Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
CALHM1	255022	broad.mit.edu	36	10	105205211	105205211	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105205211G>C	uc001kxe.1	-	c.839C>G	c.(838-840)CCC>CGC	p.P280R	CALHM2_uc001kxd.1_5'Flank	NM_001001412	NP_001001412	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	280						endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel activity|identical protein binding			ovary(1)	1														1	12.292088	12.26073	5	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105205211	105205211	2698	10	G	C	C	43	43	CALHM1	C	3	3
GSTO1	9446	broad.mit.edu	36	10	106009517	106009517	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:106009517C>A	uc001kya.1	+	c.337C>A	c.(337-339)CAG>AAG	p.Q113K		NM_004832	NP_004823	P78417	GSTO1_HUMAN	glutathione-S-transferase omega 1	113	GST C-terminal.				xenobiotic metabolic process	cytosol	glutathione transferase activity|monodehydroascorbate reductase (NADH) activity				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)									0.119048	15.092655	27.062498	10	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106009517	106009517	7122	10	C	A	A	21	21	GSTO1	A	3	3
SORCS1	114815	broad.mit.edu	36	10	108449066	108449066	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:108449066T>A	uc001kyl.1	-	c.1309A>T	c.(1309-1311)AAC>TAC	p.N437Y	SORCS1_uc001kym.1_Missense_Mutation_p.N437Y|SORCS1_uc009xxs.1_Missense_Mutation_p.N437Y|SORCS1_uc001kyn.1_Missense_Mutation_p.N437Y|SORCS1_uc001kyo.2_Missense_Mutation_p.N437Y	NM_001013031	NP_001013049	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform b	437	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)	1		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)										0.45	15.136713	15.184242	9	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108449066	108449066	15430	10	T	A	A	63	63	SORCS1	A	4	4
HABP2	3026	broad.mit.edu	36	10	115333095	115333095	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:115333095C>T	uc001lai.2	+	c.1225C>T	c.(1225-1227)CAC>TAC	p.H409Y		NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	409	Peptidase S1.				cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)	2		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)										0.571429	7.388139	7.418041	4	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115333095	115333095	7220	10	C	T	T	21	21	HABP2	T	2	2
SLC18A2	6571	broad.mit.edu	36	10	119003914	119003914	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:119003914A>T	uc001ldd.1	+	c.616A>T	c.(616-618)ATG>TTG	p.M206L	SLC18A2_uc009xyy.1_Missense_Mutation_p.M3L	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine),	206	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)									0.75	6.722362	6.946612	3	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119003914	119003914	14922	10	A	T	T	8	8	SLC18A2	T	4	4
SLC18A2	6571	broad.mit.edu	36	10	119003917	119003917	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:119003917C>T	uc001ldd.1	+	c.619C>T	c.(619-621)CTT>TTT	p.L207F	SLC18A2_uc009xyy.1_Missense_Mutation_p.L4F	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine),	207	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)									0.75	6.319831	6.543514	3	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119003917	119003917	14922	10	C	T	T	28	28	SLC18A2	T	2	2
TACC2	10579	broad.mit.edu	36	10	123960524	123960525	+	Missense_Mutation	DNP	GC	TG	TG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:123960524_123960525GC>TG	uc001lfv.1	+	c.6594_6595GC>TG	c.(6592-6597)GGGCCC>GGTGCC	p.P2199A	TACC2_uc001lfw.1_Missense_Mutation_p.P345A|TACC2_uc009xzx.1_Missense_Mutation_p.P2154A|TACC2_uc001lfx.1_5'UTR|TACC2_uc001lfy.1_5'UTR|TACC2_uc001lfz.1_Missense_Mutation_p.P277A|TACC2_uc001lga.1_Missense_Mutation_p.P277A|TACC2_uc009xzy.1_Missense_Mutation_p.P277A|TACC2_uc001lgb.1_Missense_Mutation_p.P234A	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	2199						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)												0.857143	27.586276	29.296941	12	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	123960524	123960525	16023	10	GC	TG	TG	42	42	TACC2	TG	3	3
ADAM12	8038	broad.mit.edu	36	10	127727924	127727924	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:127727924A>G	uc001ljk.1	-	c.1814T>C	c.(1813-1815)ATC>ACC	p.I605T	ADAM12_uc001ljm.1_Missense_Mutation_p.I605T|ADAM12_uc001ljn.1_Missense_Mutation_p.I602T|ADAM12_uc001ljl.2_Missense_Mutation_p.I602T	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	605	Extracellular (Potential).|Cys-rich.				cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)	8		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)						1070				0.4	7.089129	7.178733	4	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127727924	127727924	237	10	A	G	G	12	12	ADAM12	G	4	4
MGMT	4255	broad.mit.edu	36	10	131396168	131396168	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:131396168C>G	uc001lkh.1	+	c.145C>G	c.(145-147)CCC>GCC	p.P49A		NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	49										ovary(1)	1		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)										0.666667	8.18986	8.334353	4	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131396168	131396168	9947	10	C	G	G	22	22	MGMT	G	3	3
DPYSL4	10570	broad.mit.edu	36	10	133866176	133866177	+	Missense_Mutation	DNP	CG	GC	GC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:133866176_133866177CG>GC	uc009ybb.1	+	c.1318_1319CG>GC	c.(1318-1320)CGG>GCG	p.R440A		NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	440					axon guidance	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds			central_nervous_system(2)	2		all_cancers(35;4.33e-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;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)										0.75	6.420686	6.644376	3	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	133866176	133866177	4933	10	CG	GC	GC	23	23	DPYSL4	GC	3	3
C10orf93	255352	broad.mit.edu	36	10	134593260	134593260	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134593260G>C	uc001llt.1	-	c.731C>G	c.(730-732)ACC>AGC	p.T244S		NM_173572	NP_775843	Q5SR76	CJ093_HUMAN	hypothetical protein LOC255352	302							binding			pancreas(1)	1		all_cancers(35;1.8e-07)|all_epithelial(44;6.22e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Colorectal(31;0.119)|Glioma(114;0.172)|Melanoma(40;0.175)		Epithelial(32;4.28e-05)|OV - Ovarian serous cystadenocarcinoma(35;4.31e-05)|all cancers(32;5.02e-05)										0.444444	6.683799	6.709883	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134593260	134593260	1662	10	G	C	C	44	44	C10orf93	C	3	3
MEIG1	644890	broad.mit.edu	36	10	15048487	15048488	+	Missense_Mutation	DNP	AC	GG	GG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15048487_15048488AC>GG	uc009xjk.1	+	c.14_15AC>GG	c.(13-15)GAC>GGG	p.D5G		NM_001080836	NP_001074305	Q5JSS6	MEIG1_HUMAN	meiosis expressed gene 1 homolog	5											0														0.7	14.409989	14.761911	7	3	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	15048487	15048488	9855	10	AC	GG	GG	10	10	MEIG1	GG	4	4
ZNF33B	7582	broad.mit.edu	36	10	42447797	42447797	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:42447797G>T	uc001jaf.1	-	c.106C>A	c.(106-108)CTG>ATG	p.L36M	ZNF33B_uc009xmg.1_Missense_Mutation_p.L36M|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_De_novo_Start_OutOfFrame	NM_006955	NP_008886	Q06732	ZN33B_HUMAN	zinc finger protein 33B	36	KRAB.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						Melanoma(137;1247 1767 16772 25727 43810)								0.2	109.197615	133.492004	58	232	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42447797	42447797	18447	10	G	T	T	33	33	ZNF33B	T	3	3
OGDHL	55753	broad.mit.edu	36	10	50627868	50627868	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:50627868C>A	uc009xog.1	-	c.978G>T	c.(976-978)AGG>AGT	p.R326S	OGDHL_uc001jie.1_Missense_Mutation_p.R299S|OGDHL_uc009xoh.1_Missense_Mutation_p.R90S	NM_018245	NP_060715	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like isoform a	299					glycolysis|oxidation-reduction process	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1														0.962963	64.841231	64.497396	26	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50627868	50627868	11245	10	C	A	A	22	22	OGDHL	A	3	3
OGDHL	55753	broad.mit.edu	36	10	50627870	50627873	+	Splice_Site_ONP	ONP	TGGA	ACAC	ACAC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50627870_50627873TGGA>ACAC	uc009xog.1	-	c.e7_splice_site			OGDHL_uc001jie.1_Splice_Site_ONP|OGDHL_uc009xoh.1_Splice_Site_ONP	NM_018245	NP_060715			oxoglutarate dehydrogenase-like isoform a						glycolysis|oxidation-reduction process	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1														0.947368	42.823172	44.203571	18	1	TT		KEEP	---	---	---	---	capture			Splice_Site_ONP	ONP	50627870	50627873	11245	10	TGGA	ACAC	ACAC	55	55	OGDHL	ACAC	5	4
ARID5B	84159	broad.mit.edu	36	10	63521893	63521893	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:63521893C>T	uc001jlt.1	+	c.2665C>T	c.(2665-2667)CTG>TTG	p.L889L		NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	889					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription repressor activity			ovary(2)|kidney(1)	3	Prostate(12;0.016)|all_hematologic(501;0.215)													0.4	8.917545	9.056109	6	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	63521893	63521893	937	10	C	T	T	24	24	ARID5B	T	2	2
H2AFY2	55506	broad.mit.edu	36	10	71538848	71538849	+	Missense_Mutation	DNP	AT	TG	TG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:71538848_71538849AT>TG	uc001jqm.1	+	c.832_833AT>TG	c.(832-834)ATC>TGC	p.I278C	H2AFY2_uc001jqn.1_Non-coding_Transcript	NM_018649	NP_061119	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	278	Macro.				chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding				0														0.5	7.289774	7.289774	4	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	71538848	71538849	7211	10	AT	TG	TG	8	8	H2AFY2	TG	4	4
ZMIZ1	57178	broad.mit.edu	36	10	80726321	80726321	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:80726321C>T	uc001kaf.1	+	c.1318C>T	c.(1318-1320)CTC>TTC	p.L440F	ZMIZ1_uc001kag.1_Missense_Mutation_p.L316F|ZMIZ1_uc001kad.1_Missense_Mutation_p.L440F|ZMIZ1_uc001kah.1_3'UTR	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	440	Pro-rich.				transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)	3	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)											1	14.548691	14.532828	6	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	80726321	80726321	18287	10	C	T	T	20	20	ZMIZ1	T	2	2
PLCE1	51196	broad.mit.edu	36	10	96002062	96002062	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:96002062G>A	uc001kjk.1	+	c.e9_splice_site			PLCE1_uc001kjm.2_Splice_Site_SNP	NM_016341	NP_057425			phospholipase C, epsilon 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|phospholipid metabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)												0.178571	10.757332	13.481376	5	23	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	96002062	96002062	12460	10	G	A	A	35	35	PLCE1	A	5	2
ZFYVE27	118813	broad.mit.edu	36	10	99502869	99502869	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:99502869C>T	uc001kon.2	+	c.997C>T	c.(997-999)CGC>TGC	p.R333C	ZFYVE27_uc001koo.2_Missense_Mutation_p.R328C|ZFYVE27_uc001kop.2_Missense_Mutation_p.R321C|ZFYVE27_uc001koq.2_Missense_Mutation_p.R235C|ZFYVE27_uc001kok.1_Non-coding_Transcript|ZFYVE27_uc001kol.1_Missense_Mutation_p.R328C|ZFYVE27_uc001kom.1_Missense_Mutation_p.R321C	NM_001002261	NP_001002261	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27 isoform	328	Extracellular (Potential).				cell death	integral to membrane	zinc ion binding			ovary(1)	1		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)										0.625	14.673231	14.782257	5	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99502869	99502869	18259	10	C	T	T	27	27	ZFYVE27	T	1	1
CASP4	837	broad.mit.edu	36	11	104324569	104324569	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:104324569C>T	uc001pid.1	-	c.826G>A	c.(826-828)GAA>AAA	p.E276K	CASP4_uc009yxg.1_Missense_Mutation_p.E185K|CASP4_uc001pib.1_Missense_Mutation_p.E220K	NM_001225	NP_150649	P49662	CASP4_HUMAN	caspase 4 isoform alpha precursor	276					apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)						204				0.112903	7.694112	16.860317	7	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104324569	104324569	2792	11	C	T	T	30	30	CASP4	T	2	2
MLL	4297	broad.mit.edu	36	11	117878717	117878717	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117878717G>A	uc001ptb.1	+	c.6900G>A	c.(6898-6900)GTG>GTA	p.V2300V	MLL_uc001pta.1_Silent_p.V2297V	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2297					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|unmethylated CpG binding|zinc ion binding			ovary(5)|kidney(5)|lung(3)|pancreas(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)	18	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)						723				0.419437	482.091884	484.312447	164	227	GG		KEEP	---	---	---	---	capture			Silent	SNP	117878717	117878717	10010	11	G	A	A	48	48	MLL	A	2	2
BCL9L	283149	broad.mit.edu	36	11	118284538	118284538	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118284538G>A	uc001pug.1	-	c.63C>T	c.(61-63)AGC>AGT	p.S21S	BCL9L_uc009zal.1_Silent_p.S16S	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	21					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)										0.304348	10.30248	11.097511	7	16	GG		KEEP	---	---	---	---	capture			Silent	SNP	118284538	118284538	1403	11	G	A	A	42	42	BCL9L	A	2	2
DPAGT1	1798	broad.mit.edu	36	11	118473816	118473816	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118473816C>G	uc001pvi.1	-	c.876G>C	c.(874-876)CAG>CAC	p.Q292H	H2AFX_uc001pvg.1_5'Flank|H2AFX_uc001pvh.1_5'Flank|DPAGT1_uc001pvj.1_Missense_Mutation_p.Q185H|DPAGT1_uc009zaq.1_Intron|DPAGT1_uc001pvk.1_Missense_Mutation_p.Q120H|DPAGT1_uc001pvm.1_3'UTR	NM_001382	NP_976061	Q9H3H5	GPT_HUMAN	UDP-N-acetylglucosamine-dolichyl-phosphate	292	Helical; (Potential).				dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity			breast(2)|ovary(1)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)										0.857143	11.679306	12.47846	6	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118473816	118473816	4894	11	C	G	G	28	28	DPAGT1	G	3	3
CCDC153	283152	broad.mit.edu	36	11	118566671	118566671	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118566671G>A	uc001pwc.1	-	c.180C>T	c.(178-180)GCC>GCT	p.A60A	CCDC153_uc001pwd.1_Silent_p.A60A	NM_001033658	NP_001028830	Q494R4	CC153_HUMAN	coiled-coil domain containing 153	146	Potential.										0														0.210526	16.033952	18.869778	8	30	GG		KEEP	---	---	---	---	capture			Silent	SNP	118566671	118566671	2908	11	G	A	A	43	43	CCDC153	A	2	2
TECTA	7007	broad.mit.edu	36	11	120506024	120506024	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:120506024G>T	uc001pxr.1	+	c.2835G>T	c.(2833-2835)CAG>CAT	p.Q945H		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	945					cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)	8	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)										0.209259	235.477576	277.780864	113	427	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120506024	120506024	16274	11	G	T	T	33	33	TECTA	T	3	3
ST14	6768	broad.mit.edu	36	11	129584771	129584774	+	Missense_Mutation	ONP	ATTC	CCCT	CCCT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:129584771_129584774ATTC>CCCT	uc001qfw.1	+	c.2411_2414ATTC>CCCT	c.(2410-2415)GATTCC>GCCCTC	p.804_805DS>AL		NM_021978	NP_068813	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14	804_805	Extracellular (Potential).|Peptidase S1.	Charge relay system.		S->A: Abolishes catalytic activity.	proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)									1	17.315357	17.307378	7	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	ONP	129584771	129584774	15729	11	ATTC	CCCT	CCCT	12	12	ST14	CCCT	4	4
INSC	387755	broad.mit.edu	36	11	15218620	15218620	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:15218620G>T	uc001mly.1	+	c.1586G>T	c.(1585-1587)AGT>ATT	p.S529I	INSC_uc001mlz.1_Missense_Mutation_p.S482I|INSC_uc001mma.1_Missense_Mutation_p.S482I|INSC_uc001mmb.1_Missense_Mutation_p.S482I|INSC_uc001mmc.1_Missense_Mutation_p.S440I	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	529					cell differentiation|nervous system development	cytoplasm	binding			ovary(2)|central_nervous_system(1)	3														0.098124	32.552385	144.796738	68	625	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15218620	15218620	8065	11	G	T	T	36	36	INSC	T	3	3
