12	40	KEEP	---	---	---	---	capture		Silent	SNP	86672799	86672799	13520	5	C	T	T	T	246	19	RASA1	1	1
GPR98	84059	broad.mit.edu	37	5	89949519	89949519	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:89949519C>T	uc003kju.2	+	c.4128C>T	c.(4126-4128)GAC>GAT	p.D1376D	GPR98_uc003kjt.2_De_novo_Start_InFrame	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	1376	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.205882	15.213832	17.935555	7	27	KEEP	---	---	---	---	capture		Silent	SNP	89949519	89949519	6997	5	C	T	T	T	246	19	GPR98	1	1
CAST	831	broad.mit.edu	37	5	96101822	96101822	+	Silent	SNP	C	T	T	rs61733809		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:96101822C>T	uc003klu.2	+	c.2103C>T	c.(2101-2103)TAC>TAT	p.Y701Y	CAST_uc003klt.2_Silent_p.Y605Y|CAST_uc003klv.2_Silent_p.Y679Y|CAST_uc003klw.2_Silent_p.Y682Y|CAST_uc003klx.2_Silent_p.Y660Y|CAST_uc003kly.2_Silent_p.Y666Y|CAST_uc011cuo.1_Silent_p.Y664Y|CAST_uc003klz.1_Silent_p.Y618Y|CAST_uc011cur.1_Silent_p.Y604Y|CAST_uc011cus.1_Silent_p.Y605Y|CAST_uc003kma.1_Silent_p.Y576Y|CAST_uc011cut.1_Silent_p.Y546Y|CAST_uc003kmb.2_Silent_p.Y564Y|CAST_uc003kmc.2_Silent_p.Y618Y|CAST_uc003kmd.2_Silent_p.Y596Y|CAST_uc003kme.2_Silent_p.Y577Y|CAST_uc003kmf.2_Silent_p.Y583Y|CAST_uc003kmh.2_Silent_p.Y332Y|CAST_uc010jbj.2_Silent_p.Y333Y|CAST_uc010jbk.2_Silent_p.Y333Y|CAST_uc010jbl.1_Silent_p.Y341Y|CAST_uc003kmi.2_Non-coding_Transcript|CAST_uc003kmj.2_Silent_p.Y340Y|CAST_uc003kmk.2_Non-coding_Transcript|ERAP1_uc003kml.2_Intron	NM_001750	NP_001741	P20810	ICAL_HUMAN	calpastatin isoform a	618	Inhibitory domain 4.						calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)										0.2	57.240969	68.548117	27	108	KEEP	---	---	---	---	capture		Silent	SNP	96101822	96101822	2803	5	C	T	T	T	220	17	CAST	2	2
GRIK2	2898	broad.mit.edu	37	6	102483232	102483232	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:102483232C>A	uc003pqp.3	+	c.2102C>A	c.(2101-2103)ACG>AAG	p.T701K	GRIK2_uc003pqo.3_Missense_Mutation_p.T701K|GRIK2_uc010kcw.2_Missense_Mutation_p.T701K	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	701	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|breast(1)|pancreas(1)	4		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)									0.129412	17.363663	28.729352	11	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102483232	102483232	7053	6	C	A	A	A	247	19	GRIK2	1	1
SERINC1	57515	broad.mit.edu	37	6	122774962	122774962	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:122774962G>A	uc003pyy.1	-	c.542C>T	c.(541-543)TCG>TTG	p.S181L		NM_020755	NP_065806	Q9NRX5	SERC1_HUMAN	serine incorporator 1	181	Cytoplasmic (Potential).				phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	L-serine transmembrane transporter activity|protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.126)										0.142857	17.202045	25.806168	10	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122774962	122774962	14567	6	G	A	A	A	481	37	SERINC1	1	1
SHPRH	257218	broad.mit.edu	37	6	146264574	146264574	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146264574G>A	uc003qld.2	-	c.1943C>T	c.(1942-1944)ACC>ATC	p.T648I	SHPRH_uc003qle.2_Missense_Mutation_p.T648I|SHPRH_uc003qlf.2_Missense_Mutation_p.T648I|SHPRH_uc003qlg.1_Missense_Mutation_p.T204I|SHPRH_uc003qlj.1_Missense_Mutation_p.T537I	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	648					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)	2		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)										0.153061	26.266432	37.548575	15	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146264574	146264574	14786	6	G	A	A	A	572	44	SHPRH	2	2
FNDC1	84624	broad.mit.edu	37	6	159652943	159652943	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:159652943G>T	uc010kjv.2	+	c.1399G>T	c.(1399-1401)GAG>TAG	p.E467*	FNDC1_uc010kjw.1_Nonsense_Mutation_p.E352*	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	467						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)										0.09434	1.341083	10.100131	5	48	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	159652943	159652943	6210	6	G	T	T	T	533	41	FNDC1	5	2
PNLDC1	154197	broad.mit.edu	37	6	160222219	160222219	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160222219G>T	uc003qsy.1	+	c.208_splice	c.e3+1	p.G70_splice	PNLDC1_uc003qsx.1_Splice_Site_SNP_p.G59_splice	NM_173516	NP_775787			poly(A)-specific ribonuclease (PARN)-like domain							integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)										0.111111	20.662271	43.53849	17	136	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	160222219	160222219	12574	6	G	T	T	T	572	44	PNLDC1	5	2
CCR6	1235	broad.mit.edu	37	6	167549961	167549961	+	Silent	SNP	A	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:167549961A>C	uc003qvl.2	+	c.243A>C	c.(241-243)ACA>ACC	p.T81T	CCR6_uc010kkm.2_Silent_p.T81T|CCR6_uc003qvn.3_Silent_p.T81T|CCR6_uc003qvm.3_Silent_p.T81T	NM_031409	NP_113597	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	81	Cytoplasmic (Potential).				cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)						4				0.136986	15.499832	24.811978	10	63	KEEP	---	---	---	---	capture		Silent	SNP	167549961	167549961	3072	6	A	C	C	C	80	7	CCR6	4	4
GMDS	2762	broad.mit.edu	37	6	1960101	1960101	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:1960101C>A	uc003mtq.2	-	c.643G>T	c.(643-645)GGA>TGA	p.G215*		NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	215					'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion	cytoplasm	coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)										0.09434	2.535603	11.297627	5	48	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	1960101	1960101	6755	6	C	A	A	A	312	24	GMDS	5	2
HIST1H1C	3006	broad.mit.edu	37	6	26056117	26056117	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26056117C>T	uc003nfw.2	-	c.540G>A	c.(538-540)GCG>GCA	p.A180A		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	180					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)	3														0.08642	2.30811	16.300289	7	74	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	26056117	26056117	7409	6	C	T	T	T	392	31	HIST1H1C	1	1
SERPINB6	5269	broad.mit.edu	37	6	2949198	2949198	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:2949198C>T	uc003muk.2	-	c.679G>A	c.(679-681)GAA>AAA	p.E227K	SERPINB6_uc003mui.2_Missense_Mutation_p.E110K|SERPINB6_uc003muj.2_Non-coding_Transcript|SERPINB6_uc003mul.2_Missense_Mutation_p.E227K|SERPINB6_uc003mum.2_Missense_Mutation_p.E227K|SERPINB6_uc003mun.2_Missense_Mutation_p.E227K|SERPINB6_uc003muo.2_Missense_Mutation_p.E227K	NM_004568	NP_004559	P35237	SPB6_HUMAN	serine (or cysteine) proteinase inhibitor, clade	227					regulation of proteolysis	centrosome|cytosol|protein complex	protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)									0.168539	28.567077	37.830777	15	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2949198	2949198	14593	6	C	T	T	T	390	30	SERPINB6	2	2
GNL1	2794	broad.mit.edu	37	6	30514577	30514577	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30514577G>A	uc003nqh.2	-	c.1478C>T	c.(1477-1479)GCG>GTG	p.A493V	GNL1_uc011dmi.1_Missense_Mutation_p.A290V|GNL1_uc011dmj.1_Missense_Mutation_p.A491V|GNL1_uc011dmk.1_Missense_Mutation_p.A148V	NM_005275	NP_005266	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	493					response to DNA damage stimulus|signal transduction|T cell mediated immunity	extracellular space|intracellular	GTP binding|structural molecule activity			ovary(3)	3														0.111111	6.684638	17.425673	8	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30514577	30514577	6804	6	G	A	A	A	494	38	GNL1	1	1
MDC1	9656	broad.mit.edu	37	6	30679197	30679197	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30679197T>C	uc003nrg.3	-	c.2213A>G	c.(2212-2214)CAG>CGG	p.Q738R	MDC1_uc003nrf.3_Missense_Mutation_p.Q392R|MDC1_uc011dmp.1_Missense_Mutation_p.Q609R	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	738				Missing (in Ref. 2; CAH18685).	cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4														0.150685	19.176063	27.713869	11	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30679197	30679197	9792	6	T	C	C	C	715	55	MDC1	4	4
BAT3	7917	broad.mit.edu	37	6	31616491	31616491	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31616491A>G	uc003nvg.3	-	c.515T>C	c.(514-516)ATG>ACG	p.M172T	BAT3_uc003nvf.3_Missense_Mutation_p.M172T|BAT3_uc003nvh.3_Missense_Mutation_p.M172T|BAT3_uc003nvi.3_Missense_Mutation_p.M172T|BAT3_uc011dnw.1_Missense_Mutation_p.M172T|BAT3_uc011dnx.1_Missense_Mutation_p.M172T|BAT3_uc003nvj.1_Missense_Mutation_p.M172T	NM_004639	NP_004630	P46379	BAG6_HUMAN	HLA-B associated transcript-3 isoform a	172					apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process	BAT3 complex|nucleus	polyubiquitin binding|proteasome binding|ribosome binding				0										141				0.157895	30.387301	45.240363	21	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31616491	31616491	1343	6	A	G	G	G	104	8	BAT3	4	4
C2	717	broad.mit.edu	37	6	31912787	31912787	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31912787G>A	uc003nyf.2	+	c.2060G>A	c.(2059-2061)CGG>CAG	p.R687Q	C2_uc011doo.1_Missense_Mutation_p.R441Q|C2_uc011dop.1_Missense_Mutation_p.R473Q|C2_uc010jtk.2_Missense_Mutation_p.R555Q|C2_uc011doq.1_Missense_Mutation_p.R658Q|C2_uc003nyg.2_Missense_Mutation_p.R464Q|CFB_uc011dor.1_Intron|C2_uc003nyh.1_Intron|CFB_uc011dos.1_5'Flank|CFB_uc003nyi.2_5'Flank|CFB_uc003nyj.3_5'Flank	NM_000063	NP_000054	P06681	CO2_HUMAN	complement component 2 isoform 1 preproprotein	687	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular space	serine-type endopeptidase activity			ovary(1)	1		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)										0.201681	60.841239	70.67452	24	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31912787	31912787	2150	6	G	A	A	A	507	39	C2	1	1
TNXB	7148	broad.mit.edu	37	6	32035615	32035615	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32035615C>T	uc003nzl.2	-	c.6367G>A	c.(6367-6369)GAC>AAC	p.D2123N		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	2195	Fibronectin type-III 14.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0														0.162162	11.130787	15.142927	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32035615	32035615	16887	6	C	T	T	T	403	31	TNXB	1	1
HLA-DOA	3111	broad.mit.edu	37	6	32975163	32975163	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32975163C>T	uc003ocr.2	-	c.538G>A	c.(538-540)GTG>ATG	p.V180M	HLA-DOA_uc010juj.2_Missense_Mutation_p.V150M|HLA-DOA_uc010jui.2_Missense_Mutation_p.V180M	NM_002119	NP_002110	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO	180	Extracellular (Potential).|Alpha-2.|Ig-like C1-type.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0														0.135484	31.791977	51.730355	21	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32975163	32975163	7491	6	C	T	T	T	247	19	HLA-DOA	1	1
TCP11	6954	broad.mit.edu	37	6	35088271	35088271	+	Missense_Mutation	SNP	T	C	C	rs62404564		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:35088271T>C	uc003okd.2	-	c.907A>G	c.(907-909)ATG>GTG	p.M303V	TCP11_uc003ojz.1_Missense_Mutation_p.M228V|TCP11_uc003oka.2_Missense_Mutation_p.M228V|TCP11_uc003okb.2_Missense_Mutation_p.M227V|TCP11_uc003okc.2_Missense_Mutation_p.M227V|TCP11_uc011dsu.1_Missense_Mutation_p.M285V|TCP11_uc011dsv.1_Missense_Mutation_p.M252V|TCP11_uc011dsw.1_Missense_Mutation_p.M257V	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	290					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)	3														0.168	47.70441	60.749726	21	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35088271	35088271	16239	6	T	C	C	C	676	52	TCP11	4	4
SFRS3	6428	broad.mit.edu	37	6	36568950	36568950	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:36568950C>G	uc003omj.2	+	c.363C>G	c.(361-363)TTC>TTG	p.F121L	SFRS3_uc003omk.2_Non-coding_Transcript	NM_003017	NP_003008	P84103	SRSF3_HUMAN	splicing factor, arginine/serine-rich 3	121	B-1.|2 X approximate repeats, basic.|Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0														0.148148	5.779377	8.992847	4	23	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	36568950	36568950	14668	6	C	G	G	G	415	32	SFRS3	3	3
KCNK17	89822	broad.mit.edu	37	6	39272299	39272299	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:39272299C>T	uc003ooo.2	-	c.485G>A	c.(484-486)TGG>TAG	p.W162*	KCNK17_uc003oop.2_Nonsense_Mutation_p.W162*	NM_031460	NP_113648	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	162	Cytoplasmic (Potential).					integral to membrane	potassium channel activity|voltage-gated ion channel activity			skin(1)	1														0.08871	1.320773	22.558125	11	113	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	39272299	39272299	8369	6	C	T	T	T	273	21	KCNK17	5	2
TREML4	285852	broad.mit.edu	37	6	41196603	41196603	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41196603C>A	uc003oqc.2	+	c.215C>A	c.(214-216)CCC>CAC	p.P72H	TREML4_uc003oqd.2_Non-coding_Transcript	NM_198153	NP_937796	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid	72	Ig-like V-type.					extracellular region				breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)													0.097561	3.812671	17.048216	8	74	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	41196603	41196603	17018	6	C	A	A	A	286	22	TREML4	2	2
CUL9	23113	broad.mit.edu	37	6	43192148	43192148	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43192148G>A	uc003ouk.2	+	c.7519G>A	c.(7519-7521)GAT>AAT	p.D2507N	CUL9_uc003oul.2_Missense_Mutation_p.D2479N|CUL9_uc010jyk.2_Missense_Mutation_p.D1659N|CUL9_uc003oun.2_Missense_Mutation_p.D302N	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	2507					regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process	anaphase-promoting complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|central_nervous_system(1)	6														0.087719	1.429988	11.231396	5	52	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	43192148	43192148	4221	6	G	A	A	A	585	45	CUL9	2	2
MYO6	4646	broad.mit.edu	37	6	76602282	76602282	+	Silent	SNP	G	A	A	rs55905349	by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:76602282G>A	uc003pih.1	+	c.2982G>A	c.(2980-2982)GAG>GAA	p.E994E	MYO6_uc003pig.1_Silent_p.E994E|MYO6_uc003pii.1_Silent_p.E994E|MYO6_uc003pij.1_5'Flank	NM_004999	NP_004990	Q9UM54	MYO6_HUMAN	myosin VI	994	Glu-rich.|Potential.				actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)										0.12069	19.977091	36.332923	14	102	KEEP	---	---	---	---	capture		Silent	SNP	76602282	76602282	10476	6	G	A	A	A	451	35	MYO6	2	2
TPBG	7162	broad.mit.edu	37	6	83075447	83075447	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:83075447C>T	uc003pjn.3	+	c.769C>T	c.(769-771)CTG>TTG	p.L257L	TPBG_uc010kbj.2_Silent_p.L257L|TPBG_uc003pjo.2_Silent_p.L257L	NM_006670	NP_006661	Q13641	TPBG_HUMAN	trophoblast glycoprotein precursor	257	Extracellular (Potential).				cell adhesion	integral to plasma membrane				central_nervous_system(1)	1		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)										0.085714	1.998932	14.177187	6	64	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	83075447	83075447	16938	6	C	T	T	T	311	24	TPBG	2	2
DOPEY1	23033	broad.mit.edu	37	6	83838852	83838852	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:83838852G>A	uc011dyy.1	+	c.1939G>A	c.(1939-1941)GTA>ATA	p.V647I	DOPEY1_uc003pjs.1_Missense_Mutation_p.V656I|DOPEY1_uc010kbl.1_Missense_Mutation_p.V647I	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	656					protein transport					ovary(2)|breast(1)	3		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)										0.173333	24.336568	31.889404	13	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83838852	83838852	4891	6	G	A	A	A	520	40	DOPEY1	1	1
KIAA1009	22832	broad.mit.edu	37	6	84862623	84862623	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:84862623G>A	uc010kbp.2	-	c.3270C>T	c.(3268-3270)CTC>CTT	p.L1090L	KIAA1009_uc003pkj.3_Silent_p.L1014L|KIAA1009_uc003pki.3_Silent_p.L476L	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	1090	Potential.				cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)										0.10687	10.444669	30.552813	14	117	KEEP	---	---	---	---	capture		Silent	SNP	84862623	84862623	8510	6	G	A	A	A	574	45	KIAA1009	2	2
TBX18	9096	broad.mit.edu	37	6	85457788	85457788	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:85457788C>T	uc003pkl.1	-	c.789G>A	c.(787-789)ATG>ATA	p.M263I	TBX18_uc010kbq.1_Missense_Mutation_p.M105I	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	263	T-box.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)						300				0.111111	4.088421	9.458513	4	32	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	85457788	85457788	16179	6	C	T	T	T	325	25	TBX18	2	2
MANEA	79694	broad.mit.edu	37	6	96054073	96054073	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:96054073C>A	uc003poo.1	+	c.1181C>A	c.(1180-1182)CCC>CAC	p.P394H		NM_024641	NP_078917	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	394	Catalytic (Probable).|Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)										0.082474	-0.054615	17.039817	8	89	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	96054073	96054073	9604	6	C	A	A	A	286	22	MANEA	2	2
SERPINE1	5054	broad.mit.edu	37	7	100771789	100771789	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100771789G>T	uc003uxt.2	+	c.115G>T	c.(115-117)GGG>TGG	p.G39W	SERPINE1_uc011kkj.1_Intron	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1	39					angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)									0.088235	1.597269	13.265409	6	62	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	100771789	100771789	14599	7	G	T	T	T	507	39	SERPINE1	1	1
SRPK2	6733	broad.mit.edu	37	7	104782689	104782689	+	Missense_Mutation	SNP	T	G	G	rs55743527		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:104782689T>G	uc003vcv.2	-	c.1309A>C	c.(1309-1311)ACA>CCA	p.T437P	SRPK2_uc003vct.2_Missense_Mutation_p.T426P|SRPK2_uc003vcu.2_Missense_Mutation_p.T426P|SRPK2_uc003vcw.1_Missense_Mutation_p.T426P	NM_182692	NP_872634	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2	426	Protein kinase.				angiogenesis|cell differentiation|innate immune response|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|protein phosphorylation|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)	5									p.T437P(ES2-Tumor)	326				0.118343	25.439537	49.755954	20	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104782689	104782689	15674	7	T	G	G	G	767	59	SRPK2	4	4