LSP1	4046	broad.mit.edu	36	11	1861350	1861350	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1861350A>C	uc001luj.1	+	c.866A>C	c.(865-867)GAG>GCG	p.E289A	LSP1_uc001lui.1_Missense_Mutation_p.E161A|LSP1_uc001luk.1_Missense_Mutation_p.E99A|LSP1_uc001lul.1_Missense_Mutation_p.E99A|LSP1_uc001lum.1_Missense_Mutation_p.E99A	NM_001013255	NP_001013273	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 2	161					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)						91				1	7.839477	7.720787	3	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1861350	1861350	9439	11	A	C	C	11	11	LSP1	C	4	4
SLC17A6	57084	broad.mit.edu	36	11	22321379	22321379	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22321379T>A	uc001mqk.1	+	c.350T>A	c.(349-351)TTC>TAC	p.F117Y		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	117	Vesicular (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4														0.357143	15.916559	16.429908	10	18	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22321379	22321379	14917	11	T	A	A	62	62	SLC17A6	A	4	4
QSER1	79832	broad.mit.edu	36	11	32913349	32913349	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:32913349G>T	uc001mty.1	+	c.3582G>T	c.(3580-3582)AAG>AAT	p.K1194N	QSER1_uc001mtz.1_Missense_Mutation_p.K955N|QSER1_uc001mua.2_Missense_Mutation_p.K699N	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1194										ovary(3)|central_nervous_system(2)	5	Breast(20;0.158)													0.2	13.881933	17.232645	8	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32913349	32913349	13340	11	G	T	T	34	34	QSER1	T	3	3
CAPRIN1	4076	broad.mit.edu	36	11	34074778	34074778	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:34074778C>T	uc001mvh.1	+	c.1882C>T	c.(1882-1884)CCT>TCT	p.P628S	CAPRIN1_uc001mvi.1_Missense_Mutation_p.P628S|CAPRIN1_uc001mvj.1_Missense_Mutation_p.P547S|CAPRIN1_uc001mvg.1_Missense_Mutation_p.P628S	NM_005898	NP_005889	Q14444	CAPR1_HUMAN	membrane component chromosome 11 surface marker	628					negative regulation of translation|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis	cytoplasmic mRNA processing body|cytosol|dendrite|integral to plasma membrane|stress granule	protein binding|RNA binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)												0.571429	9.699104	9.73033	4	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34074778	34074778	2754	11	C	T	T	22	22	CAPRIN1	T	2	2
PRDM11	56981	broad.mit.edu	36	11	45161095	45161095	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:45161095C>G	uc001myo.1	+	c.433C>G	c.(433-435)CTC>GTC	p.L145V		NM_020229	NP_064614	Q9NQV5	PRD11_HUMAN	PR domain containing 11	145											0						NSCLC(118;1511 1736 6472 36603 43224)								0.666667	13.301499	13.448909	4	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45161095	45161095	12894	11	C	G	G	28	28	PRDM11	G	3	3
CKAP5	9793	broad.mit.edu	36	11	46745777	46745777	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46745777T>C	uc001ndi.1	-	c.3335A>G	c.(3334-3336)GAT>GGT	p.D1112G	CKAP5_uc009ylg.1_Missense_Mutation_p.D998G|CKAP5_uc001ndj.1_Missense_Mutation_p.D1112G|CKAP5_uc001ndh.1_Missense_Mutation_p.D41G	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	1112					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)	1						Ovarian(4;85 273 2202 4844 13323)								0.294118	8.660848	9.311218	5	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46745777	46745777	3581	11	T	C	C	50	50	CKAP5	C	4	4
OR4A5	81318	broad.mit.edu	36	11	51268236	51268236	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:51268236G>T	uc001nhi.1	-	c.736C>A	c.(736-738)CTC>ATC	p.L246I		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	246	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		all_lung(304;0.236)												0.177778	6.454405	10.892049	8	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51268236	51268236	11449	11	G	T	T	35	35	OR4A5	T	3	3
LRRC56	115399	broad.mit.edu	36	11	539939	539939	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:539939T>C	uc001lpw.1	+	c.364T>C	c.(364-366)TGG>CGG	p.W122R		NM_198075	NP_932341	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	122	LRR 2.										0		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.888889	15.229728	16.49512	8	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	539939	539939	9387	11	T	C	C	59	59	LRRC56	C	4	4
SERPING1	710	broad.mit.edu	36	11	57124120	57124120	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57124120A>G	uc009ymi.1	+	c.244A>G	c.(244-246)ACC>GCC	p.T82A	SERPING1_uc001nkp.1_Missense_Mutation_p.T82A|SERPING1_uc001nkq.1_Missense_Mutation_p.T82A|SERPING1_uc001nkr.1_Missense_Mutation_p.T82A|SERPING1_uc009ymj.1_Missense_Mutation_p.T82A|SERPING1_uc001nks.1_Intron	NM_001032295	NP_001027466	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G, member 1	82					blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1														0.333333	7.363383	7.735737	5	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57124120	57124120	14604	11	A	G	G	14	14	SERPING1	G	4	4
AHNAK	79026	broad.mit.edu	36	11	62041336	62041336	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62041336G>T	uc001ntl.1	-	c.17129C>A	c.(17128-17130)TCC>TAC	p.S5710Y	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	5710	Nuclear localization signal (Potential).				nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)	14		Melanoma(852;0.155)												0.103659	13.667917	39.317165	17	147	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62041336	62041336	417	11	G	T	T	41	41	AHNAK	T	3	3
AHNAK	79026	broad.mit.edu	36	11	62044600	62044600	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62044600A>C	uc001ntl.1	-	c.13865T>G	c.(13864-13866)CTC>CGC	p.L4622R	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	4622					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)	14		Melanoma(852;0.155)												0.210526	12.140329	16.603993	12	45	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62044600	62044600	417	11	A	C	C	11	11	AHNAK	C	4	4
MARK2	2011	broad.mit.edu	36	11	63424115	63424115	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:63424115C>T	uc001nxw.1	+	c.725C>T	c.(724-726)ACA>ATA	p.T242I	MARK2_uc001nxx.1_Missense_Mutation_p.T242I|MARK2_uc001nxy.1_Missense_Mutation_p.T242I|MARK2_uc001nxv.2_Missense_Mutation_p.T242I|MARK2_uc001nxz.2_Missense_Mutation_p.T209I|MARK2_uc001nya.2_Missense_Mutation_p.T209I|MARK2_uc001nyb.1_Missense_Mutation_p.T209I|MARK2_uc009yoy.1_Missense_Mutation_p.T209I	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	242	Protein kinase.				cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|protein phosphorylation|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2										218				0.555556	77.973473	78.094838	25	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63424115	63424115	9696	11	C	T	T	17	17	MARK2	T	2	2
MARK2	2011	broad.mit.edu	36	11	63433199	63433199	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:63433199A>C	uc001nxw.1	+	c.2281A>C	c.(2281-2283)AAC>CAC	p.N761H	MARK2_uc001nxx.1_Missense_Mutation_p.N692H|MARK2_uc001nxy.1_Missense_Mutation_p.N682H|MARK2_uc001nxv.2_Missense_Mutation_p.N697H|MARK2_uc001nxz.2_Missense_Mutation_p.N718H|MARK2_uc001nya.2_Missense_Mutation_p.N664H|MARK2_uc001nyb.1_Missense_Mutation_p.N728H|MARK2_uc009yoy.1_Missense_Mutation_p.N672H	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	761	KA1.				cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|protein phosphorylation|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2										218				0.75	6.621644	6.845302	3	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63433199	63433199	9696	11	A	C	C	5	5	MARK2	C	4	4
LTBP3	4054	broad.mit.edu	36	11	65070935	65070935	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65070935G>A	uc001oej.1	-	c.2098C>T	c.(2098-2100)CCG>TCG	p.P700S	LTBP3_uc001oef.1_5'Flank|LTBP3_uc001oeg.1_5'Flank|LTBP3_uc001oeh.1_Missense_Mutation_p.P144S|LTBP3_uc001oei.1_Missense_Mutation_p.P714S	NM_021070	NP_066548	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding	714	Cys-rich.					extracellular region	calcium ion binding|growth factor binding			lung(1)|central_nervous_system(1)	2														1	8.540591	8.422004	3	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65070935	65070935	9451	11	G	A	A	43	43	LTBP3	A	2	2
SPTBN2	6712	broad.mit.edu	36	11	66216613	66216613	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66216613G>A	uc001ojd.1	-	c.5160C>T	c.(5158-5160)CAC>CAT	p.H1720H		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1720	Spectrin 14.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4														0.927536	215.094339	223.545054	64	5	GG		KEEP	---	---	---	---	capture			Silent	SNP	66216613	66216613	15634	11	G	A	A	40	40	SPTBN2	A	1	1
DEAF1	10522	broad.mit.edu	36	11	669799	669799	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:669799C>G	uc001lqq.1	-	c.1015G>C	c.(1015-1017)GGA>CGA	p.G339R	DEAF1_uc009ycf.1_Non-coding_Transcript	NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1	339					embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)										0.357143	9.060328	9.316321	5	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	669799	669799	4551	11	C	G	G	22	22	DEAF1	G	3	3
C11orf24	53838	broad.mit.edu	36	11	67786616	67786616	+	Silent	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67786616A>C	uc001onr.2	-	c.423T>G	c.(421-423)ACT>ACG	p.T141T	C11orf24_uc001ons.1_Silent_p.T141T	NM_022338	NP_071733	Q96F05	CK024_HUMAN	hypothetical protein LOC53838	141	Extracellular (Potential).					integral to membrane					0						NSCLC(21;855 905 4198 36694)								0.727273	16.580209	17.087525	8	3	AA		KEEP	---	---	---	---	capture			Silent	SNP	67786616	67786616	1673	11	A	C	C	7	7	C11orf24	C	4	4
TMEM80	283232	broad.mit.edu	36	11	693053	693053	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:693053T>G	uc001lqr.1	+	c.410T>G	c.(409-411)GTG>GGG	p.V137G	TMEM80_uc001lqs.1_Missense_Mutation_p.V129G	NM_001042463	NP_001035928	Q96HE8	TMM80_HUMAN	transmembrane protein 80 isoform 2	137	Helical; (Potential).					integral to membrane					0		all_cancers(49;5.11e-06)|all_epithelial(84;0.00143)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.44e-27)|Epithelial(43;2.29e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.19e-20)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)										1	10.052571	9.991156	4	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	693053	693053	16743	11	T	G	G	59	59	TMEM80	G	4	4
INPPL1	3636	broad.mit.edu	36	11	71621010	71621010	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:71621010G>C	uc001osf.1	+	c.1694G>C	c.(1693-1695)GGA>GCA	p.G565A	INPPL1_uc001osg.1_Missense_Mutation_p.G323A	NM_001567	NP_001558	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	565					actin filament organization|cell adhesion|endocytosis	actin cortical patch|cytosol	actin binding|SH2 domain binding|SH3 domain binding			skin(2)|ovary(1)	3														0.75	8.225441	8.450716	3	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71621010	71621010	8062	11	G	C	C	41	41	INPPL1	C	3	3
TSKU	25987	broad.mit.edu	36	11	76184780	76184780	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:76184780C>T	uc001oxt.1	+	c.472C>T	c.(472-474)CGG>TGG	p.R158W	TSKU_uc009yuk.1_Missense_Mutation_p.R158W	NM_015516	NP_056331	Q8WUA8	TSK_HUMAN	tsukushin	158						extracellular region					0	Ovarian(111;0.112)													0.8	10.414903	10.815443	4	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76184780	76184780	17178	11	C	T	T	23	23	TSKU	T	1	1
SART3	9733	broad.mit.edu	36	12	107442258	107442258	+	Silent	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107442258T>A	uc001tmz.1	-	c.2679A>T	c.(2677-2679)CCA>CCT	p.P893P	SART3_uc009zux.1_Silent_p.P505P|SART3_uc001tmy.1_Silent_p.P419P	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	893					RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														0.24	6.413293	7.98187	6	19	TT		KEEP	---	---	---	---	capture			Silent	SNP	107442258	107442258	14328	12	T	A	A	55	55	SART3	A	4	4
PTPN11	5781	broad.mit.edu	36	12	111411268	111411268	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:111411268C>T	uc001ttx.1	+	c.1505C>T	c.(1504-1506)TCA>TTA	p.S502L		NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	506	Tyrosine-protein phosphatase.		S -> T (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.S502L(5)|p.S502P(1)		haematopoietic_and_lymphoid_tissue(372)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|ovary(1)|NS(1)|kidney(1)	388									p.S502*(NCIH1838-Tumor)|p.S502L(KMS20-Tumor)|p.S502L(SNU719-Tumor)	372				0.222222	11.734994	13.653284	6	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111411268	111411268	13235	12	C	T	T	29	29	PTPN11	T	2	2
CCDC60	160777	broad.mit.edu	36	12	118445882	118445882	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:118445882C>T	uc001txe.1	+	c.1105C>T	c.(1105-1107)CGC>TGC	p.R369C		NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	369										ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)										0.585714	127.377502	127.827677	41	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118445882	118445882	2954	12	C	T	T	23	23	CCDC60	T	1	1
ANAPC5	51433	broad.mit.edu	36	12	120249404	120249404	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120249404G>T	uc001uag.1	-	c.1318C>A	c.(1318-1320)CAA>AAA	p.Q440K	ANAPC5_uc001uae.1_Missense_Mutation_p.Q4K|ANAPC5_uc001uaf.1_Non-coding_Transcript|ANAPC5_uc009zxd.1_Missense_Mutation_p.Q427K|ANAPC5_uc001uah.1_Missense_Mutation_p.Q328K|ANAPC5_uc001uai.1_Missense_Mutation_p.Q42K|ANAPC5_uc001uaj.1_Non-coding_Transcript	NM_016237	NP_057321	Q9UJX4	APC5_HUMAN	anaphase-promoting complex subunit 5 isoform a	440					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|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	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity			skin(3)|breast(2)|kidney(1)	6	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)									448				0.173077	36.301344	46.79067	18	86	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120249404	120249404	608	12	G	T	T	46	46	ANAPC5	T	3	3
UBC	7316	broad.mit.edu	36	12	123963962	123963962	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:123963962T>C	uc001ugs.2	-	c.309A>G	c.(307-309)AAA>AAG	p.K103K	UBC_uc001ugr.2_5'Flank|UBC_uc001ugu.1_Silent_p.K103K|UBC_uc001ugt.2_Silent_p.K103K|UBC_uc001ugv.2_Intron|UBC_uc001ugq.2_Silent_p.K103K|UBC_uc001ugw.2_5'UTR	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	103	Ubiquitin-like 2.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|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|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)										0.886792	1328.019867	1421.573664	564	72	TT		KEEP	---	---	---	---	capture			Silent	SNP	123963962	123963962	17399	12	T	C	C	56	56	UBC	C	4	4
SLC15A4	121260	broad.mit.edu	36	12	127844780	127844781	+	Missense_Mutation	DNP	AA	TC	TC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:127844780_127844781AA>TC	uc001uhu.1	-	c.1647_1648TT>GA	c.(1645-1650)CTTTTC>CTGATC	p.F550I	SLC15A4_uc001uht.2_Non-coding_Transcript|SLC15A4_uc001uhv.1_Non-coding_Transcript	NM_145648	NP_663623	Q8N697	S15A4_HUMAN	solute carrier family 15, member 4	550	Helical; (Potential).				oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)										0.363636	6.384257	6.568976	4	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	127844780	127844781	14896	12	AA	TC	TC	1	1	SLC15A4	TC	4	4
MMP17	4326	broad.mit.edu	36	12	130901480	130901480	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130901480A>C	uc001ujc.1	+	c.1520A>C	c.(1519-1521)GAG>GCG	p.E507A	MMP17_uc001ujd.1_Missense_Mutation_p.E423A	NM_016155	NP_057239	Q9ULZ9	MMP17_HUMAN	matrix metalloproteinase 17 preproprotein	507	Hemopexin-like 4.				proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)										0.875	17.059145	18.11161	7	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130901480	130901480	10046	12	A	C	C	11	11	MMP17	C	4	4
DDX11	1663	broad.mit.edu	36	12	31128182	31128182	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:31128182C>A	uc001rjt.1	+	c.313C>A	c.(313-315)CCG>ACG	p.P105T	DDX11_uc001rjr.1_Missense_Mutation_p.P105T|DDX11_uc001rjs.1_Missense_Mutation_p.P105T|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Missense_Mutation_p.P105T|DDX11_uc001rjw.1_Missense_Mutation_p.P79T	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	105	Helicase ATP-binding.				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.129032	16.249445	28.701483	12	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31128182	31128182	4514	12	C	A	A	22	22	DDX11	A	3	3
DDX11	1663	broad.mit.edu	36	12	31142157	31142157	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:31142157G>C	uc001rjt.1	+	c.1834G>C	c.(1834-1836)GAA>CAA	p.E612Q	DDX11_uc001rjr.1_Missense_Mutation_p.E612Q|DDX11_uc001rjs.1_Missense_Mutation_p.E612Q|DDX11_uc001rju.1_Missense_Mutation_p.E290Q|DDX11_uc001rjv.1_Missense_Mutation_p.E612Q|DDX11_uc001rjw.1_Missense_Mutation_p.E586Q|DDX11_uc009zjn.1_Non-coding_Transcript	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	612					G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.666667	7.587721	7.732499	4	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31142157	31142157	4514	12	G	C	C	41	41	DDX11	C	3	3
C12orf35	55196	broad.mit.edu	36	12	32027666	32027666	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:32027666A>C	uc001rks.1	+	c.2510A>C	c.(2509-2511)AAG>ACG	p.K837T		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	837										ovary(1)	1	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)											0.272727	7.721587	8.761872	6	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32027666	32027666	1726	12	A	C	C	3	3	C12orf35	C	4	4
ABCD2	225	broad.mit.edu	36	12	38299408	38299408	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:38299408T>G	uc001rmb.2	-	c.277A>C	c.(277-279)AAA>CAA	p.K93Q		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	93	Interaction with PEX19.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.272727	7.422311	8.462703	6	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38299408	38299408	62	12	T	G	G	62	62	ABCD2	G	4	4
KCNH3	23416	broad.mit.edu	36	12	48223502	48223504	+	Missense_Mutation	TNP	GAG	AGT	AGT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:48223502_48223504GAG>AGT	uc001ruh.1	+	c.757_759GAG>AGT	c.(757-759)GAG>AGT	p.E253S		NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	253	Extracellular (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0														0.833333	10.084332	10.587987	5	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	48223502	48223504	8338	12	GAG	AGT	AGT	41	41	KCNH3	AGT	2	2
NR4A1	3164	broad.mit.edu	36	12	50734949	50734949	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:50734949T>C	uc001rzq.1	+	c.732T>C	c.(730-732)TTT>TTC	p.F244F	NR4A1_uc001rzr.2_Silent_p.F190F|NR4A1_uc009zmb.1_Silent_p.F190F|NR4A1_uc001rzs.1_Silent_p.F190F|NR4A1_uc001rzt.1_Silent_p.F190F|NR4A1_uc009zmc.1_5'Flank	NM_173157	NP_775180	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	190					nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(357;0.0967)										0.363636	6.389624	6.5721	4	7	TT		KEEP	---	---	---	---	capture			Silent	SNP	50734949	50734949	11037	12	T	C	C	64	64	NR4A1	C	4	4
KRT76	51350	broad.mit.edu	36	12	51452220	51452220	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51452220A>G	uc001sax.1	-	c.1062T>C	c.(1060-1062)ATT>ATC	p.I354I		NM_015848	NP_056932	Q01546	K22O_HUMAN	keratin 76	354	Rod.|Coil 2.				cytoskeleton organization	keratin filament	structural molecule activity			breast(1)	1														0.157143	6.57848	14.471226	11	59	AA		KEEP	---	---	---	---	capture			Silent	SNP	51452220	51452220	8804	12	A	G	G	5	5	KRT76	G	4	4
ARHGAP9	64333	broad.mit.edu	36	12	56154107	56154108	+	Missense_Mutation	DNP	AA	TC	TC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56154107_56154108AA>TC	uc001sod.1	-	c.2172_2173TT>GA	c.(2170-2175)CATTTC>CAGATC	p.724_725HF>QI	ARHGAP9_uc001sny.1_Intron|ARHGAP9_uc001snz.1_Missense_Mutation_p.450_451HF>QI|ARHGAP9_uc001soa.1_Missense_Mutation_p.323_324HF>QI|ARHGAP9_uc001sob.1_Missense_Mutation_p.634_635HF>QI|ARHGAP9_uc001soc.1_Missense_Mutation_p.634_635HF>QI|ARHGAP9_uc001soe.1_Missense_Mutation_p.713_714HF>QI	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	653_654	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)											0.916667	24.810454	26.309584	11	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	56154107	56154108	903	12	AA	TC	TC	1	1	ARHGAP9	TC	4	4
ARHGAP9	64333	broad.mit.edu	36	12	56154110	56154110	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56154110G>T	uc001sod.1	-	c.2170C>A	c.(2170-2172)CAT>AAT	p.H724N	ARHGAP9_uc001sny.1_Intron|ARHGAP9_uc001snz.1_Missense_Mutation_p.H450N|ARHGAP9_uc001soa.1_Missense_Mutation_p.H323N|ARHGAP9_uc001sob.1_Missense_Mutation_p.H634N|ARHGAP9_uc001soc.1_Missense_Mutation_p.H634N|ARHGAP9_uc001soe.1_Missense_Mutation_p.H713N	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	653	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)											0.8	8.29207	8.703553	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56154110	56154110	903	12	G	T	T	47	47	ARHGAP9	T	3	3
VWF	7450	broad.mit.edu	36	12	6010904	6010904	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6010904C>T	uc001qnn.1	-	c.2787G>A	c.(2785-2787)GTG>GTA	p.V929V		NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	929	VWFD 3.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.323529	28.913126	29.853231	11	23	CC		KEEP	---	---	---	---	capture			Silent	SNP	6010904	6010904	17818	12	C	T	T	21	21	VWF	T	2	2
DYRK2	8445	broad.mit.edu	36	12	66338176	66338176	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:66338176C>G	uc001str.2	+	c.1222C>G	c.(1222-1224)CTG>GTG	p.L408V	DYRK2_uc001sts.2_Missense_Mutation_p.L335V|DYRK2_uc009zqu.1_Missense_Mutation_p.L335V	NM_006482	NP_003574	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	408	Protein kinase.				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|protein phosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)						47				0.946939	768.228104	792.74163	232	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66338176	66338176	5042	12	C	G	G	24	24	DYRK2	G	3	3
NUP107	57122	broad.mit.edu	36	12	67413540	67413540	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:67413540A>T	uc001suf.1	+	c.2143A>T	c.(2143-2145)ATT>TTT	p.I715F	NUP107_uc001sug.1_Missense_Mutation_p.I474F	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	715					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding				0	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)											0.24	7.926986	9.483572	6	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67413540	67413540	11158	12	A	T	T	4	4	NUP107	T	4	4
GPR162	27239	broad.mit.edu	36	12	6806586	6806587	+	Missense_Mutation	DNP	TC	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6806586_6806587TC>CT	uc001qqw.1	+	c.1723_1724TC>CT	c.(1723-1725)TCC>CTC	p.S575L	LEPREL2_uc001qqz.1_5'Flank|LEPREL2_uc001qra.1_5'Flank|LEPREL2_uc001qrb.1_5'Flank|GPR162_uc001qqx.1_Missense_Mutation_p.S291L|GPR162_uc009zfd.1_Missense_Mutation_p.S271L|GPR162_uc001qqy.1_Intron	NM_019858	NP_062832	Q16538	GP162_HUMAN	G protein-coupled receptor 162 isoform 2	575	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.833333	11.596071	12.102491	5	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	6806586	6806587	6941	12	TC	CT	CT	50	50	GPR162	CT	4	4
GPR162	27239	broad.mit.edu	36	12	6806589	6806589	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6806589T>C	uc001qqw.1	+	c.1726T>C	c.(1726-1728)TGG>CGG	p.W576R	LEPREL2_uc001qqz.1_5'Flank|LEPREL2_uc001qra.1_5'Flank|LEPREL2_uc001qrb.1_5'Flank|GPR162_uc001qqx.1_Missense_Mutation_p.W292R|GPR162_uc009zfd.1_Missense_Mutation_p.W272R|GPR162_uc001qqy.1_Intron	NM_019858	NP_062832	Q16538	GP162_HUMAN	G protein-coupled receptor 162 isoform 2	576	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.833333	10.85733	10.822377	5	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6806589	6806589	6941	12	T	C	C	55	55	GPR162	C	4	4
A2ML1	144568	broad.mit.edu	36	12	8904804	8904804	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:8904804G>T	uc001quz.2	+	c.3325G>T	c.(3325-3327)GGA>TGA	p.G1109*	A2ML1_uc001qva.1_Nonsense_Mutation_p.G689*	NM_144670	NP_653271	B3KVV6	B3KVV6_HUMAN	alpha-2-macroglobulin-like 1	953						extracellular space	endopeptidase inhibitor activity			ovary(2)	2												OREG0021663	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.181159	23.439748	36.726132	25	113	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	8904804	8904804	6	12	G	T	T	43	43	A2ML1	T	5	3
CLEC2D	29121	broad.mit.edu	36	12	9731895	9731895	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:9731895G>A	uc001qwf.1	+	c.303G>A	c.(301-303)AGG>AGA	p.R101R	CLEC2D_uc001qwg.1_Silent_p.R101R|CLEC2D_uc009zgs.1_Non-coding_Transcript|CLEC2D_uc001qwh.1_Non-coding_Transcript|CLEC2D_uc009zgt.1_Non-coding_Transcript|CLEC2D_uc009zgu.1_Silent_p.R59R	NM_001004419	NP_001004419	Q9UHP7	CLC2D_HUMAN	osteoclast inhibitory lectin isoform 2	101	Extracellular (Potential).|C-type lectin.				cell surface receptor linked signaling pathway	cell surface|endoplasmic reticulum|integral to plasma membrane|membrane fraction	sugar binding|transmembrane receptor activity				0														0.214286	14.139992	16.247567	6	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	9731895	9731895	3646	12	G	A	A	44	44	CLEC2D	A	2	2
COL4A1	1282	broad.mit.edu	36	13	109605704	109605705	+	Missense_Mutation	DNP	TG	AA	AA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:109605704_109605705TG>AA	uc001vqw.2	-	c.4681_4682CA>TT	c.(4681-4683)CAC>TTC	p.H1561F	COL4A1_uc010agl.1_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	1561	Collagen IV NC1.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)											0.875	14.048551	14.792386	7	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	109605704	109605705	3827	13	TG	AA	AA	59	59	COL4A1	AA	4	4
ZNF828	283489	broad.mit.edu	36	13	114109548	114109549	+	Missense_Mutation	DNP	AT	CC	CC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:114109548_114109549AT>CC	uc001vuv.1	+	c.2129_2130AT>CC	c.(2128-2130)TAT>TCC	p.Y710S	ZNF828_uc010ahb.1_Missense_Mutation_p.Y710S	NM_032436	NP_115812	Q96JM3	ZN828_HUMAN	zinc finger protein 828	710	Mediates localization to the chromosome and the spindle and negatively regulates chromosome alignment.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|protein localization to kinetochore|protein localization to microtubule|sister chromatid biorientation	condensed chromosome kinetochore|cytoplasm|nucleus|spindle	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_epithelial(44;0.122)|all_lung(25;0.123)	BRCA - Breast invasive adenocarcinoma(86;0.104)	OV - Ovarian serous cystadenocarcinoma(48;0.193)|Epithelial(10;0.197)										0.368421	13.308898	13.60186	7	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	114109548	114109549	18780	13	AT	CC	CC	16	16	ZNF828	CC	4	4
SPATA13	221178	broad.mit.edu	36	13	23769599	23769599	+	Silent	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:23769599G>C	uc001upd.1	+	c.3189G>C	c.(3187-3189)CTG>CTC	p.L1063L	C1QTNF9_uc001upe.1_Non-coding_Transcript|SPATA13_uc001upg.1_Silent_p.L478L|SPATA13_uc001uph.1_Silent_p.L400L|SPATA13_uc009zzz.1_Intron|SPATA13_uc001upi.1_5'UTR	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	478	PH.				cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)										0.375	9.52748	9.753014	6	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	23769599	23769599	15508	13	G	C	C	48	48	SPATA13	C	3	3
CDX2	1045	broad.mit.edu	36	13	27437074	27437074	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:27437074T>G	uc001urv.1	-	c.620A>C	c.(619-621)TAC>TCC	p.Y207S		NM_001265	NP_001256	Q99626	CDX2_HUMAN	caudal type homeobox 2	207	Homeobox.				organ morphogenesis|transcription from RNA polymerase II promoter		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			lung(1)	1	all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)						130				1	8.241556	8.123061	3	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27437074	27437074	3312	13	T	G	G	57	57	CDX2	G	4	4
THSD1	55901	broad.mit.edu	36	13	51869886	51869886	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:51869886T>G	uc001vgo.1	-	c.503A>C	c.(502-504)GAT>GCT	p.D168A	THSD1_uc010adz.1_Missense_Mutation_p.D168A|THSD1_uc001vgp.1_Missense_Mutation_p.D168A|THSD1_uc010aea.1_Intron	NM_018676	NP_061146	Q9NS62	THSD1_HUMAN	thrombospondin type I domain-containing 1	168	Extracellular (Potential).					extracellular region|integral to membrane|intracellular membrane-bounded organelle				ovary(2)	2		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)										0.357143	8.05771	8.31468	5	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51869886	51869886	16405	13	T	G	G	50	50	THSD1	G	4	4
KLF12	11278	broad.mit.edu	36	13	73167697	73167697	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:73167697C>T	uc001vjf.1	-	c.1140G>A	c.(1138-1140)GCG>GCA	p.A380A	KLF12_uc010aeq.1_Silent_p.A380A	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	380	C2H2-type 3.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)										0.119048	7.060607	13.031435	5	37	CC		KEEP	---	---	---	---	capture			Silent	SNP	73167697	73167697	8652	13	C	T	T	23	23	KLF12	T	1	1
TRAF3	7187	broad.mit.edu	36	14	102406334	102406334	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:102406334A>T	uc001ymc.1	+	c.43A>T	c.(43-45)ACT>TCT	p.T15S	TRAF3_uc001ymd.1_Missense_Mutation_p.T15S|TRAF3_uc001yme.1_Missense_Mutation_p.T15S	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1	15					apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)										0.4	6.58812	6.677733	4	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102406334	102406334	16983	14	A	T	T	10	10	TRAF3	T	4	4
BRF1	2972	broad.mit.edu	36	14	104810181	104810181	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104810181G>C	uc001yqp.2	-	c.361C>G	c.(361-363)CAC>GAC	p.H121D	BRF1_uc010axg.1_Missense_Mutation_p.H94D|BRF1_uc001yqr.1_Missense_Mutation_p.H121D	NM_001519	NP_663718	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	121	1.				regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	RNA polymerase III transcription factor activity|transcription activator activity|translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)										1	7.536304	7.417312	3	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104810181	104810181	1541	14	G	C	C	46	46	BRF1	C	3	3
OR4L1	122742	broad.mit.edu	36	14	19598901	19598901	+	Silent	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19598901T>A	uc001vwn.1	+	c.858T>A	c.(856-858)ATT>ATA	p.I286I		NM_001004717	NP_001004717	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L,	286	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)										0.235294	7.546381	9.768471	8	26	TT		KEEP	---	---	---	---	capture			Silent	SNP	19598901	19598901	11484	14	T	A	A	64	64	OR4L1	A	4	4
SLC22A17	51310	broad.mit.edu	36	14	22886220	22886220	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22886220G>C	uc001wjl.1	-	c.1258C>G	c.(1258-1260)CTC>GTC	p.L420V	SLC22A17_uc010akk.1_Missense_Mutation_p.L184V|SLC22A17_uc001wjn.1_Non-coding_Transcript|SLC22A17_uc001wjm.1_Missense_Mutation_p.L402V	NM_020372	NP_065105	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17 isoform a	420	Helical; (Potential).				siderophore transport|transmembrane transport	integral to organelle membrane|integral to plasma membrane|vacuolar membrane	transmembrane receptor activity|transporter activity				0	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)										1	8.643397	8.525076	3	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22886220	22886220	14944	14	G	C	C	34	34	SLC22A17	C	3	3
ADCY4	196883	broad.mit.edu	36	14	23869224	23869224	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23869224G>C	uc001wov.1	-	c.1048C>G	c.(1048-1050)CGG>GGG	p.R350G	ADCY4_uc001wow.1_Missense_Mutation_p.R350G|ADCY4_uc001wox.1_Missense_Mutation_p.R350G|ADCY4_uc001woy.1_Missense_Mutation_p.R350G	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	350	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|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(265;0.0192)						1				0.363636	7.085013	7.269501	4	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23869224	23869224	297	14	G	C	C	39	39	ADCY4	C	3	3
CTSG	1511	broad.mit.edu	36	14	24114420	24114420	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:24114420G>A	uc001wpq.1	-	c.94C>T	c.(94-96)CGC>TGC	p.R32C		NM_001911	NP_001902	P08311	CATG_HUMAN	cathepsin G preproprotein	32	Peptidase S1.				immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2				GBM - Glioblastoma multiforme(265;0.0269)										0.173077	17.949822	23.195408	9	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24114420	24114420	4194	14	G	A	A	39	39	CTSG	A	1	1
GZMH	2999	broad.mit.edu	36	14	24146403	24146404	+	Missense_Mutation	DNP	GG	TA	TA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24146403_24146404GG>TA	uc001wpr.1	-	c.388_389CC>TA	c.(388-390)CCT>TAT	p.P130Y	GZMH_uc010aly.1_Intron|GZMH_uc010alz.1_Intron	NM_033423	NP_219491	P20718	GRAH_HUMAN	granzyme H	130	Peptidase S1.				apoptosis|cytolysis|proteolysis	cytoplasm	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.0267)										0.538462	14.513217	14.529187	7	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	24146403	24146404	7197	14	GG	TA	TA	35	35	GZMH	TA	3	3