HYAL4	23553	broad.mit.edu	37	7	123516947	123516947	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123516947C>T	uc003vlc.2	+	c.1184C>T	c.(1183-1185)CCC>CTC	p.P395L	HYAL4_uc011knz.1_3'UTR	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	395	Extracellular (Potential).				fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity				0														0.155556	8.994266	14.110133	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123516947	123516947	7766	7	C	T	T	T	286	22	HYAL4	2	2
BRAF	673	broad.mit.edu	37	7	140500244	140500244	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:140500244T>C	uc003vwc.3	-	c.898A>G	c.(898-900)ATA>GTA	p.I300V		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	300					activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(211)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(7681)|large_intestine(4665)|skin(3221)|NS(366)|central_nervous_system(264)|ovary(219)|lung(77)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(27)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(16)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	16798	Melanoma(164;0.00956)				Sorafenib(DB00398)	Colon(40;35 892 2973 5743 27438)		61		451				0.092784	5.902481	22.086551	9	88	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	140500244	140500244	1527	7	T	C	C	C	676	52	BRAF	4	4
MGAM	8972	broad.mit.edu	37	7	141734094	141734094	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141734094C>G	uc003vwy.2	+	c.1702C>G	c.(1702-1704)CTC>GTC	p.L568V		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	568	Lumenal (Potential).|Maltase.				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.159091	15.296901	20.168254	7	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141734094	141734094	9931	7	C	G	G	G	416	32	MGAM	3	3
PIP	5304	broad.mit.edu	37	7	142836663	142836663	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142836663C>A	uc003wcf.1	+	c.369C>A	c.(367-369)TGC>TGA	p.C123*		NM_002652	NP_002643	P12273	PIP_HUMAN	prolactin-induced protein precursor	123						extracellular region	actin binding			ovary(1)	1	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)										0.072581	-4.818159	18.489483	9	115	FSTAR-RETAIN	---	---	---	---	capture		Nonsense_Mutation	SNP	142836663	142836663	12359	7	C	A	A	A	337	26	PIP	5	2
EPHA1	2041	broad.mit.edu	37	7	143096786	143096786	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143096786C>T	uc003wcz.2	-	c.793G>A	c.(793-795)GAG>AAG	p.E265K		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1 precursor	265	Extracellular (Potential).|Cys-rich.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)								379				0.122449	7.51345	14.353697	6	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143096786	143096786	5358	7	C	T	T	T	377	29	EPHA1	2	2
TMEM195	392636	broad.mit.edu	37	7	15427115	15427115	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:15427115G>C	uc003stb.1	-	c.873C>G	c.(871-873)TTC>TTG	p.F291L		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	291					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0														0.083333	3.323358	20.262899	8	88	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	15427115	15427115	16652	7	G	C	C	C	425	33	TMEM195	3	3
DNAH11	8701	broad.mit.edu	37	7	21695523	21695523	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:21695523C>A	uc003svc.2	+	c.5033C>A	c.(5032-5034)GCA>GAA	p.A1678E		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1678	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.121951	6.550655	12.285933	5	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21695523	21695523	4781	7	C	A	A	A	325	25	DNAH11	2	2
C7orf46	340277	broad.mit.edu	37	7	23731172	23731172	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:23731172C>T	uc003swo.3	+	c.594C>T	c.(592-594)AGC>AGT	p.S198S	C7orf46_uc003swq.3_Silent_p.S198S|C7orf46_uc003swr.3_Silent_p.S140S|C7orf46_uc003swp.3_Non-coding_Transcript|C7orf46_uc010kup.2_Non-coding_Transcript	NM_199136	NP_954587	A4D161	CG046_HUMAN	hypothetical protein LOC340277 isoform 1	198											0														0.105263	7.04956	18.817094	8	68	KEEP	---	---	---	---	capture		Silent	SNP	23731172	23731172	2503	7	C	T	T	T	363	28	C7orf46	2	2
HOXA1	3198	broad.mit.edu	37	7	27134293	27134293	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27134293G>T	uc003sye.2	-	c.774C>A	c.(772-774)CGC>CGA	p.R258R	HOXA1_uc003syd.2_3'UTR	NM_005522	NP_005513	P49639	HXA1_HUMAN	homeobox A1 isoform a	258	Homeobox.					nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.09375	4.300798	20.22981	9	87	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	27134293	27134293	7580	7	G	T	T	T	587	46	HOXA1	2	2
NOD1	10392	broad.mit.edu	37	7	30491863	30491863	+	Silent	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:30491863C>A	uc003tav.2	-	c.1170G>T	c.(1168-1170)GTG>GTT	p.V390V	NOD1_uc010kvs.2_3'UTR	NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain	390	NACHT.				activation of caspase activity|activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|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	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)	1														0.111111	3.707433	10.384494	5	40	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	30491863	30491863	10919	7	C	A	A	A	314	25	NOD1	2	2
FAM188B	84182	broad.mit.edu	37	7	30811121	30811121	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:30811121C>G	uc003tbt.2	+	c.12C>G	c.(10-12)CTC>CTG	p.L4L	FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182	4											0														0.263158	14.866295	15.830133	5	14	KEEP	---	---	---	---	capture		Silent	SNP	30811121	30811121	5725	7	C	G	G	G	405	32	FAM188B	3	3
FAM188B	84182	broad.mit.edu	37	7	30825544	30825544	+	Missense_Mutation	SNP	C	A	A	rs75843887		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:30825544C>A	uc003tbt.2	+	c.599C>A	c.(598-600)TCC>TAC	p.S200Y	FAM188B_uc010kwe.2_Missense_Mutation_p.S171Y	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182	200											0														0.236111	38.344294	42.925313	17	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30825544	30825544	5725	7	C	A	A	A	390	30	FAM188B	2	2
HECW1	23072	broad.mit.edu	37	7	43540857	43540857	+	Silent	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43540857C>A	uc003tid.1	+	c.3567C>A	c.(3565-3567)GCC>GCA	p.A1189A	HECW1_uc011kbi.1_Silent_p.A1155A	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	1189					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.083333	1.6895	20.74655	9	99	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	43540857	43540857	7325	7	C	A	A	A	301	24	HECW1	2	2
UBE2D4	51619	broad.mit.edu	37	7	43988239	43988239	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43988239C>T	uc003tja.1	+	c.207C>T	c.(205-207)TTC>TTT	p.F69F	POLR2J4_uc003tjc.2_Intron|UBE2D4_uc003tjb.1_Silent_p.F31F	NM_015983	NP_057067	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)	69					post-translational protein modification|protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0						Esophageal Squamous(27;401 815 16344 30604)								0.196429	22.090412	26.905165	11	45	KEEP	---	---	---	---	capture		Silent	SNP	43988239	43988239	17408	7	C	T	T	T	376	29	UBE2D4	2	2
UBE2D4	51619	broad.mit.edu	37	7	43988284	43988284	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43988284C>G	uc003tja.1	+	c.252C>G	c.(250-252)ATC>ATG	p.I84M	POLR2J4_uc003tjc.2_Intron|UBE2D4_uc003tjb.1_Missense_Mutation_p.I46M	NM_015983	NP_057067	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)	84					post-translational protein modification|protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0						Esophageal Squamous(27;401 815 16344 30604)								0.16	23.651377	31.908025	12	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43988284	43988284	17408	7	C	G	G	G	408	32	UBE2D4	3	3
NUDCD3	23386	broad.mit.edu	37	7	44432049	44432049	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44432049G>A	uc003tkz.2	-	c.822C>T	c.(820-822)AAC>AAT	p.N274N	NUDCD3_uc010kye.2_Non-coding_Transcript	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	274	CS.						protein binding				0														0.070707	-10.929698	26.646029	14	184	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	44432049	44432049	11129	7	G	A	A	A	516	40	NUDCD3	1	1
TBRG4	9238	broad.mit.edu	37	7	45148653	45148653	+	Silent	SNP	G	T	T	rs11541073	byFrequency;by1000genomes	TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:45148653G>T	uc011kcd.1	-	c.217C>A	c.(217-219)CGA>AGA	p.R73R	TBRG4_uc003tmu.2_5'Flank|TBRG4_uc003tmv.2_Silent_p.R62R|TBRG4_uc003tmw.2_Silent_p.R62R|TBRG4_uc003tmx.2_Silent_p.R62R|SNORA5B_uc003tna.3_5'Flank	NM_004749	NP_004740	Q969Z0	TBRG4_HUMAN	cell cycle progression 2 protein isoform 1	62					apoptosis|cell cycle arrest|cellular respiration|G1 phase of mitotic cell cycle|positive regulation of cell proliferation	mitochondrion	ATP binding|protein binding|protein kinase activity				0														0.25	32.431068	35.405603	13	39	KEEP	---	---	---	---	capture		Silent	SNP	45148653	45148653	16175	7	G	T	T	T	519	40	TBRG4	1	1