G2E3	55632	broad.mit.edu	36	14	30154357	30154357	+	Nonsense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:30154357T>A	uc001wqk.1	+	c.1725T>A	c.(1723-1725)TAT>TAA	p.Y575*	G2E3_uc001wql.1_Nonsense_Mutation_p.Y87*	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	575	HECT.				apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3														0.25	15.03949	16.402349	6	18	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	30154357	30154357	6391	14	T	A	A	50	50	G2E3	A	5	4
NPAS3	64067	broad.mit.edu	36	14	33336498	33336498	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:33336498C>T	uc001wru.1	+	c.1386C>T	c.(1384-1386)TCC>TCT	p.S462S	NPAS3_uc001wrt.1_Silent_p.S430S|NPAS3_uc001wrv.1_Silent_p.S432S|NPAS3_uc001wrs.1_Silent_p.S449S	NM_022123	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 1	462					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			ovary(1)	1	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)										0.416667	10.264329	10.338791	5	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	33336498	33336498	10968	14	C	T	T	23	23	NPAS3	T	1	1
ARG2	384	broad.mit.edu	36	14	67182257	67182257	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:67182257A>C	uc001xjs.1	+	c.507A>C	c.(505-507)AGA>AGC	p.R169S		NM_001172	NP_001163	P78540	ARGI2_HUMAN	arginase 2 precursor	169					arginine metabolic process|nitric oxide biosynthetic process|urea cycle	mitochondrial matrix	arginase activity|metal ion binding				0				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)									0.195652	10.633039	14.62986	9	37	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67182257	67182257	869	14	A	C	C	11	11	ARG2	C	4	4
SLC8A3	6547	broad.mit.edu	36	14	69703510	69703510	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:69703510C>G	uc001xly.1	-	c.1383G>C	c.(1381-1383)CAG>CAC	p.Q461H	SLC8A3_uc001xlw.1_Missense_Mutation_p.Q461H|SLC8A3_uc001xlx.1_Missense_Mutation_p.Q461H|SLC8A3_uc001xlz.1_Missense_Mutation_p.Q461H|SLC8A3_uc010ara.1_Non-coding_Transcript	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	461	Calx-beta 1.|Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			ovary(2)|breast(2)	4				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)										0.234043	13.678641	16.749146	11	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69703510	69703510	15205	14	C	G	G	32	32	SLC8A3	G	3	3
MLH3	27030	broad.mit.edu	36	14	74585513	74585513	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74585513T>C	uc001xrd.1	-	c.599A>G	c.(598-600)CAG>CGG	p.Q200R	MLH3_uc001xre.1_Missense_Mutation_p.Q200R	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	200					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)										0.4	6.385905	6.476161	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74585513	74585513	10008	14	T	C	C	55	55	MLH3	C	4	4
ISM2	145501	broad.mit.edu	36	14	77020829	77020831	+	Nonsense_Mutation	TNP	GCA	AAC	AAC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77020829_77020831GCA>AAC	uc001xtz.1	-	c.326_328TGC>GTT	c.(325-330)CTGCAG>CGTTAG	p.109_110LQ>R*	ISM2_uc001xty.1_Nonsense_Mutation_p.21_22LQ>R*|ISM2_uc001xua.1_Nonsense_Mutation_p.109_110LQ>R*	NM_199296	NP_954874	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1	109_110						extracellular region					0														1	22.356292	22.35428	9	0	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	TNP	77020829	77020831	8165	14	GCA	AAC	AAC	46	46	ISM2	AAC	5	2
KCNK10	54207	broad.mit.edu	36	14	87799474	87799474	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:87799474G>A	uc001xwm.1	-	c.227C>T	c.(226-228)ACG>ATG	p.T76M	KCNK10_uc001xwn.1_Missense_Mutation_p.T76M|KCNK10_uc001xwo.1_Missense_Mutation_p.T71M	NM_138318	NP_612191	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	71	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|pancreas(1)	3														0.409396	382.866985	384.982122	122	176	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87799474	87799474	8364	14	G	A	A	40	40	KCNK10	A	1	1
RIN3	79890	broad.mit.edu	36	14	92195272	92195272	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:92195272G>T	uc001yap.1	+	c.2040G>T	c.(2038-2040)GAG>GAT	p.E680D	RIN3_uc010auk.1_Missense_Mutation_p.E342D|RIN3_uc001yaq.1_Missense_Mutation_p.E605D|RIN3_uc001yar.1_Missense_Mutation_p.E342D|RIN3_uc001yas.1_Missense_Mutation_p.E342D	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	680	Interaction with RAB5B.				endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding				0		all_cancers(154;0.0701)												0.571429	7.587892	7.61736	4	3	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92195272	92195272	13850	14	G	T	T	36	36	RIN3	T	3	3
KIAA1409	57578	broad.mit.edu	36	14	93242883	93242883	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93242883C>T	uc001ybv.1	+	c.7323C>T	c.(7321-7323)GGC>GGT	p.G2441G	KIAA1409_uc001ybs.1_Silent_p.G2419G	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	2596						integral to membrane				ovary(10)|large_intestine(3)	13		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)						1186				0.809091	261.957956	271.758863	89	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	93242883	93242883	8539	14	C	T	T	28	28	KIAA1409	T	2	2
SERPINA1	5265	broad.mit.edu	36	14	93919189	93919189	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93919189A>C	uc001ycx.2	-	c.139T>G	c.(139-141)TTC>GTC	p.F47V	SERPINA1_uc001ycw.2_Non-coding_Transcript|SERPINA1_uc010auw.1_Missense_Mutation_p.F47V|SERPINA1_uc010aux.1_Missense_Mutation_p.F47V|SERPINA1_uc001ycy.2_Missense_Mutation_p.F47V|SERPINA1_uc010auy.1_Missense_Mutation_p.F47V|SERPINA1_uc001ycz.2_Missense_Mutation_p.F47V|SERPINA1_uc010auz.1_Missense_Mutation_p.F47V|SERPINA1_uc010ava.1_Missense_Mutation_p.F47V|SERPINA1_uc001ydb.2_Missense_Mutation_p.F47V|SERPINA1_uc010avb.1_Missense_Mutation_p.F47V|SERPINA1_uc001ydc.2_Missense_Mutation_p.F47V|SERPINA1_uc001yda.1_Missense_Mutation_p.F47V	NM_000295	NP_001121179	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1	47					acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)									0.272727	8.922223	9.961583	6	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	93919189	93919189	14574	14	A	C	C	3	3	SERPINA1	C	4	4
OR4F15	390649	broad.mit.edu	36	15	100176728	100176728	+	Silent	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:100176728T>A	uc002cde.1	+	c.816T>A	c.(814-816)GCT>GCA	p.A272A		NM_001001674	NP_001001674	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F,	272	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)											0.5	112.538192	112.538192	38	38	TT		KEEP	---	---	---	---	capture			Silent	SNP	100176728	100176728	11468	15	T	A	A	53	53	OR4F15	A	4	4
CDAN1	146059	broad.mit.edu	36	15	40813739	40813739	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40813739C>A	uc001zql.1	-	c.1234G>T	c.(1234-1236)GCC>TCC	p.A412S	CDAN1_uc001zqk.1_5'UTR|CDAN1_uc010bcx.1_Intron	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	412						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)										0.454545	9.461369	9.482331	5	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40813739	40813739	3182	15	C	A	A	25	25	CDAN1	A	3	3
SPG11	80208	broad.mit.edu	36	15	42742939	42742939	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:42742939A>C	uc001ztx.1	-	c.199T>G	c.(199-201)TCT>GCT	p.S67A	SPG11_uc001zua.1_Missense_Mutation_p.S67A	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	67	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)	4		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)										0.263158	7.169762	8.1346	5	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42742939	42742939	15553	15	A	C	C	9	9	SPG11	C	4	4
DUOXA1	90527	broad.mit.edu	36	15	43197555	43197555	+	Silent	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43197555G>T	uc001zup.1	-	c.996C>A	c.(994-996)CGC>CGA	p.R332R	DUOXA2_uc001zuo.1_3'UTR|DUOXA2_uc010beb.1_Non-coding_Transcript|DUOXA1_uc010bec.1_Silent_p.R332R	NM_144565	NP_653166	Q1HG43	DOXA1_HUMAN	Numb-interacting protein	Error:Variant_position_missing_in_Q1HG43_after_alignment					protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)								OREG0023102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.75	6.68769	6.851393	3	1	GG		KEEP	---	---	---	---	capture			Silent	SNP	43197555	43197555	4987	15	G	T	T	42	42	DUOXA1	T	3	3
DUOXA1	90527	broad.mit.edu	36	15	43197557	43197558	+	Nonsense_Mutation	DNP	GA	TT	TT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43197557_43197558GA>TT	uc001zup.1	-	c.993_994TC>AA	c.(991-996)TATCGC>TAAAGC	p.331_332YR>*S	DUOXA2_uc001zuo.1_3'UTR|DUOXA2_uc010beb.1_Non-coding_Transcript|DUOXA1_uc010bec.1_Nonsense_Mutation_p.331_332YR>*S	NM_144565	NP_653166	Q1HG43	DOXA1_HUMAN	Numb-interacting protein	Error:Variant_position_missing_in_Q1HG43_after_alignment					protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)								OREG0023102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1	7.638001	7.519171	3	0	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	DNP	43197557	43197558	4987	15	GA	TT	TT	37	37	DUOXA1	TT	5	3
IGDCC4	57722	broad.mit.edu	36	15	63490541	63490543	+	Missense_Mutation	TNP	CTG	AAT	AAT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:63490541_63490543CTG>AAT	uc002aou.1	-	c.289_291CAG>ATT	c.(289-291)CAG>ATT	p.Q97I		NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member	97	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(1)|pancreas(1)	2														0.857143	11.947898	12.782135	6	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	63490541	63490543	7870	15	CTG	AAT	AAT	28	28	IGDCC4	AAT	3	3
CD276	80381	broad.mit.edu	36	15	71783631	71783631	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:71783631G>A	uc002avv.1	+	c.1134G>A	c.(1132-1134)ACG>ACA	p.T378T	CD276_uc010bjd.1_Silent_p.T232T|CD276_uc002avu.1_Silent_p.T378T|CD276_uc002avw.1_Silent_p.T160T|CD276_uc002avx.2_Non-coding_Transcript	NM_001024736	NP_001019907	Q5ZPR3	CD276_HUMAN	CD276 antigen isoform a	378	Extracellular (Potential).|Ig-like C2-type 2.				cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding				0														0.5	7.589379	7.589379	4	4	GG		KEEP	---	---	---	---	capture			Silent	SNP	71783631	71783631	3120	15	G	A	A	39	39	CD276	A	1	1
NEIL1	79661	broad.mit.edu	36	15	73433662	73433662	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73433662G>T	uc002bae.1	+	c.1123G>T	c.(1123-1125)GCA>TCA	p.A375S	NEIL1_uc002bad.1_Missense_Mutation_p.A289S	NM_024608	NP_078884	Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1	289					base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress	cytoplasm|nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding				0														0.333333	25.163011	25.828726	9	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73433662	73433662	10717	15	G	T	T	42	42	NEIL1	T	3	3
MAN2C1	4123	broad.mit.edu	36	15	73439604	73439604	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73439604A>C	uc002baf.1	-	c.1586T>G	c.(1585-1587)ATC>AGC	p.I529S	MAN2C1_uc002bag.1_Missense_Mutation_p.I529S|MAN2C1_uc002bah.1_Missense_Mutation_p.I529S|MAN2C1_uc010bkk.1_Missense_Mutation_p.I430S	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	529					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0														1	10.552956	10.491559	4	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73439604	73439604	9601	15	A	C	C	12	12	MAN2C1	C	4	4
SNX33	257364	broad.mit.edu	36	15	73728950	73728950	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73728950A>T	uc002bau.1	+	c.452A>T	c.(451-453)TAC>TTC	p.Y151F	IMP3_uc002bat.2_5'Flank|SNX33_uc002bav.1_5'Flank	NM_153271	NP_695003	Q8WV41	SNX33_HUMAN	sorting nexin 33	151					cell communication		phosphatidylinositol binding|protein binding			ovary(1)	1														0.994652	465.646326	465.761374	186	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73728950	73728950	15403	15	A	T	T	14	14	SNX33	T	4	4
MESP2	145873	broad.mit.edu	36	15	88121479	88121479	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:88121479C>A	uc002bon.1	+	c.887C>A	c.(886-888)GCG>GAG	p.A296E	MESP2_uc002bom.1_Intron	NM_001039958	NP_001035047	Q0VG99	MESP2_HUMAN	mesoderm posterior 2 homolog	296					Notch signaling pathway	nucleus	DNA binding|transcription regulator activity				0	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)											0.418182	63.305312	63.628233	23	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88121479	88121479	9872	15	C	A	A	27	27	MESP2	A	3	3
ZNF774	342132	broad.mit.edu	36	15	88704952	88704952	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:88704952C>G	uc002bpk.2	+	c.885C>G	c.(883-885)GAC>GAG	p.D295E		NM_001004309	NP_001004309	Q6NX45	ZN774_HUMAN	zinc finger protein 774	295	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)											0.3125	7.567623	8.070038	5	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88704952	88704952	18745	15	C	G	G	20	20	ZNF774	G	3	3
LYSMD4	145748	broad.mit.edu	36	15	98087141	98087142	+	Missense_Mutation	DNP	GC	AT	AT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:98087141_98087142GC>AT	uc002bvl.1	-	c.603_604GC>AT	c.(601-606)CTGCTC>CTATTC	p.L202F	LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvk.1_Missense_Mutation_p.L201F|LYSMD4_uc002bvm.1_3'UTR|LYSMD4_uc010bov.1_Missense_Mutation_p.L201F	NM_152449	NP_689662	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain	201	Extracellular (Potential).				cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)											0.75	6.528566	6.745482	3	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	98087141	98087142	9504	15	GC	AT	AT	34	34	LYSMD4	AT	2	2
LYSMD4	145748	broad.mit.edu	36	15	98087144	98087144	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:98087144G>A	uc002bvl.1	-	c.601C>T	c.(601-603)CTG>TTG	p.L201L	LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvk.1_Silent_p.L200L|LYSMD4_uc002bvm.1_3'UTR|LYSMD4_uc010bov.1_Silent_p.L200L	NM_152449	NP_689662	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain	200	Extracellular (Potential).				cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)											0.875	16.544732	17.612318	7	1	GG		KEEP	---	---	---	---	capture			Silent	SNP	98087144	98087144	9504	15	G	A	A	36	36	LYSMD4	A	2	2
SNN	8303	broad.mit.edu	36	16	11677503	11677503	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:11677503C>G	uc002dbf.1	+	c.87C>G	c.(85-87)ATC>ATG	p.I29M	SNN_uc010but.1_Missense_Mutation_p.I29M	NM_003498	NP_003489	O75324	SNN_HUMAN	Stannin	29	Helical; (Potential).				response to abiotic stimulus|response to stress	integral to membrane|mitochondrial outer membrane					0														0.714286	9.961785	10.246327	5	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11677503	11677503	15349	16	C	G	G	30	30	SNN	G	3	3
TELO2	9894	broad.mit.edu	36	16	1492973	1492974	+	Missense_Mutation	DNP	AC	CG	CG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1492973_1492974AC>CG	uc002cly.1	+	c.1811_1812AC>CG	c.(1810-1812)TAC>TCG	p.Y604S		NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	604						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)												0.384615	8.762429	8.916805	5	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	1492973	1492974	16284	16	AC	CG	CG	14	14	TELO2	CG	4	4
MYH11	4629	broad.mit.edu	36	16	15777508	15777508	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:15777508G>A	uc002ddx.1	-	c.838C>T	c.(838-840)CGC>TGC	p.R280C	MYH11_uc002ddv.1_Missense_Mutation_p.R280C|MYH11_uc002ddw.1_Missense_Mutation_p.R273C|MYH11_uc002ddy.1_Missense_Mutation_p.R273C|MYH11_uc010bvg.1_Missense_Mutation_p.R105C|MYH11_uc002dea.1_5'UTR	NM_001040114	NP_001035203	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	273	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(4)|skin(2)|lung(1)	7									p.R280C(SNU81-Tumor)	1257				0.11236	10.892329	24.098989	10	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15777508	15777508	10426	16	G	A	A	37	37	MYH11	A	1	1
ABCC1	4363	broad.mit.edu	36	16	16123367	16123367	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:16123367G>A	uc010bvi.1	+	c.3425G>A	c.(3424-3426)CGC>CAC	p.R1142H	ABCC1_uc010bvj.1_Missense_Mutation_p.R1083H|ABCC1_uc010bvk.1_Missense_Mutation_p.R1086H|ABCC1_uc010bvl.1_Missense_Mutation_p.R1142H|ABCC1_uc010bvm.1_Missense_Mutation_p.R1027H|ABCC1_uc002del.2_Missense_Mutation_p.R1036H	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	1142	Cytoplasmic.|ABC transmembrane type-1 2.			R->E,K: Reduced transport of leukotriene C4, estradiol glucuronide and of glutathione.	hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)									0.176471	7.332291	12.396879	9	42	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16123367	16123367	50	16	G	A	A	38	38	ABCC1	A	1	1
TMC5	79838	broad.mit.edu	36	16	19390949	19390950	+	Missense_Mutation	DNP	GA	CC	CC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:19390949_19390950GA>CC	uc002dgc.2	+	c.1821_1822GA>CC	c.(1819-1824)TTGACG>TTCCCG	p.607_608LT>FP	TMC5_uc002dgb.2_Missense_Mutation_p.607_608LT>FP|TMC5_uc002dgd.1_Missense_Mutation_p.361_362LT>FP|TMC5_uc002dge.2_Missense_Mutation_p.361_362LT>FP|TMC5_uc002dgf.2_Missense_Mutation_p.290_291LT>FP|TMC5_uc002dgg.2_Missense_Mutation_p.248_249LT>FP	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	607_608	Cytoplasmic (Potential).					integral to membrane					0														0.294118	9.362552	10.011472	5	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	19390949	19390950	16518	16	GA	CC	CC	45	45	TMC5	CC	3	3
ACSM5	54988	broad.mit.edu	36	16	20356189	20356189	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20356189A>C	uc002dhe.1	+	c.1535A>C	c.(1534-1536)GAG>GCG	p.E512A		NM_017888	NP_060358	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member	512					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2														0.909091	47.163365	49.390343	20	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20356189	20356189	188	16	A	C	C	11	11	ACSM5	C	4	4
ACSM5	54988	broad.mit.edu	36	16	20356191	20356192	+	Splice_Site_DNP	DNP	GT	CA	CA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20356191_20356192GT>CA	uc002dhe.1	+	c.e12_splice_site				NM_017888	NP_060358			acyl-CoA synthetase medium-chain family member						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2														1	28.656913	28.656655	12	0	GG		KEEP	---	---	---	---	capture			Splice_Site_DNP	DNP	20356191	20356192	188	16	GT	CA	CA	44	44	ACSM5	CA	5	3
OTOA	146183	broad.mit.edu	36	16	21597353	21597353	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:21597353C>T	uc002djh.1	+	c.17C>T	c.(16-18)ACG>ATG	p.T6M		NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	6					sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0414)										0.387097	32.994158	33.339551	12	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21597353	21597353	11714	16	C	T	T	19	19	OTOA	T	1	1
UBFD1	56061	broad.mit.edu	36	16	23489332	23489332	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23489332T>A	uc002dlv.1	+	c.850T>A	c.(850-852)TAC>AAC	p.Y284N		NM_019116	NP_061989	O14562	UBFD1_HUMAN	ubiquitin-binding protein homolog	284											0				GBM - Glioblastoma multiforme(48;0.0331)		Melanoma(22;290 1069 22358 48158)								0.454545	9.360568	9.381657	5	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23489332	23489332	17442	16	T	A	A	61	61	UBFD1	A	4	4
PALB2	79728	broad.mit.edu	36	16	23522283	23522284	+	Nonstop_Mutation	DNP	AT	CC	CC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23522283_23522284AT>CC	uc002dlx.1	-	c.3558_3559AT>GG	c.(3556-3561)TCATAA>TCGGAA	p.*1187E		NM_024675	NP_078951	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	1187					double-strand break repair via homologous recombination	nucleoplasm	DNA binding|protein binding			breast(2)|ovary(2)|lung(1)|skin(1)|kidney(1)|pancreas(1)	8				GBM - Glioblastoma multiforme(48;0.0167)						263				0.363636	7.692775	7.874245	4	7	AA		KEEP	---	---	---	---	capture			Nonstop_Mutation	DNP	23522283	23522284	11822	16	AT	CC	CC	16	16	PALB2	CC	5	4
CACNG3	10368	broad.mit.edu	36	16	24280432	24280432	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:24280432G>A	uc002dmf.1	+	c.695G>A	c.(694-696)CGG>CAG	p.R232Q		NM_006539	NP_006530	O60359	CCG3_HUMAN	voltage-dependent calcium channel gamma-3	232					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)										0.4375	63.670809	63.833111	21	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24280432	24280432	2674	16	G	A	A	39	39	CACNG3	A	1	1
KIAA0556	23247	broad.mit.edu	36	16	27659653	27659653	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27659653C>T	uc002dow.1	+	c.2534C>T	c.(2533-2535)CCC>CTC	p.P845L		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	845										ovary(4)|large_intestine(2)	6														0.728395	181.720109	185.531094	59	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27659653	27659653	8490	16	C	T	T	22	22	KIAA0556	T	2	2
QPRT	23475	broad.mit.edu	36	16	29616030	29616031	+	Missense_Mutation	DNP	CC	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:29616030_29616031CC>AG	uc002dto.1	+	c.691_692CC>AG	c.(691-693)CCC>AGC	p.P231S	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron	NM_014298	NP_055113	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	231					protein oligomerization|quinolinate catabolic process	cytosol	nicotinate-nucleotide diphosphorylase (carboxylating) activity|protein homodimerization activity				0					Niacin(DB00627)									1	9.345083	9.283306	4	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	29616030	29616031	13334	16	CC	AG	AG	22	22	QPRT	AG	3	3
TIGD7	91151	broad.mit.edu	36	16	3289957	3289957	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3289957C>G	uc002cus.1	-	c.659G>C	c.(658-660)GGA>GCA	p.G220A	ZNF263_uc002cur.1_3'UTR	NM_033208	NP_149985	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	220	DDE.					chromosome, centromeric region|nucleus	DNA binding				0														0.170543	17.334488	30.664884	22	107	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3289957	3289957	16430	16	C	G	G	30	30	TIGD7	G	3	3
LPCAT2	54947	broad.mit.edu	36	16	54166124	54166124	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:54166124C>G	uc002eib.1	+	c.1296C>G	c.(1294-1296)ATC>ATG	p.I432M	LPCAT2_uc002eic.1_Missense_Mutation_p.I162M	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	432	EF-hand 2.|Lumenal (Potential).				cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0														0.178571	22.416856	27.863312	10	46	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54166124	54166124	9284	16	C	G	G	29	29	LPCAT2	G	3	3
AMFR	267	broad.mit.edu	36	16	54954464	54954465	+	Missense_Mutation	DNP	AA	CC	CC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:54954464_54954465AA>CC	uc002eiy.1	-	c.1789_1790TT>GG	c.(1789-1791)TTC>GGC	p.F597G	AMFR_uc002eiw.1_Non-coding_Transcript|AMFR_uc002eix.1_Missense_Mutation_p.F231G	NM_001144	NP_001135	Q9UKV5	AMFR2_HUMAN	autocrine motility factor receptor	597					endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein oligomerization|protein polyubiquitination	integral to endoplasmic reticulum membrane|integral to membrane of membrane fraction	protein binding|protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			breast(2)	2						Pancreas(2;144 323 39528)								0.8	9.301049	9.711643	4	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	54954464	54954465	574	16	AA	CC	CC	9	9	AMFR	CC	4	4
MT1E	4493	broad.mit.edu	36	16	55217921	55217921	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:55217921G>C	uc002ejl.1	+	c.71G>C	c.(70-72)TGC>TCC	p.C24S	MT1A_uc002eji.1_Intron|MT1E_uc002ejm.2_Missense_Mutation_p.C24S	NM_175617	NP_783316	P04732	MT1E_HUMAN	metallothionein 1E	24	Beta.	Divalent metal cation; cluster B.				cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0														0.4	6.483794	6.574728	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55217921	55217921	10292	16	G	C	C	46	46	MT1E	C	3	3
DYNC1LI2	1783	broad.mit.edu	36	16	65327593	65327593	+	Silent	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65327593T>G	uc002eqb.1	-	c.585A>C	c.(583-585)CCA>CCC	p.P195P		NM_006141	NP_006132	O43237	DC1L2_HUMAN	dynein, cytoplasmic, light intermediate	195					transport	cytoplasmic dynein complex|microtubule	ATP binding|motor activity			central_nervous_system(3)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)										0.255814	15.178907	17.530592	11	32	TT		KEEP	---	---	---	---	capture			Silent	SNP	65327593	65327593	5031	16	T	G	G	59	59	DYNC1LI2	G	4	4
ACD	65057	broad.mit.edu	36	16	66251879	66251879	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66251879G>C	uc002etq.2	-	c.4C>G	c.(4-6)CCT>GCT	p.P2A	ACD_uc002etp.2_Missense_Mutation_p.P2A|ACD_uc002etr.2_Missense_Mutation_p.P2A|PARD6A_uc002ets.1_5'Flank|PARD6A_uc002ett.1_5'Flank|PARD6A_uc002etu.1_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	2					intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)										0.8	7.991163	8.401583	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66251879	66251879	136	16	G	C	C	42	42	ACD	C	3	3
DDX19B	11269	broad.mit.edu	36	16	68923138	68923138	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:68923138G>C	uc002eyo.1	+	c.1036G>C	c.(1036-1038)GCT>CCT	p.A346P	DDX19A_uc002eys.1_Intron|DDX19B_uc002eyp.1_Missense_Mutation_p.A315P|DDX19B_uc002eyq.1_Missense_Mutation_p.A237P|DDX19B_uc002eyr.1_Missense_Mutation_p.A195P	NM_007242	NP_001014449	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform	346	Helicase C-terminal.				mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			kidney(1)	1		Ovarian(137;0.0694)				Esophageal Squamous(26;382 757 1343 9728 15939)						OREG0023914	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.321429	12.42827	13.241804	9	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68923138	68923138	4518	16	G	C	C	34	34	DDX19B	C	3	3
KCNG4	93107	broad.mit.edu	36	16	82828140	82828140	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82828140G>A	uc002fht.1	-	c.453C>T	c.(451-453)GGC>GGT	p.G151G	KCNG4_uc002fhu.1_Silent_p.G151G	NM_172347	NP_758857	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G,	151						voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(3)	3														0.908696	614.582027	653.508864	209	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	82828140	82828140	8335	16	G	A	A	46	46	KCNG4	A	2	2
APRT	353	broad.mit.edu	36	16	87404347	87404348	+	Missense_Mutation	DNP	GG	TA	TA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:87404347_87404348GG>TA	uc002flv.1	-	c.305_306CC>TA	c.(304-306)TCC>TTA	p.S102L	APRT_uc002flw.1_Missense_Mutation_p.S102L	NM_000485	NP_000476	P07741	APT_HUMAN	adenine phosphoribosyltransferase isoform a	102					purine ribonucleoside salvage	cytosol|nucleus	adenine phosphoribosyltransferase activity|AMP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)									1	8.633065	8.570697	4	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	87404347	87404348	830	16	GG	TA	TA	43	43	APRT	TA	3	3
APRT	353	broad.mit.edu	36	16	87404350	87404350	+	Nonsense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87404350A>C	uc002flv.1	-	c.303T>G	c.(301-303)TAT>TAG	p.Y101*	APRT_uc002flw.1_Nonsense_Mutation_p.Y101*	NM_000485	NP_000476	P07741	APT_HUMAN	adenine phosphoribosyltransferase isoform a	101					purine ribonucleoside salvage	cytosol|nucleus	adenine phosphoribosyltransferase activity|AMP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)									1	23.36202	23.360017	9	0	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	87404350	87404350	830	16	A	C	C	4	4	APRT	C	5	4
APRT	353	broad.mit.edu	36	16	87404352	87404352	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87404352A>G	uc002flv.1	-	c.301T>C	c.(301-303)TAT>CAT	p.Y101H	APRT_uc002flw.1_Missense_Mutation_p.Y101H	NM_000485	NP_000476	P07741	APT_HUMAN	adenine phosphoribosyltransferase isoform a	101					purine ribonucleoside salvage	cytosol|nucleus	adenine phosphoribosyltransferase activity|AMP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)									1	28.750501	28.749509	10	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87404352	87404352	830	16	A	G	G	15	15	APRT	G	4	4
CPNE7	27132	broad.mit.edu	36	16	88190436	88190436	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88190436C>T	uc002fnp.1	+	c.1808C>T	c.(1807-1809)CCG>CTG	p.P603L	CPNE7_uc002fnq.1_Missense_Mutation_p.P528L	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	603					lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)										1	12.894144	12.862835	5	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88190436	88190436	3955	16	C	T	T	23	23	CPNE7	T	1	1
CPNE7	27132	broad.mit.edu	36	16	88190438	88190438	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88190438A>C	uc002fnp.1	+	c.1810A>C	c.(1810-1812)AAG>CAG	p.K604Q	CPNE7_uc002fnq.1_Missense_Mutation_p.K529Q	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	604					lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)										1	7.535783	7.416741	3	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88190438	88190438	3955	16	A	C	C	9	9	CPNE7	C	4	4
ELAC2	60528	broad.mit.edu	36	17	12836921	12836922	+	Missense_Mutation	DNP	TC	GT	GT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:12836921_12836922TC>GT	uc002gnz.2	-	c.2419_2420GA>AC	c.(2419-2421)GAG>ACG	p.E807T	ELAC2_uc002gnv.2_Missense_Mutation_p.E435T|ELAC2_uc002gnw.2_Missense_Mutation_p.E463T|ELAC2_uc002gnx.2_Missense_Mutation_p.E567T|ELAC2_uc002gny.2_Missense_Mutation_p.E773T|ELAC2_uc002goa.2_Missense_Mutation_p.E791T|ELAC2_uc002gnu.2_Missense_Mutation_p.E204T	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2	807					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0														1	14.142938	14.127004	6	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	12836921	12836922	5238	17	TC	GT	GT	54	54	ELAC2	GT	4	4
RAI1	10743	broad.mit.edu	36	17	17641185	17641185	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:17641185T>A	uc002grm.1	+	c.4198T>A	c.(4198-4200)TGC>AGC	p.C1400S	RAI1_uc002grn.1_Missense_Mutation_p.C1400S	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1400						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(1115;0.0276)										0.625	11.068564	11.176788	5	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17641185	17641185	13467	17	T	A	A	51	51	RAI1	A	4	4
ULK2	9706	broad.mit.edu	36	17	19640169	19640169	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19640169T>A	uc002gwm.2	-	c.1828A>T	c.(1828-1830)ATC>TTC	p.I610F	ULK2_uc002gwn.1_Missense_Mutation_p.I610F	NM_014683	NP_055498	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2	610					protein phosphorylation|signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)									475				0.315789	9.630257	10.211328	6	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19640169	19640169	17534	17	T	A	A	52	52	ULK2	A	4	4
RAB34	83871	broad.mit.edu	36	17	24065836	24065836	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24065836G>A	uc002hcf.1	-	c.735C>T	c.(733-735)AGC>AGT	p.S245S	PROCA1_uc002hca.1_5'Flank|RAB34_uc002hcd.1_Silent_p.S236S|RAB34_uc002hcc.2_Intron|RAB34_uc002hce.1_Silent_p.S244S|RAB34_uc002hcg.1_Silent_p.S236S|RAB34_uc002hch.1_Silent_p.S244S	NM_031934	NP_114140	Q9BZG1	RAB34_HUMAN	RAB39 isoform 1	244					protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	Lung NSC(42;0.00431)					Pancreas(175;216 2049 29940 32498 41589)								0.388889	12.100661	12.301148	7	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	24065836	24065836	13383	17	G	A	A	46	46	RAB34	A	2	2
SSH2	85464	broad.mit.edu	36	17	25046647	25046647	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:25046647G>A	uc002heo.1	-	c.232C>T	c.(232-234)CAA>TAA	p.Q78*	SSH2_uc002hep.1_Nonsense_Mutation_p.Q78*|SSH2_uc002her.2_Nonsense_Mutation_p.Q78*|SSH2_uc010csc.1_Nonsense_Mutation_p.Q78*|SSH2_uc002heq.2_Nonsense_Mutation_p.Q85*	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	78					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0														0.106557	14.28643	33.040061	13	109	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	25046647	25046647	15701	17	G	A	A	47	47	SSH2	A	5	2
NF1	4763	broad.mit.edu	36	17	26580225	26580225	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26580225A>G	uc002hgg.1	+	c.2466A>G	c.(2464-2466)GGA>GGG	p.G822G	NF1_uc002hgh.1_Silent_p.G822G|NF1_uc002hgi.1_5'UTR|NF1_uc010csn.1_Silent_p.G682G	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	822					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.444444	7.189815	7.21496	4	5	AA		KEEP	---	---	---	---	capture			Silent	SNP	26580225	26580225	10756	17	A	G	G	11	11	NF1	G	4	4
TMEM132E	124842	broad.mit.edu	36	17	29977992	29977993	+	Silent	DNP	CC	AT	AT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:29977992_29977993CC>AT	uc002hif.1	+	c.531_532CC>AT	c.(529-534)CCCCTG>CCATTG	p.177_178PL>PL		NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	177_178	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)										1	12.090923	12.059537	5	0	CC		KEEP	---	---	---	---	capture			Silent	DNP	29977992	29977993	16580	17	CC	AT	AT	22	22	TMEM132E	AT	3	3
FNDC8	54752	broad.mit.edu	36	17	30480602	30480602	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30480602C>T	uc002hix.1	+	c.634C>T	c.(634-636)CTC>TTC	p.L212F		NM_017559	NP_060029	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	212	Fibronectin type-III.									ovary(2)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)										0.580645	34.901142	35.07002	18	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30480602	30480602	6216	17	C	T	T	28	28	FNDC8	T	2	2