USP42	84132	broad.mit.edu	37	7	6187422	6187422	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:6187422G>C	uc011jwo.1	+	c.1285G>C	c.(1285-1287)GGC>CGC	p.G429R	USP42_uc010kth.1_Missense_Mutation_p.G362R|USP42_uc011jwp.1_Missense_Mutation_p.G429R|USP42_uc011jwq.1_Missense_Mutation_p.G236R|USP42_uc011jwr.1_Missense_Mutation_p.G274R	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	429					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|pancreas(1)	3		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)										0.169492	21.023567	27.115929	10	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6187422	6187422	17637	7	G	C	C	C	507	39	USP42	3	3
PTPN12	5782	broad.mit.edu	37	7	77256749	77256749	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:77256749G>A	uc003ugh.2	+	c.1753G>A	c.(1753-1755)GAT>AAT	p.D585N	PTPN12_uc011kgp.1_Missense_Mutation_p.D466N|PTPN12_uc011kgq.1_Missense_Mutation_p.D455N|PTPN12_uc010lds.2_Missense_Mutation_p.D317N	NM_002835	NP_002826	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type	585						soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3														0.102564	8.405805	26.835776	12	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77256749	77256749	13236	7	G	A	A	A	585	45	PTPN12	2	2
PCLO	27445	broad.mit.edu	37	7	82545269	82545269	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82545269C>T	uc003uhx.2	-	c.12033G>A	c.(12031-12033)TTG>TTA	p.L4011L	PCLO_uc003uhv.2_Silent_p.L4011L|PCLO_uc010lec.2_Silent_p.L976L	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3942					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.115741	26.905876	58.329098	25	191	KEEP	---	---	---	---	capture		Silent	SNP	82545269	82545269	12003	7	C	T	T	T	376	29	PCLO	2	2
SEMA3D	223117	broad.mit.edu	37	7	84644447	84644447	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:84644447C>T	uc003uic.2	-	c.1631G>A	c.(1630-1632)TGT>TAT	p.C544Y	SEMA3D_uc010led.2_Missense_Mutation_p.C544Y|SEMA3D_uc003uib.2_Missense_Mutation_p.C183Y	NM_152754	NP_689967	O95025	SEM3D_HUMAN	semaphorin 3D precursor	544	PSI.				cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5						Ovarian(63;442 1191 17318 29975 31528)								0.083333	-0.819576	24.60693	12	132	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	84644447	84644447	14513	7	C	T	T	T	221	17	SEMA3D	2	2
STEAP2	261729	broad.mit.edu	37	7	89856779	89856779	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:89856779G>A	uc003ujz.2	+	c.987G>A	c.(985-987)GAG>GAA	p.E329E	STEAP2_uc003ujy.2_Silent_p.E371E|STEAP2_uc010len.2_Silent_p.E329E|STEAP2_uc003uka.2_Silent_p.E329E|STEAP2_uc003ukb.2_Silent_p.E329E|STEAP2_uc003ukc.2_Silent_p.E329E|STEAP2_uc003ukd.2_Silent_p.E329E	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the	329	Ferric oxidoreductase.				electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)													0.133333	8.319224	14.192391	6	39	KEEP	---	---	---	---	capture		Silent	SNP	89856779	89856779	15798	7	G	A	A	A	425	33	STEAP2	2	2
CDK14	5218	broad.mit.edu	37	7	90585061	90585061	+	Silent	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:90585061G>T	uc003uky.2	+	c.876G>T	c.(874-876)GTG>GTT	p.V292V	CDK14_uc003ukz.1_Silent_p.V274V|CDK14_uc010les.1_Silent_p.V246V|CDK14_uc011khl.1_Silent_p.V163V	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1	292	Protein kinase.				cell division|G2/M transition of mitotic cell cycle|protein phosphorylation|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						GBM(83;1228 1256 8311 16577 31299)				302				0.082759	1.187827	26.859117	12	133	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	90585061	90585061	3259	7	G	T	T	T	600	47	CDK14	2	2
AKAP9	10142	broad.mit.edu	37	7	91726960	91726960	+	Missense_Mutation	SNP	G	A	A	rs61757664		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91726960G>A	uc003ulg.2	+	c.10459G>A	c.(10459-10461)GAA>AAA	p.E3487K	AKAP9_uc003ulf.2_Missense_Mutation_p.E3479K|AKAP9_uc003uli.2_Missense_Mutation_p.E3110K|AKAP9_uc003ulj.2_Missense_Mutation_p.E1257K|AKAP9_uc003ull.2_Missense_Mutation_p.E383K	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	3491					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)						p.E3491K(NCIH2066-Tumor)|p.E3491K(CALU1-Tumor)	807				0.138889	34.597887	52.749484	20	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91726960	91726960	462	7	G	A	A	A	429	33	AKAP9	2	2
ANKIB1	54467	broad.mit.edu	37	7	91981814	91981814	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91981814A>T	uc003ulw.2	+	c.1255A>T	c.(1255-1257)ATT>TTT	p.I419F		NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	419	IBR-type; degenerate.						protein binding|zinc ion binding				0	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)											0.092593	8.370561	26.405248	10	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91981814	91981814	633	7	A	T	T	T	104	8	ANKIB1	3	3
PPP1R9A	55607	broad.mit.edu	37	7	94540452	94540452	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:94540452C>G	uc010lfj.2	+	c.1027C>G	c.(1027-1029)CTG>GTG	p.L343V	PPP1R9A_uc003unp.2_Missense_Mutation_p.L343V|PPP1R9A_uc011kif.1_Missense_Mutation_p.L343V|PPP1R9A_uc003unq.2_Missense_Mutation_p.L343V|PPP1R9A_uc011kig.1_Missense_Mutation_p.L343V	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	343						cell junction|synapse|synaptosome	actin binding			ovary(2)|skin(1)	3	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)											0.111111	7.441652	14.169334	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94540452	94540452	12814	7	C	G	G	G	259	20	PPP1R9A	3	3
PPP1R9A	55607	broad.mit.edu	37	7	94540565	94540565	+	Silent	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:94540565A>G	uc010lfj.2	+	c.1140A>G	c.(1138-1140)GGA>GGG	p.G380G	PPP1R9A_uc003unp.2_Silent_p.G380G|PPP1R9A_uc011kif.1_Silent_p.G380G|PPP1R9A_uc003unq.2_Silent_p.G380G|PPP1R9A_uc011kig.1_Silent_p.G380G	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	380						cell junction|synapse|synaptosome	actin binding			ovary(2)|skin(1)	3	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)											0.111111	7.249587	13.970412	5	40	KEEP	---	---	---	---	capture		Silent	SNP	94540565	94540565	12814	7	A	G	G	G	106	9	PPP1R9A	4	4
VPS13B	157680	broad.mit.edu	37	8	100844858	100844858	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:100844858C>T	uc003yiv.2	+	c.9667C>T	c.(9667-9669)CGG>TGG	p.R3223W	VPS13B_uc003yiw.2_Missense_Mutation_p.R3198W	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	3223					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			Colon(161;2205 2542 7338 31318)				1116				0.125	13.837748	23.717286	9	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100844858	100844858	17757	8	C	T	T	T	295	23	VPS13B	1	1
GATA4	2626	broad.mit.edu	37	8	11614467	11614467	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:11614467C>T	uc011kxc.1	+	c.1024C>T	c.(1024-1026)CCT>TCT	p.P342S	GATA4_uc003wub.1_Missense_Mutation_p.P135S|GATA4_uc003wuc.2_Missense_Mutation_p.P341S	NM_002052	NP_002043	P43694	GATA4_HUMAN	GATA binding protein 4	341					atrial septum primum morphogenesis|blood coagulation|cardiac right ventricle morphogenesis|cell-cell signaling|embryonic foregut morphogenesis|embryonic heart tube anterior/posterior pattern formation|endocardial cushion development|heart looping|intestinal epithelial cell differentiation|male gonad development|positive regulation of angiogenesis|positive regulation of cardioblast differentiation|positive regulation of gene-specific transcription|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|transcription from RNA polymerase II promoter|ventricular septum development	nucleoplasm	activating transcription factor binding|promoter binding|specific RNA polymerase II transcription factor activity|zinc ion binding			central_nervous_system(1)	1	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)										0.105263	7.265827	22.040754	10	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11614467	11614467	6520	8	C	T	T	T	390	30	GATA4	2	2
DEFB136	613210	broad.mit.edu	37	8	11831566	11831566	+	Silent	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:11831566T>C	uc011kxm.1	-	c.117A>G	c.(115-117)GTA>GTG	p.V39V		NM_001033018	NP_001028190	Q30KP8	DB136_HUMAN	beta-defensin 136 precursor	39					defense response to bacterium	extracellular region					0			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)										0.139073	35.966726	55.246922	21	130	KEEP	---	---	---	---	capture		Silent	SNP	11831566	11831566	4599	8	T	C	C	C	626	49	DEFB136	4	4