RASL10B	91608	broad.mit.edu	36	17	31091632	31091633	+	Missense_Mutation	DNP	TC	CA	CA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31091632_31091633TC>CA	uc002hju.1	+	c.308_309TC>CA	c.(307-309)GTC>GCA	p.V103A		NM_033315	NP_201572	Q96S79	RSLAB_HUMAN	RAS-like, family 10, member B	103	Small GTPase-like.				small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			breast(2)|lung(1)	3				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.6	22.264835	22.395066	9	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	31091632	31091633	13541	17	TC	CA	CA	58	58	RASL10B	CA	4	4
P2RX5	5026	broad.mit.edu	36	17	3538775	3538775	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3538775A>G	uc002fwh.1	-	c.778T>C	c.(778-780)TGG>CGG	p.W260R	P2RX5_uc002fwd.1_Non-coding_Transcript|P2RX5_uc002fwi.1_Missense_Mutation_p.W261R|P2RX5_uc002fwj.1_Missense_Mutation_p.W236R|P2RX5_uc002fwk.1_Missense_Mutation_p.W260R|P2RX5_uc002fwl.1_Missense_Mutation_p.W237R	NM_002561	NP_002552	Q93086	P2RX5_HUMAN	purinergic receptor P2X5 isoform A	261	Extracellular (Potential).				nervous system development|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0														0.578947	22.301439	22.402063	11	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3538775	3538775	11756	17	A	G	G	8	8	P2RX5	G	4	4
CCR7	1236	broad.mit.edu	36	17	35965485	35965485	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35965485C>A	uc002huw.1	-	c.172G>T	c.(172-174)GCC>TCC	p.A58S		NM_001838	NP_001829	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7 precursor	58	Extracellular (Potential).				activation of Rho GTPase activity|cell maturation|establishment of T cell polarity|immunological synapse formation|inflammatory response|interleukin-12 secretion|lymphocyte migration into lymph node|myeloid dendritic cell chemotaxis|negative regulation of leukocyte apoptosis|positive regulation of actin filament polymerization|positive regulation of cell-matrix adhesion|positive regulation of dendritic cell antigen processing and presentation|positive regulation of ERK1 and ERK2 cascade|positive regulation of filopodium assembly|positive regulation of glycoprotein biosynthetic process|positive regulation of humoral immune response|positive regulation of hypersensitivity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of neutrophil chemotaxis|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of pseudopodium assembly|regulation of interferon-gamma production|regulation of interleukin-1 beta secretion|release of sequestered calcium ion into cytosol|response to nitric oxide|response to prostaglandin E stimulus|ruffle organization|T cell costimulation	integral to membrane|intracellular	C-C chemokine receptor activity|chemokine (C-C motif) ligand 19 binding|chemokine (C-C motif) ligand 21 binding				0		Breast(137;0.000496)												0.143939	30.635441	46.761026	19	113	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35965485	35965485	3073	17	C	A	A	28	28	CCR7	A	3	3
KRT38	8687	broad.mit.edu	36	17	36847983	36847983	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36847983G>A	uc002hwq.1	-	c.1129C>T	c.(1129-1131)CGG>TGG	p.R377W		NM_006771	NP_006762	O76015	KRT38_HUMAN	keratin 38	377	Coil 2.|Rod.					intermediate filament	structural molecule activity				0		Breast(137;0.000496)												0.444444	36.302093	36.37347	12	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36847983	36847983	8790	17	G	A	A	39	39	KRT38	A	1	1
CAMKK1	84254	broad.mit.edu	36	17	3732354	3732354	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3732354A>C	uc002fwv.1	-	c.745T>G	c.(745-747)TCC>GCC	p.S249A	CAMKK1_uc002fwt.1_Intron|CAMKK1_uc002fwu.1_Intron	NM_172207	NP_757344	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase 1	228	Protein kinase.				protein phosphorylation|synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)						485				0.315789	9.931645	10.51196	6	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3732354	3732354	2723	17	A	C	C	11	11	CAMKK1	C	4	4
STAT3	6774	broad.mit.edu	36	17	37728639	37728640	+	Missense_Mutation	DNP	GC	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37728639_37728640GC>AG	uc002hzl.1	-	c.1796_1797GC>CT	c.(1795-1797)AGC>ACT	p.S599T	STAT3_uc002hzk.1_Missense_Mutation_p.S599T|STAT3_uc002hzm.1_Missense_Mutation_p.S599T|STAT3_uc002hzn.1_Missense_Mutation_p.S599T	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	599	SH2.				cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)						793		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.4	7.388972	7.478559	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	37728639	37728640	15786	17	GC	AG	AG	46	46	STAT3	AG	2	2
HOXB2	3212	broad.mit.edu	36	17	43975704	43975707	+	Nonsense_Mutation	ONP	GAAC	ATCA	ATCA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43975704_43975707GAAC>ATCA	uc002inm.1	-	c.793_796GTTC>TGAT	c.(793-798)GTTCGC>TGATGC	p.265_266VR>*C		NM_002145	NP_002136	P14652	HXB2_HUMAN	homeobox B2	265_266					blood circulation|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.952381	44.450597	45.692835	20	1	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	ONP	43975704	43975707	7593	17	GAAC	ATCA	ATCA	37	37	HOXB2	ATCA	5	1
SNF8	11267	broad.mit.edu	36	17	44373326	44373326	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44373326A>G	uc002ioj.1	-	c.203T>C	c.(202-204)TTC>TCC	p.F68S	SNF8_uc002iok.1_Missense_Mutation_p.F68S	NM_007241	NP_009172	Q96H20	SNF8_HUMAN	EAP30 subunit of ELL complex	68					cellular membrane organization|endosome transport|protein transport|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytosol|late endosome membrane|transcription factor complex	RNA polymerase II transcription factor activity|transcription factor binding				0														0.242424	10.173338	12.185365	8	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44373326	44373326	15346	17	A	G	G	9	9	SNF8	G	4	4
ABI3	51225	broad.mit.edu	36	17	44655001	44655001	+	Silent	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44655001C>G	uc002iop.1	+	c.1026C>G	c.(1024-1026)TCC>TCG	p.S342S	ABI3_uc002ioq.1_Silent_p.S336S	NM_016428	NP_057512	Q9P2A4	ABI3_HUMAN	NESH protein isoform 1	342	SH3.				cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)											0.970588	80.635962	82.357835	33	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	44655001	44655001	91	17	C	G	G	23	23	ABI3	G	3	3
ABI3	51225	broad.mit.edu	36	17	44655003	44655004	+	Missense_Mutation	DNP	AT	GA	GA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:44655003_44655004AT>GA	uc002iop.1	+	c.1028_1029AT>GA	c.(1027-1029)GAT>GGA	p.D343G	ABI3_uc002ioq.1_Missense_Mutation_p.D337G	NM_016428	NP_057512	Q9P2A4	ABI3_HUMAN	NESH protein isoform 1	343	SH3.				cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)											0.958333	56.415744	57.89317	23	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	44655003	44655004	91	17	AT	GA	GA	12	12	ABI3	GA	4	4
NLRP1	22861	broad.mit.edu	36	17	5383623	5383623	+	Silent	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:5383623G>T	uc002gci.1	-	c.2706C>A	c.(2704-2706)GTC>GTA	p.V902V	NLRP1_uc002gcg.1_Silent_p.V902V|NLRP1_uc002gch.2_Silent_p.V902V|NLRP1_uc002gck.1_Silent_p.V902V|NLRP1_uc002gcj.1_Silent_p.V902V|NLRP1_uc002gcl.1_Silent_p.V902V|NLRP1_uc010clh.1_Silent_p.V902V	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	902	LRR 4.				activation of caspase activity|defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|regulation of inflammatory response|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)								431				0.380952	13.673521	13.940996	8	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	5383623	5383623	10874	17	G	T	T	45	45	NLRP1	T	3	3
FAM64A	54478	broad.mit.edu	36	17	6293411	6293411	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:6293411C>A	uc002gcw.1	+	c.646C>A	c.(646-648)CTG>ATG	p.L216M	FAM64A_uc002gct.1_Missense_Mutation_p.L216M|FAM64A_uc002gcu.1_Missense_Mutation_p.L216M|FAM64A_uc002gcv.1_Missense_Mutation_p.L247M|FAM64A_uc002gcz.1_Non-coding_Transcript|FAM64A_uc002gcx.1_Missense_Mutation_p.L216M|FAM64A_uc002gcy.1_Non-coding_Transcript|FAM64A_uc002gda.1_Missense_Mutation_p.L216M|FAM64A_uc002gdb.1_Missense_Mutation_p.L216M	NM_019013	NP_061886	Q9BSJ6	FA64A_HUMAN	hypothetical protein LOC54478	216						nucleolus	protein binding				0				COAD - Colon adenocarcinoma(228;0.141)										0.375	10.933362	11.15709	6	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6293411	6293411	5821	17	C	A	A	28	28	FAM64A	A	3	3
MRPS7	51081	broad.mit.edu	36	17	70770190	70770190	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70770190G>C	uc002jnn.2	+	c.188G>C	c.(187-189)TGG>TCG	p.W63S	GGA3_uc002jni.1_5'Flank|GGA3_uc002jnj.1_5'Flank|GGA3_uc002jnk.1_5'Flank|MRPS7_uc002jnl.2_Missense_Mutation_p.W34S|MRPS7_uc002jnm.2_Missense_Mutation_p.W34S	NM_015971	NP_057055	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7	34					translation	cytosolic small ribosomal subunit|mitochondrion	protein binding|RNA binding|structural constituent of ribosome			central_nervous_system(1)	1	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)											0.5	8.292119	8.292119	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70770190	70770190	10241	17	G	C	C	47	47	MRPS7	C	3	3
KIAA0195	9772	broad.mit.edu	36	17	71003051	71003051	+	Silent	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71003051C>G	uc002jnz.2	+	c.2820C>G	c.(2818-2820)CCC>CCG	p.P940P	KIAA0195_uc002joa.2_Silent_p.P580P|KIAA0195_uc002job.2_5'Flank	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	940					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)											0.428571	6.518595	6.550611	3	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	71003051	71003051	8467	17	C	G	G	21	21	KIAA0195	G	3	3
YBX2	51087	broad.mit.edu	36	17	7134340	7134340	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7134340C>T	uc002gfq.2	-	c.698G>A	c.(697-699)CGG>CAG	p.R233Q		NM_015982	NP_057066	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	233	Pro-rich.|Required for mRNA-binding.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter|translational attenuation	cytoplasm|nucleus	DNA binding				0														0.375	7.924251	8.033397	3	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7134340	7134340	18053	17	C	T	T	23	23	YBX2	T	1	1
EVPL	2125	broad.mit.edu	36	17	71523016	71523016	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71523016G>C	uc002jqi.2	-	c.1915C>G	c.(1915-1917)CGG>GGG	p.R639G		NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	639	Globular 1.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)	3														0.869565	42.059412	45.095458	20	3	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71523016	71523016	5485	17	G	C	C	38	38	EVPL	C	3	3
ENGASE	64772	broad.mit.edu	36	17	74589708	74589708	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:74589708A>G	uc002jwv.1	+	c.1006A>G	c.(1006-1008)AAC>GAC	p.N336D	ENGASE_uc002jwu.1_Missense_Mutation_p.N336D|ENGASE_uc002jww.1_5'UTR	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	336	BRCT.					cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity				0														0.666667	8.096922	8.247275	4	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74589708	74589708	5311	17	A	G	G	9	9	ENGASE	G	4	4
TBC1D16	125058	broad.mit.edu	36	17	75541193	75541193	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75541193C>G	uc002jxj.1	-	c.799G>C	c.(799-801)GCC>CCC	p.A267P	TBC1D16_uc002jxh.1_5'Flank|TBC1D16_uc002jxi.1_5'Flank|TBC1D16_uc002jxk.1_5'Flank	NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	267						intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			Ovarian(14;397 562 4850 31922 49378)								0.916667	22.203128	22.958087	11	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75541193	75541193	16127	17	C	G	G	27	27	TBC1D16	G	3	3
TBC1D16	125058	broad.mit.edu	36	17	75541196	75541198	+	Nonsense_Mutation	TNP	CGG	TCT	TCT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:75541196_75541198CGG>TCT	uc002jxj.1	-	c.794_796CCG>AGA	c.(793-798)TCCGAC>TAGAAC	p.265_266SD>*N	TBC1D16_uc002jxh.1_5'Flank|TBC1D16_uc002jxi.1_5'Flank|TBC1D16_uc002jxk.1_5'Flank	NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	265_266						intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			Ovarian(14;397 562 4850 31922 49378)								0.96	58.888257	59.761934	24	1	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	TNP	75541196	75541198	16127	17	CGG	TCT	TCT	31	31	TBC1D16	TCT	5	1
HGS	9146	broad.mit.edu	36	17	77278226	77278226	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77278226G>A	uc002kbg.1	+	c.2113G>A	c.(2113-2115)GGC>AGC	p.G705S	MRPL12_uc002kbh.1_5'Flank	NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	705	Interaction with NF2.|Gln-rich.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	protein domain specific binding|zinc ion binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)											0.5	7.086178	7.086178	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77278226	77278226	7371	17	G	A	A	43	43	HGS	A	2	2
HEXDC	284004	broad.mit.edu	36	17	77992248	77992252	+	Missense_Mutation	ONP	CCCTG	TTTCC	TTTCC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77992248_77992252CCCTG>TTTCC	uc002kev.2	+	c.1069_1073CCCTG>TTTCC	c.(1069-1074)CCCTGC>TTTCCC	p.357_358PC>FP	HEXDC_uc010diq.1_Intron|HEXDC_uc002kew.1_Intron	NM_173620	NP_775891	Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20,	357_358					carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)											0.923077	27.356379	28.45357	12	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	ONP	77992248	77992252	7358	17	CCCTG	TTTCC	TTTCC	18	18	HEXDC	TTTCC	2	2
PER1	5187	broad.mit.edu	36	17	7985282	7985282	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7985282A>G	uc002gkd.1	-	c.3702T>C	c.(3700-3702)GGT>GGC	p.G1234G	PER1_uc010cns.1_Silent_p.G108G	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	1234	CRY binding domain (By similarity).				circadian rhythm|entrainment of circadian clock|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			breast(2)|ovary(1)|large_intestine(1)|kidney(1)|skin(1)	6										239				0.76	40.988625	42.520551	19	6	AA		KEEP	---	---	---	---	capture			Silent	SNP	7985282	7985282	12150	17	A	G	G	6	6	PER1	G	4	4
PFAS	5198	broad.mit.edu	36	17	8113247	8113247	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:8113247C>T	uc002gkr.1	+	c.3957C>T	c.(3955-3957)ACC>ACT	p.T1319T	PFAS_uc002gks.2_3'UTR	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1319					'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)									0.25	52.579304	57.81331	23	69	CC		KEEP	---	---	---	---	capture			Silent	SNP	8113247	8113247	12176	17	C	T	T	24	24	PFAS	T	2	2
SLC14A1	6563	broad.mit.edu	36	18	41583885	41583885	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:41583885A>C	uc010dnk.1	+	c.1309A>C	c.(1309-1311)AAG>CAG	p.K437Q	SLC14A1_uc002lbf.2_Missense_Mutation_p.K381Q|SLC14A1_uc002lbg.2_Non-coding_Transcript|SLC14A1_uc002lbh.2_Missense_Mutation_p.K273Q|SLC14A1_uc002lbi.2_Missense_Mutation_p.K249Q|SLC14A1_uc002lbj.2_Missense_Mutation_p.K437Q|SLC14A1_uc002lbk.2_Missense_Mutation_p.K381Q	NM_001128588	NP_001122060	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter),	381						integral to plasma membrane	ubiquitin-ubiquitin ligase activity|urea transmembrane transporter activity			central_nervous_system(1)|pancreas(1)	2										201				0.24	16.456844	19.564363	12	38	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41583885	41583885	14891	18	A	C	C	5	5	SLC14A1	C	4	4
MALT1	10892	broad.mit.edu	36	18	54514582	54514582	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:54514582A>G	uc002lhm.1	+	c.381A>G	c.(379-381)ATA>ATG	p.I127M	MALT1_uc002lhn.1_Missense_Mutation_p.I127M	NM_006785	NP_006776	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma	127	Ig-like C2-type 1.	Breakpoint for translocation to form BIRC2-MALT1.			activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell activation|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|central_nervous_system(1)	3										549				0.75	6.472513	6.648148	3	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54514582	54514582	9585	18	A	G	G	13	13	MALT1	G	4	4
CETN1	1068	broad.mit.edu	36	18	570740	570742	+	Missense_Mutation	TNP	GGC	TCG	TCG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:570740_570742GGC>TCG	uc002kko.1	+	c.332_334GGC>TCG	c.(331-336)AGGCTC>ATCGTC	p.111_112RL>IV		NM_004066	NP_004057	Q12798	CETN1_HUMAN	centrin 1	111_112	EF-hand 3.				cell division|mitosis	spindle pole	ATP binding|ATP-dependent helicase activity|calcium ion binding|nucleic acid binding			ovary(1)	1														0.833333	10.575278	11.191329	5	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	570740	570742	3407	18	GGC	TCG	TCG	35	35	CETN1	TCG	3	3
CETN1	1068	broad.mit.edu	36	18	570745	570745	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:570745T>A	uc002kko.1	+	c.337T>A	c.(337-339)TTT>ATT	p.F113I		NM_004066	NP_004057	Q12798	CETN1_HUMAN	centrin 1	113	EF-hand 3.				cell division|mitosis	spindle pole	ATP binding|ATP-dependent helicase activity|calcium ion binding|nucleic acid binding			ovary(1)	1														0.916667	25.722287	27.118503	11	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	570745	570745	3407	18	T	A	A	56	56	CETN1	A	4	4
BCL2	596	broad.mit.edu	36	18	59136528	59136528	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59136528G>C	uc002lit.1	-	c.352C>G	c.(352-354)CAG>GAG	p.Q118E	BCL2_uc002liu.1_Missense_Mutation_p.Q118E|BCL2_uc002liv.1_Missense_Mutation_p.Q118E	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform	118					activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|transcription activator activity			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)					37				0.225806	8.695204	10.852902	7	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59136528	59136528	1386	18	G	C	C	47	47	BCL2	C	3	3
CNDP1	84735	broad.mit.edu	36	18	70395161	70395161	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70395161A>T	uc002llq.1	+	c.919A>T	c.(919-921)ATA>TTA	p.I307L	CNDP1_uc002lls.1_Missense_Mutation_p.I110L	NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1	307					proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		Melanoma(32;1029 1042 25286 38395 44237)								0.315789	8.322196	8.908036	6	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70395161	70395161	3731	18	A	T	T	4	4	CNDP1	T	4	4
NFATC1	4772	broad.mit.edu	36	18	75328496	75328497	+	Missense_Mutation	DNP	AC	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:75328496_75328497AC>CT	uc002lnf.1	+	c.1979_1980AC>CT	c.(1978-1980)CAC>CCT	p.H660P	NFATC1_uc002lnd.1_Missense_Mutation_p.H673P|NFATC1_uc002lne.1_Missense_Mutation_p.H201P|NFATC1_uc002lng.1_Missense_Mutation_p.H660P|NFATC1_uc002lnc.1_Missense_Mutation_p.H673P	NM_172387	NP_765975	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic	673					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)		GBM(151;1210 2593 28719 45011)			p.H660H(HCC1954-Tumor)|p.H660R(DMS53-Tumor)	1639				0.363636	7.290542	7.47286	4	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	75328496	75328497	10761	18	AC	CT	CT	6	6	NFATC1	CT	4	4
ANKRD12	23253	broad.mit.edu	36	18	9248744	9248744	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9248744C>G	uc002knv.2	+	c.5479C>G	c.(5479-5481)CCA>GCA	p.P1827A	ANKRD12_uc002knw.2_Missense_Mutation_p.P1804A|ANKRD12_uc002knx.2_Missense_Mutation_p.P1804A|ANKRD12_uc010dkx.1_Missense_Mutation_p.P1534A	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	1827						nucleus				ovary(2)|central_nervous_system(1)	3														0.219512	9.527937	12.535266	9	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9248744	9248744	643	18	C	G	G	26	26	ANKRD12	G	3	3
ABCA7	10347	broad.mit.edu	36	19	1008047	1008047	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1008047C>T	uc002lqw.2	+	c.4728C>T	c.(4726-4728)CCC>CCT	p.P1576P	ABCA7_uc002lqy.1_Silent_p.P47P|ABCA7_uc010dsc.1_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1576					phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.454545	8.758506	8.779766	5	6	CC		KEEP	---	---	---	---	capture			Silent	SNP	1008047	1008047	38	19	C	T	T	21	21	ABCA7	T	2	2
ICAM1	3383	broad.mit.edu	36	19	10246457	10246457	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10246457G>A	uc002mnq.2	+	c.84G>A	c.(82-84)CAG>CAA	p.Q28Q		NM_000201	NP_000192	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1 precursor	28	Extracellular (Potential).				adhesion to symbiont|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking|positive regulation of cellular extravasation|regulation of immune response|regulation of leukocyte mediated cytotoxicity|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell|virion attachment, binding of host cell surface receptor	extracellular space|integral to plasma membrane	integrin binding|transmembrane receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Natalizumab(DB00108)|Simvastatin(DB00641)					72				0.142857	11.292481	17.318791	7	42	GG		KEEP	---	---	---	---	capture			Silent	SNP	10246457	10246457	7779	19	G	A	A	33	33	ICAM1	A	2	2
SMARCA4	6597	broad.mit.edu	36	19	10993463	10993464	+	Missense_Mutation	DNP	GA	AT	AT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10993463_10993464GA>AT	uc010dxo.1	+	c.2679_2680GA>AT	c.(2677-2682)CTGACG>CTATCG	p.T894S	SMARCA4_uc002mqf.2_Missense_Mutation_p.T894S|SMARCA4_uc010dxp.1_Missense_Mutation_p.T894S|SMARCA4_uc010dxq.1_Missense_Mutation_p.T894S|SMARCA4_uc010dxr.1_Missense_Mutation_p.T894S|SMARCA4_uc002mqj.2_Missense_Mutation_p.T894S|SMARCA4_uc010dxs.1_Missense_Mutation_p.T894S|SMARCA4_uc002mqh.2_Missense_Mutation_p.T17S|SMARCA4_uc002mqg.1_Missense_Mutation_p.T894S|SMARCA4_uc010dxt.1_Missense_Mutation_p.T114S|SMARCA4_uc002mqi.1_Missense_Mutation_p.T97S	NM_001128849	NP_001122321	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	894	Helicase ATP-binding.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of S phase of mitotic cell cycle|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription activator activity|transcription corepressor activity	p.?(1)		lung(29)|ovary(7)|pancreas(7)|large_intestine(5)|prostate(3)|central_nervous_system(2)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|skin(1)|autonomic_ganglia(1)|kidney(1)	61		all_lung(6;0.0512)|Lung NSC(9;0.0568)								582				1	8.040954	7.922402	3	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	10993463	10993464	15268	19	GA	AT	AT	45	45	SMARCA4	AT	2	2
EPOR	2057	broad.mit.edu	36	19	11353493	11353493	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11353493G>A	uc002mrj.1	-	c.460C>T	c.(460-462)CGG>TGG	p.R154W	EPOR_uc002mrh.1_5'Flank|EPOR_uc002mri.1_5'UTR|EPOR_uc002mrk.1_5'UTR|EPOR_uc002mrl.1_Non-coding_Transcript	NM_000121	NP_000112	P19235	EPOR_HUMAN	erythropoietin receptor precursor	154	Fibronectin type-III.|Extracellular (Potential).					extracellular region|integral to plasma membrane	erythropoietin receptor activity|identical protein binding			ovary(1)	1					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)							OREG0025255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.454545	8.256461	8.277769	5	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11353493	11353493	5382	19	G	A	A	38	38	EPOR	A	1	1
ZNF443	10224	broad.mit.edu	36	19	12403714	12403714	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12403714A>C	uc002mtu.1	-	c.272T>G	c.(271-273)ATT>AGT	p.I91S		NM_005815	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	91					induction of apoptosis|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1														0.155172	6.832142	13.449353	9	49	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12403714	12403714	18509	19	A	C	C	4	4	ZNF443	C	4	4
MUM1	84939	broad.mit.edu	36	19	1315571	1315571	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1315571C>A	uc002lsa.1	+	c.1280C>A	c.(1279-1281)CCA>CAA	p.P427Q	MUM1_uc002lrz.1_Missense_Mutation_p.P426Q|MUM1_uc010dsi.1_Missense_Mutation_p.P358Q|MUM1_uc002lsb.1_Missense_Mutation_p.P358Q	NM_032853	NP_116242	Q2TAK8	MUM1_HUMAN	melanoma ubiquitous mutated protein	426	PWWP.				chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.833333	13.079361	13.704146	5	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1315571	1315571	10379	19	C	A	A	21	21	MUM1	A	3	3
MUM1	84939	broad.mit.edu	36	19	1315573	1315574	+	Missense_Mutation	DNP	GC	AT	AT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1315573_1315574GC>AT	uc002lsa.1	+	c.1282_1283GC>AT	c.(1282-1284)GCA>ATA	p.A428I	MUM1_uc002lrz.1_Missense_Mutation_p.A427I|MUM1_uc010dsi.1_Missense_Mutation_p.A359I|MUM1_uc002lsb.1_Missense_Mutation_p.A359I	NM_032853	NP_116242	Q2TAK8	MUM1_HUMAN	melanoma ubiquitous mutated protein	427	PWWP.				chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.75	6.922594	7.1472	3	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	1315573	1315574	10379	19	GC	AT	AT	34	34	MUM1	AT	2	2
CC2D1A	54862	broad.mit.edu	36	19	13899960	13899960	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13899960G>C	uc002mxo.1	+	c.2478G>C	c.(2476-2478)AAG>AAC	p.K826N	CC2D1A_uc002mxp.1_Missense_Mutation_p.K825N|CC2D1A_uc010dzh.1_Missense_Mutation_p.K395N	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	826					positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)											0.555556	9.257867	9.280326	5	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13899960	13899960	2846	19	G	C	C	35	35	CC2D1A	C	3	3
CD97	976	broad.mit.edu	36	19	14368209	14368209	+	Silent	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14368209C>A	uc002myl.1	+	c.402C>A	c.(400-402)GTC>GTA	p.V134V	CD97_uc002mym.1_Silent_p.V134V|CD97_uc002myn.1_Intron	NM_078481	NP_510966	P48960	CD97_HUMAN	CD97 antigen isoform 1 precursor	134	Extracellular (Potential).|EGF-like 3; calcium-binding (Potential).				cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(2)|breast(1)	3														0.31307	256.880291	267.131646	103	226	CC		KEEP	---	---	---	---	capture			Silent	SNP	14368209	14368209	3177	19	C	A	A	29	29	CD97	A	3	3
WIZ	58525	broad.mit.edu	36	19	15408649	15408649	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15408649C>A	uc002nbb.2	-	c.497G>T	c.(496-498)TGG>TTG	p.W166L		NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	1009						nucleus	zinc ion binding				0														1	9.04008	8.978058	4	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15408649	15408649	17949	19	C	A	A	21	21	WIZ	A	3	3
SLC27A1	376497	broad.mit.edu	36	19	17458654	17458654	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17458654G>T	uc002ngu.1	+	c.450G>T	c.(448-450)AAG>AAT	p.K150N	SLC27A1_uc002ngt.1_Intron	NM_198580	NP_940982	Q6PCB7	S27A1_HUMAN	solute carrier family 27, member 1	150	Cytoplasmic (Potential).				cardiolipin biosynthetic process|fatty acid metabolic process|long-chain fatty acid transport|negative regulation of phospholipid biosynthetic process|phosphatidic acid biosynthetic process|phosphatidylcholine biosynthetic process|phosphatidylethanolamine biosynthetic process|phosphatidylinositol biosynthetic process|phosphatidylserine biosynthetic process|transmembrane transport	endomembrane system|integral to membrane	fatty acid transporter activity|nucleotide binding				0														0.25	11.403744	12.305004	4	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17458654	17458654	15022	19	G	T	T	35	35	SLC27A1	T	3	3
RPL18A	6142	broad.mit.edu	36	19	17833184	17833184	+	Missense_Mutation	SNP	C	A	A	rs11553808	unknown	TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17833184C>A	uc002nhp.1	+	c.101C>A	c.(100-102)GCG>GAG	p.A34E	SNORA68_uc002nhq.1_5'Flank	NM_000980	NP_000971	Q02543	RL18A_HUMAN	ribosomal protein L18a	34					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0														0.283394	425.832881	449.12697	157	397	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17833184	17833184	14044	19	C	A	A	27	27	RPL18A	A	3	3
TMPRSS9	360200	broad.mit.edu	36	19	2359534	2359534	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2359534C>T	uc002lvw.1	+	c.921C>T	c.(919-921)CAC>CAT	p.H307H	TMPRSS9_uc002lvv.1_Silent_p.H341H	NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	307	Extracellular (Potential).|Peptidase S1 1.				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.884	666.060043	702.290899	221	29	CC		KEEP	---	---	---	---	capture			Silent	SNP	2359534	2359534	16794	19	C	T	T	17	17	TMPRSS9	T	2	2
LMNB2	84823	broad.mit.edu	36	19	2382614	2382614	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2382614C>A	uc002lwa.1	-	c.1753G>T	c.(1753-1755)GAG>TAG	p.E585*	LMNB2_uc002lvy.1_Nonsense_Mutation_p.E565*|LMNB2_uc010dtc.1_5'Flank	NM_032737	NP_116126	Q03252	LMNB2_HUMAN	lamin B2	565	Tail.					nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)						1275				0.444444	7.690502	7.715759	4	5	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	2382614	2382614	9179	19	C	A	A	29	29	LMNB2	A	5	3
GADD45B	4616	broad.mit.edu	36	19	2428554	2428554	+	Silent	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2428554G>T	uc002lwb.1	+	c.438G>T	c.(436-438)CGG>CGT	p.R146R		NM_015675	NP_056490	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta	146					activation of MAPKKK activity|apoptosis|cell differentiation|multicellular organismal development|response to stress						0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.363636	6.889388	7.07212	4	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	2428554	2428554	6433	19	G	T	T	43	43	GADD45B	T	3	3
ZNF536	9745	broad.mit.edu	36	19	35627715	35627718	+	Missense_Mutation	ONP	TGCT	GCGA	GCGA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35627715_35627718TGCT>GCGA	uc002nsu.1	+	c.1406_1409TGCT>GCGA	c.(1405-1410)CTGCTG>CGCGAG	p.469_470LL>RE	ZNF536_uc010edd.1_Missense_Mutation_p.469_470LL>RE	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	469_470					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													1	8.241577	8.123084	3	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	ONP	35627715	35627718	18568	19	TGCT	GCGA	GCGA	55	55	ZNF536	GCGA	4	4
TSHZ3	57616	broad.mit.edu	36	19	36459930	36459930	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:36459930T>G	uc002nsy.2	-	c.2609A>C	c.(2608-2610)GAG>GCG	p.E870A		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	870					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)													0.222222	7.423968	9.356437	6	21	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36459930	36459930	17176	19	T	G	G	54	54	TSHZ3	G	4	4
TJP3	27134	broad.mit.edu	36	19	3694949	3694949	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3694949G>A	uc002lym.1	+	c.1955G>A	c.(1954-1956)CGC>CAC	p.R652H	TJP3_uc002lyk.1_Missense_Mutation_p.R619H|TJP3_uc002lyl.1_Missense_Mutation_p.R628H|TJP3_uc002lyn.1_Missense_Mutation_p.R619H	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	633	Guanylate kinase-like.					tight junction	protein binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)										0.5	19.051468	19.051468	6	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3694949	3694949	16460	19	G	A	A	38	38	TJP3	A	1	1
NUDT19	390916	broad.mit.edu	36	19	37874988	37874988	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:37874988G>A	uc010edf.1	+	c.282G>A	c.(280-282)GCG>GCA	p.A94A		NM_001105570	NP_001099040	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety	94	Nudix hydrolase.					mitochondrion|peroxisome	hydrolase activity|metal ion binding				0	Esophageal squamous(110;0.137)													0.833333	9.252245	9.867677	5	1	GG		KEEP	---	---	---	---	capture			Silent	SNP	37874988	37874988	11141	19	G	A	A	38	38	NUDT19	A	1	1
ITGB1BP3	27231	broad.mit.edu	36	19	3888285	3888285	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3888285C>T	uc002lyz.2	+	c.165C>T	c.(163-165)GAC>GAT	p.D55D		NM_170678	NP_733778	Q9NPI5	NRK2_HUMAN	integrin beta 1 binding protein 3	55		Substrate (By similarity).			pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)										0.5	38.502511	38.502511	12	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	3888285	3888285	8197	19	C	T	T	19	19	ITGB1BP3	T	1	1
GAPDHS	26330	broad.mit.edu	36	19	40725246	40725247	+	Missense_Mutation	DNP	AG	CC	CC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40725246_40725247AG>CC	uc002oaf.1	+	c.555_556AG>CC	c.(553-558)GCAGGT>GCCCGT	p.G186R		NM_014364	NP_055179	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase,	186					gluconeogenesis|glycolysis|oxidation-reduction process|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)									0.35	12.105332	12.50811	7	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	40725246	40725247	6501	19	AG	CC	CC	7	7	GAPDHS	CC	4	4
NPHS1	4868	broad.mit.edu	36	19	41031814	41031814	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41031814C>T	uc002oby.2	-	c.916G>A	c.(916-918)GTG>ATG	p.V306M		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	306	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.571429	7.487298	7.516765	4	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41031814	41031814	10986	19	C	T	T	19	19	NPHS1	T	1	1
WDR62	284403	broad.mit.edu	36	19	41286088	41286088	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41286088C>A	uc002odd.2	+	c.3518C>A	c.(3517-3519)CCC>CAC	p.P1173H	WDR62_uc002odc.2_Missense_Mutation_p.P1168H	NM_001083961	NP_001077430	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 1	1168	WD 14.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)											0.4	10.328639	10.464365	6	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41286088	41286088	17886	19	C	A	A	22	22	WDR62	A	3	3