NOV	4856	broad.mit.edu	37	8	120430441	120430441	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:120430441G>A	uc003yoq.2	+	c.454G>A	c.(454-456)GAG>AAG	p.E152K		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	152	VWFC.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)					71				0.098592	0.656411	12.154408	7	64	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	120430441	120430441	10957	8	G	A	A	A	585	45	NOV	2	2
FAM135B	51059	broad.mit.edu	37	8	139164679	139164679	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139164679G>A	uc003yuy.2	-	c.2039C>T	c.(2038-2040)TCA>TTA	p.S680L	FAM135B_uc003yux.2_Missense_Mutation_p.S581L|FAM135B_uc003yuz.2_Non-coding_Transcript|FAM135B_uc003yva.2_Missense_Mutation_p.S242L|FAM135B_uc003yvb.2_Missense_Mutation_p.S242L	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	680										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.107143	8.30907	21.17722	9	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139164679	139164679	5646	8	G	A	A	A	585	45	FAM135B	2	2
TRAPPC9	83696	broad.mit.edu	37	8	141407834	141407834	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:141407834G>A	uc003yvh.2	-	c.1313C>T	c.(1312-1314)GCG>GTG	p.A438V	TRAPPC9_uc003yvj.2_Missense_Mutation_p.A340V|TRAPPC9_uc003yvi.1_Missense_Mutation_p.A331V	NM_031466	NP_113654	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform	340					cell differentiation	endoplasmic reticulum|Golgi apparatus					0														0.166667	13.768157	18.827686	8	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141407834	141407834	17009	8	G	A	A	A	494	38	TRAPPC9	1	1
SCRIB	23513	broad.mit.edu	37	8	144890953	144890953	+	Silent	SNP	A	G	G	rs111919660		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144890953A>G	uc003yzo.1	-	c.1941T>C	c.(1939-1941)AAT>AAC	p.N647N	SCRIB_uc003yzp.1_Silent_p.N647N	NM_182706	NP_874365	Q14160	SCRIB_HUMAN	scribble isoform a	647	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			Pancreas(51;966 1133 10533 14576 29674)				520				0.206897	10.942676	13.246773	6	23	KEEP	---	---	---	---	capture		Silent	SNP	144890953	144890953	14419	8	A	G	G	G	102	8	SCRIB	4	4
PLEC	5339	broad.mit.edu	37	8	144993230	144993230	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144993230G>A	uc003zaf.1	-	c.11170C>T	c.(11170-11172)CTG>TTG	p.L3724L	PLEC_uc003zab.1_Silent_p.L3587L|PLEC_uc003zac.1_Silent_p.L3591L|PLEC_uc003zad.2_Silent_p.L3587L|PLEC_uc003zae.1_Silent_p.L3555L|PLEC_uc003zag.1_Silent_p.L3565L|PLEC_uc003zah.2_Silent_p.L3573L|PLEC_uc003zaj.2_Silent_p.L3614L	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	3724	Globular 2.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|central_nervous_system(1)	7														0.285714	21.188623	22.342314	8	20	KEEP	---	---	---	---	capture		Silent	SNP	144993230	144993230	12478	8	G	A	A	A	451	35	PLEC	2	2
DOCK5	80005	broad.mit.edu	37	8	25174610	25174610	+	Missense_Mutation	SNP	C	T	T	rs61732769		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:25174610C>T	uc003xeg.2	+	c.1406C>T	c.(1405-1407)ACG>ATG	p.T469M	DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Missense_Mutation_p.T183M|DOCK5_uc003xei.2_Missense_Mutation_p.T39M	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	469	DHR-1.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		Pancreas(145;34 1887 3271 10937 30165)								0.181818	19.736399	24.952938	10	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25174610	25174610	4874	8	C	T	T	T	247	19	DOCK5	1	1
BAG4	9530	broad.mit.edu	37	8	38065246	38065246	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:38065246C>G	uc003xky.1	+	c.595C>G	c.(595-597)CCT>GCT	p.P199A	BAG4_uc003xkz.1_Missense_Mutation_p.P163A	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	199					anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)								66				0.162791	13.402919	18.046406	7	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38065246	38065246	1310	8	C	G	G	G	286	22	BAG4	3	3
ANK1	286	broad.mit.edu	37	8	41525790	41525790	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41525790C>T	uc003xom.2	-	c.5512G>A	c.(5512-5514)GTG>ATG	p.V1838M	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Missense_Mutation_p.V951M|ANK1_uc003xoi.2_Missense_Mutation_p.V1797M|ANK1_uc003xoj.2_Missense_Mutation_p.V1797M|ANK1_uc003xok.2_Missense_Mutation_p.V1797M|ANK1_uc003xol.2_Missense_Mutation_p.V1635M|ANK1_uc011lcl.1_5'Flank|ANK1_uc003xod.2_5'Flank|ANK1_uc003xoc.2_5'Flank|ANK1_uc003xof.2_5'Flank	NM_001142446	NP_001135918	P16157	ANK1_HUMAN	ankyrin 1 isoform 9	1797	55 kDa regulatory domain.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)											0.087838	3.867291	29.290322	13	135	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	41525790	41525790	623	8	C	T	T	T	234	18	ANK1	2	2
SDR16C5	195814	broad.mit.edu	37	8	57228594	57228594	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:57228594C>A	uc010lyk.1	-	c.313G>T	c.(313-315)GTG>TTG	p.V105L	SDR16C5_uc003xsy.1_Missense_Mutation_p.V105L|SDR16C5_uc010lyl.1_Missense_Mutation_p.V105L	NM_138969	NP_620419	Q8N3Y7	RDHE2_HUMAN	epidermal retinal dehydrogenase 2	105					detection of light stimulus involved in visual perception|keratinocyte proliferation|oxidation-reduction process|retinal metabolic process|retinol metabolic process	endoplasmic reticulum membrane|integral to membrane|integral to membrane of membrane fraction	binding|retinol dehydrogenase activity			ovary(1)|central_nervous_system(1)	2														0.115942	8.559004	18.572417	8	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57228594	57228594	14457	8	C	A	A	A	260	20	SDR16C5	2	2
LRRCC1	85444	broad.mit.edu	37	8	86050664	86050664	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:86050664G>T	uc003ycw.2	+	c.2794G>T	c.(2794-2796)GAA>TAA	p.E932*	LRRCC1_uc003ycx.2_Nonsense_Mutation_p.E839*|LRRCC1_uc003ycy.2_Nonsense_Mutation_p.E912*	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	932					cell division|mitosis	centriole|nucleus					0														0.186047	16.172744	20.146592	8	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	86050664	86050664	9402	8	G	T	T	T	533	41	LRRCC1	5	2
GABBR2	9568	broad.mit.edu	37	9	101216455	101216455	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101216455G>A	uc004ays.2	-	c.1044C>T	c.(1042-1044)GGC>GGT	p.G348G		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor	348	Extracellular (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)									0.196721	45.113413	55.521732	24	98	KEEP	---	---	---	---	capture		Silent	SNP	101216455	101216455	6407	9	G	A	A	A	483	38	GABBR2	1	1
COL15A1	1306	broad.mit.edu	37	9	101767192	101767192	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101767192G>A	uc004azb.1	+	c.1213G>A	c.(1213-1215)GAA>AAA	p.E405K		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	405	Nonhelical region 1 (NC1).|1.|4 X tandem repeats.				angiogenesis|cell adhesion|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding|extracellular matrix structural constituent			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)												0.069767	-8.537956	32.545025	15	200	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	101767192	101767192	3810	9	G	A	A	A	585	45	COL15A1	2	2
SMC2	10592	broad.mit.edu	37	9	106860779	106860779	+	Missense_Mutation	SNP	A	C	C	rs61755310		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:106860779A>C	uc004bbv.2	+	c.371A>C	c.(370-372)AAC>ACC	p.N124T	SMC2_uc004bbu.1_Missense_Mutation_p.N124T|SMC2_uc004bbw.2_Missense_Mutation_p.N124T|SMC2_uc011lvl.1_Missense_Mutation_p.N124T|SMC2_uc010mtg.1_5'UTR|SMC2_uc010mth.1_Missense_Mutation_p.N74T|SMC2_uc004bbx.2_Missense_Mutation_p.N124T	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	124					cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|lung(1)|breast(1)	8									p.N124T(SKMEL5-Tumor)|p.N124T(A172-Tumor)|p.N124T(CORL24-Tumor)	1437				0.146341	11.424637	16.35168	6	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106860779	106860779	15281	9	A	C	C	C	26	2	SMC2	4	4
OR13F1	138805	broad.mit.edu	37	9	107267284	107267284	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107267284G>A	uc011lvm.1	+	c.741G>A	c.(739-741)GTG>GTA	p.V247V		NM_001004485	NP_001004485	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2														0.086207	0.731292	10.793868	5	53	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	107267284	107267284	11347	9	G	A	A	A	600	47	OR13F1	2	2
OR13D1	286365	broad.mit.edu	37	9	107457527	107457527	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107457527G>A	uc011lvs.1	+	c.825G>A	c.(823-825)GCG>GCA	p.A275A		NM_001004484	NP_001004484	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D,	275	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.108696	8.501018	22.444671	10	82	KEEP	---	---	---	---	capture		Silent	SNP	107457527	107457527	11346	9	G	A	A	A	483	38	OR13D1	1	1
LPAR1	1902	broad.mit.edu	37	9	113704059	113704059	+	Silent	SNP	C	T	T	rs41279057		TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113704059C>T	uc011lwm.1	-	c.438G>A	c.(436-438)GAG>GAA	p.E146E	LPAR1_uc004bfa.2_Silent_p.E145E|LPAR1_uc004bfb.2_Silent_p.E145E|LPAR1_uc004bfc.2_Silent_p.E145E|LPAR1_uc011lwn.1_Silent_p.E127E|LPAR1_uc011lwo.1_Silent_p.E146E|LPAR1_uc010mub.2_Silent_p.E145E	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	145	Cytoplasmic (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						NSCLC(115;661 2323 9836 34256)								0.139241	35.239245	55.111653	22	136	KEEP	---	---	---	---	capture		Silent	SNP	113704059	113704059	9277	9	C	T	T	T	415	32	LPAR1	2	2
RGS3	5998	broad.mit.edu	37	9	116346507	116346507	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:116346507C>T	uc004bhq.2	+	c.2815C>T	c.(2815-2817)CGC>TGC	p.R939C	RGS3_uc004bhs.2_Missense_Mutation_p.R829C|RGS3_uc004bht.2_Missense_Mutation_p.R658C|RGS3_uc010muy.2_Intron|RGS3_uc004bhv.2_Missense_Mutation_p.R260C|RGS3_uc010muz.1_Missense_Mutation_p.R278C|RGS3_uc004bhw.2_Intron|RGS3_uc011lxh.1_Missense_Mutation_p.R249C|RGS3_uc004bhx.2_Missense_Mutation_p.R260C|RGS3_uc004bhy.1_Missense_Mutation_p.R249C|RGS3_uc004bhz.2_Missense_Mutation_p.R281C	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	939					inactivation of MAPK activity|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3														0.315789	16.090038	16.638647	6	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116346507	116346507	13780	9	C	T	T	T	351	27	RGS3	1	1
ORM1	5004	broad.mit.edu	37	9	117094123	117094123	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:117094123A>T	uc011lxo.1	+	c.454A>T	c.(454-456)ACC>TCC	p.T152S	ORM2_uc004bil.2_Missense_Mutation_p.T152S	NM_000607	NP_000598	P02763	A1AG1_HUMAN	orosomucoid 1 precursor	152					acute-phase response|regulation of immune system process	extracellular space	protein binding				0		Myeloproliferative disorder(63;0.163)			Acenocoumarol(DB01418)|Alfentanil(DB00802)|Aprindine(DB01429)|Disopyramide(DB00280)|Penbutolol(DB01359)|Phenprocoumon(DB00946)|Quinidine(DB00908)|Tamsulosin(DB00706)									0.185185	9.459019	11.968568	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117094123	117094123	11678	9	A	T	T	T	130	10	ORM1	3	3
OR1N2	138882	broad.mit.edu	37	9	125316032	125316032	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125316032A>G	uc011lyx.1	+	c.584A>G	c.(583-585)TAT>TGT	p.Y195C		NM_001004457	NP_001004457	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N,	195	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.15	41.193028	57.62767	21	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125316032	125316032	11376	9	A	G	G	G	208	16	OR1N2	4	4
ZNF79	7633	broad.mit.edu	37	9	130191113	130191113	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130191113C>T	uc004bqw.3	+	c.19C>T	c.(19-21)CTG>TTG	p.L7L	ZNF79_uc011maf.1_5'UTR|ZNF79_uc011mag.1_5'UTR	NM_007135	NP_009066	Q15937	ZNF79_HUMAN	zinc finger protein 79	7					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1														0.190476	8.789094	10.668778	4	17	KEEP	---	---	---	---	capture		Silent	SNP	130191113	130191113	18759	9	C	T	T	T	259	20	ZNF79	2	2
PKN3	29941	broad.mit.edu	37	9	131475832	131475832	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131475832G>T	uc004bvw.2	+	c.1147G>T	c.(1147-1149)GTG>TTG	p.V383L	PKN3_uc010myh.2_Missense_Mutation_p.V383L|PKN3_uc011mbk.1_5'UTR	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN	protein kinase PKNbeta	383					protein phosphorylation|signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			lung(2)	2										307				0.375	16.644632	16.864564	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131475832	131475832	12406	9	G	T	T	T	520	40	PKN3	1	1
CRAT	1384	broad.mit.edu	37	9	131860363	131860363	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131860363T>C	uc004bxh.2	-	c.1393A>G	c.(1393-1395)ACC>GCC	p.T465A	CRAT_uc004bxg.2_Missense_Mutation_p.T444A|CRAT_uc004bxk.3_Missense_Mutation_p.T444A	NM_000755	NP_000746	P43155	CACP_HUMAN	carnitine acetyltransferase precursor	465		Carnitine.		T->A: Increases the KM for carnitine almost 70-fold and reduces enzyme activity 450-fold.	energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA oxidase|transport	endoplasmic reticulum|mitochondrial inner membrane|peroxisomal matrix	carnitine O-acetyltransferase activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)									0.15625	6.45886	10.069202	5	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131860363	131860363	3986	9	T	C	C	C	767	59	CRAT	4	4
TTF1	7270	broad.mit.edu	37	9	135275495	135275495	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135275495C>A	uc004cbl.2	-	c.1518G>T	c.(1516-1518)AAG>AAT	p.K506N	TTF1_uc011mcp.1_Non-coding_Transcript|TTF1_uc004cbm.2_De_novo_Start_OutOfFrame	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	506					negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|pancreas(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)										0.133333	20.704874	36.390139	16	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135275495	135275495	17273	9	C	A	A	A	311	24	TTF1	2	2
KCNT1	57582	broad.mit.edu	37	9	138648751	138648751	+	Silent	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:138648751G>C	uc011mdq.1	+	c.573G>C	c.(571-573)ACG>ACC	p.T191T	KCNT1_uc011mdr.1_Silent_p.T18T|KCNT1_uc010nbf.2_Silent_p.T143T|KCNT1_uc004cgo.1_5'UTR	NM_020822	NP_065873	B9EGP2	B9EGP2_HUMAN	potassium channel, subfamily T, member 1	191						membrane	binding|calcium-activated potassium channel activity|catalytic activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)										0.181818	15.430451	18.568189	6	27	KEEP	---	---	---	---	capture		Silent	SNP	138648751	138648751	8396	9	G	C	C	C	470	37	KCNT1	3	3
SEC16A	9919	broad.mit.edu	37	9	139371657	139371657	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139371657C>G	uc004chx.2	-	c.411G>C	c.(409-411)GAG>GAC	p.E137D	SEC16A_uc004chv.3_5'Flank|SEC16A_uc004chw.2_Missense_Mutation_p.E137D|SEC16A_uc010nbn.2_Missense_Mutation_p.E137D|SEC16A_uc010nbo.1_Missense_Mutation_p.E137D	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	2111	Required for interaction with SEC23A.				protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)										0.155172	17.734917	24.325076	9	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139371657	139371657	14472	9	C	G	G	G	415	32	SEC16A	3	3
BNC2	54796	broad.mit.edu	37	9	16436019	16436019	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:16436019C>T	uc003zml.2	-	c.2173G>A	c.(2173-2175)GAG>AAG	p.E725K	BNC2_uc011lmw.1_Missense_Mutation_p.E630K|BNC2_uc003zmm.2_Missense_Mutation_p.E683K|BNC2_uc003zmq.1_Missense_Mutation_p.E739K|BNC2_uc003zmr.1_Missense_Mutation_p.E762K|BNC2_uc003zmp.1_Missense_Mutation_p.E753K|BNC2_uc010mij.1_Missense_Mutation_p.E647K|BNC2_uc011lmv.1_Missense_Mutation_p.E551K|BNC2_uc003zmo.1_Missense_Mutation_p.E647K|BNC2_uc003zmj.2_Missense_Mutation_p.E490K|BNC2_uc003zmk.2_Non-coding_Transcript|BNC2_uc003zmi.2_Missense_Mutation_p.E490K|BNC2_uc003zmn.1_Missense_Mutation_p.E490K	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	725					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)										0.215385	32.615062	37.474539	14	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16436019	16436019	1500	9	C	T	T	T	403	31	BNC2	1	1
SPINK4	27290	broad.mit.edu	37	9	33248451	33248451	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:33248451G>A	uc003zsh.2	+	c.243G>A	c.(241-243)ATG>ATA	p.M81I	SUGT1P1_uc010mjq.1_Intron	NM_014471	NP_055286	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	81	Kazal-like.					extracellular region	serine-type endopeptidase inhibitor activity				0			LUSC - Lung squamous cell carcinoma(29;0.00506)											0.152174	11.392334	16.722892	7	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33248451	33248451	15573	9	G	A	A	A	585	45	SPINK4	2	2
KIAA2026	158358	broad.mit.edu	37	9	5969196	5969196	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:5969196C>A	uc003zjq.3	-	c.1035G>T	c.(1033-1035)ATG>ATT	p.M345I		NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358	345										ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)										0.104167	4.136772	11.622585	5	43	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	5969196	5969196	8581	9	C	A	A	A	377	29	KIAA2026	2	2
PTPRD	5789	broad.mit.edu	37	9	8460493	8460493	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8460493C>T	uc003zkk.2	-	c.3793G>A	c.(3793-3795)GAA>AAA	p.E1265K	PTPRD_uc003zkp.2_Missense_Mutation_p.E854K|PTPRD_uc003zkq.2_Missense_Mutation_p.E854K|PTPRD_uc003zkr.2_Missense_Mutation_p.E849K|PTPRD_uc003zks.2_Missense_Mutation_p.E844K|PTPRD_uc003zkl.2_Missense_Mutation_p.E1256K|PTPRD_uc003zkm.2_Missense_Mutation_p.E1252K|PTPRD_uc003zkn.2_Missense_Mutation_p.E854K|PTPRD_uc003zko.2_Missense_Mutation_p.E851K	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1265	Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.089005	3.744339	36.346183	17	174	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	8460493	8460493	13256	9	C	T	T	T	416	32	PTPRD	2	2
PTPRD	5789	broad.mit.edu	37	9	8518415	8518415	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8518415G>T	uc003zkk.2	-	c.976C>A	c.(976-978)CCA>ACA	p.P326T	PTPRD_uc003zkp.2_Missense_Mutation_p.P326T|PTPRD_uc003zkq.2_Missense_Mutation_p.P326T|PTPRD_uc003zkr.2_Missense_Mutation_p.P320T|PTPRD_uc003zks.2_Missense_Mutation_p.P316T|PTPRD_uc003zkl.2_Missense_Mutation_p.P326T|PTPRD_uc003zkm.2_Missense_Mutation_p.P313T|PTPRD_uc003zkn.2_Missense_Mutation_p.P326T|PTPRD_uc003zko.2_Missense_Mutation_p.P323T	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	326	Fibronectin type-III 1.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.102941	3.669627	14.359776	7	61	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	8518415	8518415	13256	9	G	T	T	T	533	41	PTPRD	2	2
SECISBP2	79048	broad.mit.edu	37	9	91972334	91972334	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:91972334G>A	uc004aqj.1	+	c.2122G>A	c.(2122-2124)GAT>AAT	p.D708N	SECISBP2_uc011ltk.1_Missense_Mutation_p.D707N|SECISBP2_uc004aqk.1_Missense_Mutation_p.D635N|SECISBP2_uc010mqo.1_Missense_Mutation_p.D413N|SECISBP2_uc011ltl.1_Missense_Mutation_p.D640N	NM_024077	NP_076982	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	708					translation	nucleus	mRNA 3'-UTR binding			ovary(2)	2														0.084906	1.697803	20.223921	9	97	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	91972334	91972334	14492	9	G	A	A	A	533	41	SECISBP2	2	2
SYK	6850	broad.mit.edu	37	9	93636989	93636989	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:93636989G>T	uc004aqz.2	+	c.1039G>T	c.(1039-1041)GTG>TTG	p.V347L	SYK_uc004ara.2_Missense_Mutation_p.V324L|SYK_uc004arb.2_Missense_Mutation_p.V324L|SYK_uc004arc.2_Missense_Mutation_p.V347L|SYK_uc011ltr.1_Non-coding_Transcript|SYK_uc011lts.1_Non-coding_Transcript|SYK_uc011ltt.1_Non-coding_Transcript	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1	347	Linker.				cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(1)|skin(1)	2										618				0.084337	1.195986	30.248413	14	152	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	93636989	93636989	15959	9	G	T	T	T	572	44	SYK	2	2
HSD17B3	3293	broad.mit.edu	37	9	99003133	99003133	+	Silent	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:99003133C>G	uc004awa.1	-	c.729G>C	c.(727-729)GTG>GTC	p.V243V	HSD17B3_uc010msc.1_Intron	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3	243					androgen biosynthetic process|male genitalia development|oxidation-reduction process	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NADP+) activity|testosterone 17-beta-dehydrogenase activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)									0.1	7.875454	19.059577	7	63	KEEP	---	---	---	---	capture		Silent	SNP	99003133	99003133	7680	9	C	G	G	G	366	29	HSD17B3	3	3
ARMCX3	51566	broad.mit.edu	37	X	100880885	100880885	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100880885C>T	uc004ehz.1	+	c.916C>T	c.(916-918)CTG>TTG	p.L306L	ARMCX3_uc004eia.1_Silent_p.L306L|ARMCX3_uc004eib.1_Silent_p.L306L|ARMCX3_uc004eic.1_Silent_p.L306L	NM_016607	NP_057691	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	306						integral to membrane	binding			ovary(1)|lung(1)	2														0.109756	9.411308	21.7764	9	73	KEEP	---	---	---	---	capture		Silent	SNP	100880885	100880885	979	23	C	T	T	T	415	32	ARMCX3	2	2
NXF5	55998	broad.mit.edu	37	X	101092485	101092485	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:101092485C>A	uc011mrk.1	-	c.1061G>T	c.(1060-1062)CGG>CTG	p.R354L	NXF5_uc004eih.1_Non-coding_Transcript|NXF5_uc004eii.1_Non-coding_Transcript|NXF5_uc004eij.1_Non-coding_Transcript|NXF5_uc004eik.1_Non-coding_Transcript|NXF5_uc004eil.1_Non-coding_Transcript	NM_032946	NP_116564	Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	354	NTF2; truncated.				mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1														0.115607	25.70276	50.850179	20	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101092485	101092485	11191	23	C	A	A	A	299	23	NXF5	1	1
TEX13A	56157	broad.mit.edu	37	X	104463680	104463680	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:104463680C>T	uc004ema.2	-	c.1196G>A	c.(1195-1197)TGT>TAT	p.C399Y	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_3'UTR	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	399	RanBP2-type.					intracellular	zinc ion binding			ovary(2)	2														0.129771	22.779161	40.261048	17	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104463680	104463680	16303	23	C	T	T	T	221	17	TEX13A	2	2
COL4A6	1288	broad.mit.edu	37	X	107400278	107400278	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107400278C>T	uc004enw.3	-	c.5028G>A	c.(5026-5028)CAG>CAA	p.Q1676Q	COL4A6_uc004env.3_Silent_p.Q1675Q|COL4A6_uc011msn.1_Silent_p.Q1651Q|COL4A6_uc010npk.2_Silent_p.Q1618Q|COL4A6_uc011msm.1_Silent_p.Q210Q|COL4A6_uc010npj.2_Silent_p.Q155Q	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	1676	Collagen IV NC1.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.148148	6.381698	9.591303	4	23	KEEP	---	---	---	---	capture		Silent	SNP	107400278	107400278	3833	23	C	T	T	T	363	28	COL4A6	2	2
COL4A5	1287	broad.mit.edu	37	X	107829971	107829971	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107829971C>A	uc004enz.1	+	c.1159C>A	c.(1159-1161)CCT>ACT	p.P387T	COL4A5_uc011mso.1_Missense_Mutation_p.P387T|COL4A5_uc004eob.1_5'UTR	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	387	Triple-helical region.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														0.144737	17.371749	26.605054	11	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107829971	107829971	3832	23	C	A	A	A	234	18	COL4A5	2	2
GUCY2F	2986	broad.mit.edu	37	X	108619318	108619318	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:108619318C>T	uc004eod.3	-	c.3229G>A	c.(3229-3231)GAC>AAC	p.D1077N	GUCY2F_uc011msq.1_Non-coding_Transcript	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	1077	Cytoplasmic (Potential).				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8										308				0.16	55.479963	77.518492	32	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108619318	108619318	7178	23	C	T	T	T	390	30	GUCY2F	2	2
ODZ1	10178	broad.mit.edu	37	X	123657346	123657346	+	Silent	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123657346C>T	uc010nqy.2	-	c.2901G>A	c.(2899-2901)CAG>CAA	p.Q967Q	ODZ1_uc011muj.1_Silent_p.Q966Q|ODZ1_uc004euj.2_Silent_p.Q967Q	NM_001163278	NP_001156750	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 1	967	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	22										623				0.141026	18.269036	27.971993	11	67	KEEP	---	---	---	---	capture		Silent	SNP	123657346	123657346	11239	23	C	T	T	T	415	32	ODZ1	2	2
PRPS2	5634	broad.mit.edu	37	X	12828224	12828224	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:12828224G>A	uc004cva.2	+	c.498G>A	c.(496-498)AAG>AAA	p.K166K	PRPS2_uc004cvb.2_Silent_p.K163K|PRPS2_uc010nec.2_Silent_p.K99K	NM_001039091	NP_001034180	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	163					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity				0														0.121212	5.176274	9.816956	4	29	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	12828224	12828224	13023	23	G	A	A	A	425	33	PRPS2	2	2
GPR112	139378	broad.mit.edu	37	X	135429475	135429475	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135429475A>T	uc004ezu.1	+	c.3610A>T	c.(3610-3612)ACC>TCC	p.T1204S	GPR112_uc010nsb.1_Missense_Mutation_p.T999S|GPR112_uc010nsc.1_Missense_Mutation_p.T971S	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	1204	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.210843	78.342073	91.176348	35	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135429475	135429475	6903	23	A	T	T	T	78	6	GPR112	3	3
LDOC1	23641	broad.mit.edu	37	X	140270979	140270979	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140270979G>A	uc004fbj.2	-	c.228C>T	c.(226-228)CTC>CTT	p.L76L		NM_012317	NP_036449	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	76					negative regulation of cell proliferation	nucleus	protein binding				0	Acute lymphoblastic leukemia(192;7.65e-05)													0.111111	6.479192	15.900657	7	56	KEEP	---	---	---	---	capture		Silent	SNP	140270979	140270979	9033	23	G	A	A	A	470	37	LDOC1	1	1
MAGEC1	9947	broad.mit.edu	37	X	140992863	140992863	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140992863G>T	uc004fbt.2	+	c.4_splice	c.e3+1	p.G2_splice	MAGEC1_uc010nsl.1_Splice_Site_SNP	NM_005462	NP_005453			melanoma antigen family C, 1								protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.108974	15.869613	39.492848	17	139	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	140992863	140992863	9561	23	G	T	T	T	572	44	MAGEC1	5	2
MAGEC1	9947	broad.mit.edu	37	X	140994329	140994329	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140994329C>T	uc004fbt.2	+	c.1139C>T	c.(1138-1140)TCC>TTC	p.S380F	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	380							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.092308	5.603218	27.353828	12	118	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	140994329	140994329	9561	23	C	T	T	T	390	30	MAGEC1	2	2
CD99L2	83692	broad.mit.edu	37	X	149983368	149983368	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149983368C>G	uc004fel.2	-	c.244G>C	c.(244-246)GAT>CAT	p.D82H	CD99L2_uc004fek.2_Non-coding_Transcript|CD99L2_uc004fem.2_Intron|CD99L2_uc004fen.2_Intron|CD99L2_uc004feo.2_Non-coding_Transcript|CD99L2_uc011myb.1_Missense_Mutation_p.D82H	NM_031462	NP_113650	Q8TCZ2	C99L2_HUMAN	CD99 antigen-like 2 isoform E3'-E4'-E3-E4	82	Extracellular (Potential).				cell adhesion	cell junction|integral to membrane				large_intestine(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.2	27.762829	32.789864	12	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149983368	149983368	3179	23	C	G	G	G	377	29	CD99L2	3	3
CNGA2	1260	broad.mit.edu	37	X	150911747	150911747	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150911747G>C	uc004fey.1	+	c.772G>C	c.(772-774)GAG>CAG	p.E258Q		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	258	Extracellular (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.169355	49.596496	62.426881	21	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150911747	150911747	3735	23	G	C	C	C	585	45	CNGA2	3	3
ATP2B3	492	broad.mit.edu	37	X	152845701	152845701	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152845701C>T	uc004fht.1	+	c.3608C>T	c.(3607-3609)TCA>TTA	p.S1203L	ATP2B3_uc004fhs.1_3'UTR|ATP2B3_uc010nuf.1_Missense_Mutation_p.S340L|ATP2B3_uc004fhu.1_Missense_Mutation_p.S155L	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	1203	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.233333	14.303726	16.262902	7	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152845701	152845701	1160	23	C	T	T	T	377	29	ATP2B3	2	2
CDKL5	6792	broad.mit.edu	37	X	18593605	18593605	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:18593605G>A	uc004cym.2	+	c.277G>A	c.(277-279)GAA>AAA	p.E93K	CDKL5_uc004cyn.2_Missense_Mutation_p.E93K	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	93	Protein kinase.				neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5	Hepatocellular(33;0.183)									244				0.166667	13.897376	18.322796	7	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18593605	18593605	3286	23	G	A	A	A	585	45	CDKL5	2	2
CNKSR2	22866	broad.mit.edu	37	X	21545093	21545093	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:21545093C>A	uc004czx.1	+	c.1066C>A	c.(1066-1068)CCT>ACT	p.P356T	CNKSR2_uc004czw.2_Missense_Mutation_p.P356T|CNKSR2_uc011mjn.1_Missense_Mutation_p.P307T|CNKSR2_uc011mjo.1_Missense_Mutation_p.P356T|CNKSR2_uc004czy.2_5'UTR	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	356	Poly-Pro.|DUF1170.				regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)	1														0.113208	20.960957	52.256063	24	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21545093	21545093	3745	23	C	A	A	A	390	30	CNKSR2	2	2
FAM48B2	170067	broad.mit.edu	37	X	24330931	24330931	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24330931G>T	uc011mjw.1	-	c.502C>A	c.(502-504)CGT>AGT	p.R168S		NM_001136233	NP_001129705	P0C7V6	F48B2_HUMAN	family with sequence similarity 48, member B2	168											0														0.16129	30.069662	40.220152	15	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24330931	24330931	5796	23	G	T	T	T	520	40	FAM48B2	1	1
MAGEB6	158809	broad.mit.edu	37	X	26212459	26212459	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:26212459T>A	uc004dbr.2	+	c.496T>A	c.(496-498)TAT>AAT	p.Y166N	MAGEB6_uc010ngc.1_5'UTR	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	166										ovary(3)	3														0.142857	7.658656	11.954977	5	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26212459	26212459	9560	23	T	A	A	A	637	49	MAGEB6	3	3
MXRA5	25878	broad.mit.edu	37	X	3240577	3240577	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3240577G>A	uc004crg.3	-	c.3149C>T	c.(3148-3150)ACT>ATT	p.T1050I		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1050						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.146341	21.74262	31.602717	12	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3240577	3240577	10397	23	G	A	A	A	468	36	MXRA5	2	2
FAM47C	442444	broad.mit.edu	37	X	37028042	37028042	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37028042C>A	uc004ddl.1	+	c.1559C>A	c.(1558-1560)TCC>TAC	p.S520Y		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	520										ovary(3)	3														0.111111	5.710084	17.834686	9	72	FSTAR-RETAIN	---	---	---	---	capture		Missense_Mutation	SNP	37028042	37028042	5792	23	C	A	A	A	390	30	FAM47C	2	2
EDA2R	60401	broad.mit.edu	37	X	65819703	65819703	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:65819703C>A	uc004dwt.1	-	c.580G>T	c.(580-582)GGA>TGA	p.G194*	EDA2R_uc004dwq.2_Splice_Site_SNP_p.G173_splice|EDA2R_uc004dwr.2_Splice_Site_SNP_p.G173_splice|EDA2R_uc004dws.2_Splice_Site_SNP_p.G173_splice|EDA2R_uc011mpb.1_Splice_Site_SNP|EDA2R_uc011mpc.1_Splice_Site_SNP_p.G49_splice|EDA2R_uc010nkt.1_Intron	NM_021783	NP_068555	Q9HAV5	TNR27_HUMAN	X-linked ectodysplasin receptor	173	Cytoplasmic (Potential).				cell differentiation|embryo development|epidermis development|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	tumor necrosis factor receptor activity			upper_aerodigestive_tract(1)	1														0.230769	13.637806	15.364262	6	20	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	65819703	65819703	5091	23	C	A	A	A	312	24	EDA2R	5	2
ZMYM3	9203	broad.mit.edu	37	X	70468873	70468873	+	Silent	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70468873G>A	uc004dzh.1	-	c.1617C>T	c.(1615-1617)CTC>CTT	p.L539L	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Silent_p.L539L|ZMYM3_uc004dzj.1_Silent_p.L539L	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	539	MYM-type 5.				multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)													0.089286	0.93033	10.474409	5	51	FSTAR-RETAIN	---	---	---	---	capture		Silent	SNP	70468873	70468873	18292	23	G	A	A	A	574	45	ZMYM3	2	2
NAP1L2	4674	broad.mit.edu	37	X	72433014	72433014	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:72433014C>A	uc004ebi.2	-	c.1315G>T	c.(1315-1317)GCT>TCT	p.A439S	NAP1L2_uc011mqj.1_Missense_Mutation_p.A297S	NM_021963	NP_068798	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	439					nucleosome assembly	chromatin assembly complex				lung(1)	1	Renal(35;0.156)													0.176471	12.228603	15.582976	6	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72433014	72433014	10553	23	C	A	A	A	338	26	NAP1L2	2	2
TBX22	50945	broad.mit.edu	37	X	79282266	79282266	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:79282266G>T	uc010nmg.1	+	c.697G>T	c.(697-699)GTT>TTT	p.V233F	TBX22_uc004edi.1_Missense_Mutation_p.V113F|TBX22_uc004edj.1_Missense_Mutation_p.V233F	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	233	T-box.				multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			large_intestine(3)|central_nervous_system(2)|lung(1)|ovary(1)	7										298				0.230769	22.71778	25.265191	9	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79282266	79282266	16184	23	G	T	T	T	624	48	TBX22	2	2
POU3F4	5456	broad.mit.edu	37	X	82763633	82763633	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:82763633G>A	uc004eeg.2	+	c.301G>A	c.(301-303)GTA>ATA	p.V101I		NM_000307	NP_000298	P49335	PO3F4_HUMAN	POU domain, class 3, transcription factor 4	101					regulation of transcription, DNA-dependent|sensory perception of sound	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.181818	8.389158	10.479673	4	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82763633	82763633	12707	23	G	A	A	A	520	40	POU3F4	1	1
KLHL4	56062	broad.mit.edu	37	X	86887276	86887276	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:86887276G>T	uc004efa.2	+	c.1391G>T	c.(1390-1392)GGC>GTC	p.G464V	KLHL4_uc004efb.2_Missense_Mutation_p.G464V	NM_057162	NP_476503	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 2	464	Kelch 1.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5														0.227273	22.232786	25.233264	10	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86887276	86887276	8705	23	G	T	T	T	546	42	KLHL4	2	2
CCDC159	126075	broad.mit.edu	37	19	11459665	11459666	+	Frame_Shift_Ins	INS	-	A	A			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11459665_11459666insA	uc010xlw.1	+	c.64_65insA	c.(64-66)GAGfs	p.E22fs	TMEM205_uc002mrb.2_5'Flank|TMEM205_uc002mra.2_5'Flank|TMEM205_uc002mqz.2_5'Flank|TMEM205_uc002mrc.2_5'Flank|CCDC159_uc010xlr.1_Intron|CCDC159_uc010xls.1_Intron|CCDC159_uc010xlt.1_Intron|CCDC159_uc010xlu.1_Intron|CCDC159_uc010xlv.1_Intron	NM_001080503	NP_001073972	P0C7I6	CC159_HUMAN	coiled-coil domain-containing-like	54										ovary(1)	1														0.38			3	5		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	11459665	11459666	2913	19	-	A	A	A	521	41	CCDC159	5	5
SLC2A4RG	56731	broad.mit.edu	37	20	62373355	62373356	+	Frame_Shift_Ins	INS	-	C	C			TCGA-17-Z012-01	TCGA-17-Z012-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62373355_62373356insC	uc002ygq.2	+	c.525_526insC	c.(523-528)CTGCCCfs	p.L175fs	SLC2A4RG_uc002ygr.2_Frame_Shift_Ins_p.L70fs|SLC2A4RG_uc011abj.1_Frame_Shift_Ins_p.L70fs|SLC2A4RG_uc002ygs.2_Intron|SLC2A4RG_uc002ygt.2_5'UTR	NM_020062	NP_064446	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	175_176					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)													0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	62373355	62373356	15044	20	-	C	C	C	587	46	SLC2A4RG	5	5