ZNF829	374899	broad.mit.edu	36	19	42074826	42074826	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:42074826C>T	uc002ofa.1	-	c.707G>A	c.(706-708)GGT>GAT	p.G236D	ZNF345_uc002oez.2_Intron	NM_001037232	NP_001032309	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	236					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.285714	61.718825	64.891914	22	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42074826	42074826	18781	19	C	T	T	18	18	ZNF829	T	2	2
UBXN6	80700	broad.mit.edu	36	19	4404493	4404493	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:4404493T>G	uc002man.1	-	c.274A>C	c.(274-276)ACC>CCC	p.T92P	UBXN6_uc010dty.1_Missense_Mutation_p.T39P|UBXN6_uc002mam.1_Missense_Mutation_p.T39P	NM_025241	NP_079517	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	92						microtubule organizing center|nucleus	protein binding				0														0.444444	7.396172	7.420141	4	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4404493	4404493	17475	19	T	G	G	59	59	UBXN6	G	4	4
SERTAD1	29950	broad.mit.edu	36	19	45621055	45621055	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45621055G>C	uc002ont.2	-	c.239C>G	c.(238-240)TCC>TGC	p.S80C		NM_013376	NP_037508	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	80	SERTA.				positive regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.75	6.573679	6.74962	3	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45621055	45621055	14608	19	G	C	C	41	41	SERTAD1	C	3	3
SPTBN4	57731	broad.mit.edu	36	19	45685554	45685554	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45685554G>C	uc002ony.1	+	c.280G>C	c.(280-282)GTG>CTG	p.V94L	SPTBN4_uc002onx.1_Missense_Mutation_p.V94L|SPTBN4_uc002onz.1_Missense_Mutation_p.V94L	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	94	CH 1.|Actin-binding.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)	4			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.857143	11.649134	12.478083	6	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45685554	45685554	15635	19	G	C	C	40	40	SPTBN4	C	3	3
CEACAM5	1048	broad.mit.edu	36	19	46910978	46910978	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:46910978C>T	uc002ork.2	+	c.673C>T	c.(673-675)CGC>TGC	p.R225C	CEACAM5_uc002orl.1_Missense_Mutation_p.R225C|CEACAM5_uc010ehz.1_Missense_Mutation_p.R225C|CEACAM5_uc002orj.1_Missense_Mutation_p.R225C	NM_004363	NP_004354	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion	225	Ig-like 2.					anchored to membrane|basolateral plasma membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)										0.402062	113.797286	114.612476	39	58	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46910978	46910978	3328	19	C	T	T	27	27	CEACAM5	T	1	1
PSG11	5680	broad.mit.edu	36	19	48214817	48214817	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48214817T>A	uc002ovn.1	-	c.672A>T	c.(670-672)GAA>GAT	p.E224D	PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG11_uc002ouw.1_Missense_Mutation_p.E224D|PSG6_uc002ovh.1_Intron|PSG11_uc002ovk.1_Missense_Mutation_p.E224D|PSG11_uc002ovm.1_Missense_Mutation_p.E218D|PSG11_uc002ovo.1_Missense_Mutation_p.E96D|PSG11_uc002ovp.1_Missense_Mutation_p.E96D	NM_002785	NP_002776	Q9UQ72	PSG11_HUMAN	pregnancy specific beta-1-glycoprotein 11	218	Ig-like C2-type 1.				female pregnancy	extracellular region					0		Prostate(69;0.00682)												0.144578	8.32633	18.465305	12	71	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48214817	48214817	13107	19	T	A	A	64	64	PSG11	A	4	4
PSG4	5672	broad.mit.edu	36	19	48394019	48394019	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48394019G>A	uc002ovy.1	-	c.679C>T	c.(679-681)CGC>TGC	p.R227C	PSG4_uc002ovz.1_Missense_Mutation_p.R227C|PSG4_uc002owa.1_Non-coding_Transcript|PSG4_uc002owb.1_Intron	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform	227	Ig-like C2-type 1.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.333333	25.266351	25.930395	9	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48394019	48394019	13110	19	G	A	A	39	39	PSG4	A	1	1
PSG9	5678	broad.mit.edu	36	19	48463964	48463964	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48463964G>A	uc002owd.2	-	c.242C>T	c.(241-243)TCG>TTG	p.S81L	PSG9_uc002owc.2_Missense_Mutation_p.S10L|PSG9_uc002owe.2_Missense_Mutation_p.S81L|PSG9_uc002owf.2_Missense_Mutation_p.S81L|PSG9_uc002owg.2_Missense_Mutation_p.S81L|PSG9_uc002owh.2_Missense_Mutation_p.S81L	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	81	Ig-like V-type.				female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.870246	2540.751921	2660.006447	778	116	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48463964	48463964	13115	19	G	A	A	37	37	PSG9	A	1	1
IRF2BP1	26145	broad.mit.edu	36	19	51080054	51080054	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:51080054C>G	uc002pds.1	-	c.819G>C	c.(817-819)AAG>AAC	p.K273N		NM_015649	NP_056464	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein	273					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)										0.571429	7.387166	7.416764	4	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51080054	51080054	8132	19	C	G	G	28	28	IRF2BP1	G	3	3
GRIN2D	2906	broad.mit.edu	36	19	53614828	53614828	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53614828C>T	uc002pjc.2	+	c.2036C>T	c.(2035-2037)GCC>GTC	p.A679V	GRIN2D_uc010elx.1_5'UTR	NM_000836	NP_000827	O15399	NMDE4_HUMAN	N-methyl-D-aspartate receptor subunit 2D	679	Extracellular (Potential).					cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)									0.366667	18.088676	18.567772	11	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53614828	53614828	7061	19	C	T	T	26	26	GRIN2D	T	2	2
PLEKHA4	57664	broad.mit.edu	36	19	54056751	54056751	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54056751C>A	uc002pkx.1	-	c.203G>T	c.(202-204)GGG>GTG	p.G68V	PLEKHA4_uc002pkw.1_5'Flank|PLEKHA4_uc010eml.1_Missense_Mutation_p.G68V	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A	68	PH.					cytoplasm|membrane	1-phosphatidylinositol binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)										0.4	7.997062	8.083921	4	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54056751	54056751	12484	19	C	A	A	22	22	PLEKHA4	A	3	3
DHDH	27294	broad.mit.edu	36	19	54139572	54139572	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54139572C>T	uc002ple.1	+	c.891C>T	c.(889-891)CGC>CGT	p.R297R		NM_014475	NP_055290	Q9UQ10	DHDH_HUMAN	dimeric dihydrodiol dehydrogenase	297					carbohydrate metabolic process|oxidation-reduction process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)										0.984733	443.295711	446.961074	129	2	CC		KEEP	---	---	---	---	capture			Silent	SNP	54139572	54139572	4658	19	C	T	T	25	25	DHDH	T	2	2
SCAF1	58506	broad.mit.edu	36	19	54848217	54848218	+	Missense_Mutation	DNP	CA	GG	GG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54848217_54848218CA>GG	uc002poq.1	+	c.2759_2760CA>GG	c.(2758-2760)CCA>CGG	p.P920R	SCAF1_uc002por.1_Missense_Mutation_p.P920R	NM_021228	NP_067051	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	920	Lys-rich.				mRNA processing|RNA splicing	nucleus	RNA binding				0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)										0.625	9.458904	9.565034	5	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	54848217	54848218	14349	19	CA	GG	GG	21	21	SCAF1	GG	3	3
PTOV1	53635	broad.mit.edu	36	19	55049556	55049559	+	Nonsense_Mutation	ONP	GAGC	TGAG	TGAG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55049556_55049559GAGC>TGAG	uc002pqf.1	+	c.253_256GAGC>TGAG	c.(253-258)GAGCAC>TGAGAC	p.85_86EH>*D	PTOV1_uc002ppz.2_Non-coding_Transcript|PTOV1_uc002pqb.2_Nonsense_Mutation_p.53_54EH>*D|PTOV1_uc002pqa.1_Non-coding_Transcript|PTOV1_uc002pqc.1_Non-coding_Transcript|PTOV1_uc002pqd.2_Non-coding_Transcript|PTOV1_uc002pqe.1_Non-coding_Transcript	NM_017432	NP_059128	Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	85_86					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|plasma membrane					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)										1	51.71498	51.71498	21	0	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	ONP	55049556	55049559	13224	19	GAGC	TGAG	TGAG	37	37	PTOV1	TGAG	5	3
NUP62	23636	broad.mit.edu	36	19	55104840	55104840	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55104840T>G	uc002pqx.1	-	c.37A>C	c.(37-39)ACA>CCA	p.T13P	IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqu.1_Intron|NUP62_uc002pqy.1_Missense_Mutation_p.T13P|NUP62_uc002pqz.1_Missense_Mutation_p.T13P|NUP62_uc002pra.1_Missense_Mutation_p.T13P|NUP62_uc002prb.1_Missense_Mutation_p.T13P|NUP62_uc002prc.2_Missense_Mutation_p.T13P|NUP62_uc010enp.1_Missense_Mutation_p.T13P	NM_153719	NP_714941	P37198	NUP62_HUMAN	nucleoporin 62kDa	13	15 X 9 AA approximate repeats.|2.|Thr-rich.				carbohydrate metabolic process|cell death|cell surface receptor linked signaling pathway|glucose transport|hormone-mediated signaling pathway|mRNA transport|negative regulation of apoptosis|negative regulation of cell proliferation|nucleocytoplasmic transport|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription, DNA-dependent|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleocytoplasmic shuttling complex|ribonucleoprotein complex|spindle pole	chromatin binding|protein serine/threonine kinase activity|receptor signaling complex scaffold activity|SH2 domain binding|structural constituent of nuclear pore|thyroid hormone receptor binding|transcription regulator activity|ubiquitin binding				0		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)										0.75	6.324389	6.54388	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55104840	55104840	11173	19	T	G	G	57	57	NUP62	G	4	4
BIRC8	112401	broad.mit.edu	36	19	58484972	58484972	+	Silent	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:58484972A>C	uc002qbk.1	-	c.468T>G	c.(466-468)GCT>GCG	p.A156A		NM_033341	NP_203127	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat-containing 8	156					apoptosis		zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(134;0.00304)										0.212121	6.487557	9.046481	7	26	AA		KEEP	---	---	---	---	capture			Silent	SNP	58484972	58484972	1465	19	A	C	C	11	11	BIRC8	C	4	4
CCDC106	29903	broad.mit.edu	36	19	60855840	60855840	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60855840C>T	uc002qlr.1	+	c.759C>T	c.(757-759)GCC>GCT	p.A253A	CCDC106_uc002qls.1_Silent_p.A253A|U2AF2_uc002qlt.1_5'Flank|U2AF2_uc002qlu.1_5'Flank	NM_013301	NP_037433	Q9BWC9	CC106_HUMAN	coiled-coil domain containing 106	253						nucleus					0		Colorectal(82;0.00403)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)										0.833333	16.281993	16.90781	5	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	60855840	60855840	2861	19	C	T	T	22	22	CCDC106	T	2	2
NLRP11	204801	broad.mit.edu	36	19	60995538	60995538	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60995538G>A	uc002qma.1	-	c.2454C>T	c.(2452-2454)TAC>TAT	p.Y818Y	NLRP11_uc002qlz.1_Silent_p.Y665Y|NLRP11_uc002qmb.1_Silent_p.Y719Y|NLRP11_uc002qmc.1_Non-coding_Transcript|NLRP11_uc010ete.1_Non-coding_Transcript	NM_145007	NP_659444	P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	818	LRR 4.						ATP binding			ovary(3)|central_nervous_system(1)	4		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)										0.817955	1077.30197	1115.378581	328	73	GG		KEEP	---	---	---	---	capture			Silent	SNP	60995538	60995538	10876	19	G	A	A	40	40	NLRP11	A	1	1
ZNF470	388566	broad.mit.edu	36	19	61781279	61781279	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61781279G>T	uc002qnl.2	+	c.1670G>T	c.(1669-1671)AGA>ATA	p.R557I	ZNF470_uc010etn.1_Intron	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	557	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)										0.253125	195.935367	213.644911	81	239	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61781279	61781279	18523	19	G	T	T	33	33	ZNF470	T	3	3
UBE2M	9040	broad.mit.edu	36	19	63759371	63759371	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63759371G>C	uc002qtl.2	-	c.449C>G	c.(448-450)GCA>GGA	p.A150G	CHMP2A_uc002qti.1_5'Flank|CHMP2A_uc002qtj.1_5'Flank|CHMP2A_uc002qtk.1_5'Flank	NM_003969	NP_003960	P61081	UBC12_HUMAN	ubiquitin-conjugating enzyme E2M	150					post-translational protein modification|protein neddylation		ATP binding|NEDD8 ligase activity|protein binding|ribosomal S6-glutamic acid ligase activity|ubiquitin-protein ligase activity			ovary(1)|pancreas(1)	2		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)										0.625	9.257135	9.36288	5	3	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63759371	63759371	17422	19	G	C	C	46	46	UBE2M	C	3	3
INSR	3643	broad.mit.edu	36	19	7121629	7121629	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7121629T>G	uc002mgd.1	-	c.1402A>C	c.(1402-1404)AAG>CAG	p.K468Q	INSR_uc002mge.1_Missense_Mutation_p.K468Q|INSR_uc002mgf.2_Missense_Mutation_p.K468Q	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	468					activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of gene-specific transcription|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)					649				0.170732	6.490525	10.71574	7	34	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7121629	7121629	8074	19	T	G	G	63	63	INSR	G	4	4
S1PR1	1901	broad.mit.edu	36	1	101477908	101477908	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:101477908C>T	uc001dud.2	+	c.780C>T	c.(778-780)ATC>ATT	p.I260I	S1PR1_uc009weg.1_Silent_p.I260I	NM_001400	NP_001391	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	260	Helical; Name=6; (By similarity).				cell adhesion	integral to membrane	lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)	2														0.375	6.620252	6.730785	3	5	CC		KEEP	---	---	---	---	capture			Silent	SNP	101477908	101477908	14273	1	C	T	T	31	31	S1PR1	T	1	1
CASZ1	54897	broad.mit.edu	36	1	10627574	10627577	+	Missense_Mutation	ONP	CTCC	TCTT	TCTT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10627574_10627577CTCC>TCTT	uc001aro.1	-	c.3852_3855GGAG>AAGA	c.(3850-3855)GAGGAG>GAAAGA	p.E1285R		NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	1285					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)										0.8	7.706792	8.098923	4	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	ONP	10627574	10627577	2804	1	CTCC	TCTT	TCTT	20	20	CASZ1	TCTT	2	2
MTOR	2475	broad.mit.edu	36	1	11107161	11107161	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11107161A>T	uc001asd.1	-	c.6643T>A	c.(6643-6645)TCT>ACT	p.S2215T	MTOR_uc001asc.1_Missense_Mutation_p.S420T	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2215	PI3K/PI4K.		S -> Y (in a colorectal adenocarcinoma sample; somatic mutation).		cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|ovary(4)|kidney(3)|large_intestine(2)|skin(2)|lung(1)	19										1389				0.87931	163.530211	171.698334	51	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11107161	11107161	10347	1	A	T	T	12	12	MTOR	T	4	4
C1orf103	55791	broad.mit.edu	36	1	111296871	111296871	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:111296871C>T	uc001eaa.1	-	c.158G>A	c.(157-159)GGA>GAA	p.G53E	C1orf103_uc001dzz.1_5'UTR|C1orf103_uc001eab.1_Intron|C1orf103_uc001eac.1_Intron	NM_018372	NP_060842	Q5T3J3	CA103_HUMAN	receptor-interacting factor 1 isoform 1	53							protein binding				0		all_cancers(81;1.02e-05)|all_epithelial(167;1.87e-05)|all_lung(203;0.000234)|Lung NSC(277;0.000451)		Lung(183;0.0155)|Colorectal(144;0.0314)|all cancers(265;0.082)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0891)|COAD - Colon adenocarcinoma(174;0.134)										0.203125	12.906963	18.195565	13	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111296871	111296871	2044	1	C	T	T	30	30	C1orf103	T	2	2
MOV10	4343	broad.mit.edu	36	1	113033156	113033156	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:113033156A>G	uc001eck.1	+	c.214A>G	c.(214-216)ACT>GCT	p.T72A	MOV10_uc001ecl.1_Missense_Mutation_p.T72A|MOV10_uc001ecm.1_Missense_Mutation_p.T12A|MOV10_uc001ecn.1_Missense_Mutation_p.T72A|MOV10_uc009wgj.1_Missense_Mutation_p.T12A|MOV10_uc001eco.1_Missense_Mutation_p.T72A	NM_020963	NP_066014	Q9HCE1	MOV10_HUMAN	Mov10, Moloney leukemia virus 10, homolog	72					mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)	4	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)										0.3125	7.053002	7.563556	5	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113033156	113033156	10110	1	A	G	G	10	10	MOV10	G	4	4
SYT6	148281	broad.mit.edu	36	1	114441875	114441875	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114441875T>G	uc001eev.1	-	c.1257A>C	c.(1255-1257)AAA>AAC	p.K419N	SYT6_uc001eeu.1_Missense_Mutation_p.K64N	NM_205848	NP_995320	Q5T7P8	SYT6_HUMAN	synaptotagmin VI	504	Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.244898	15.958957	18.885318	12	37	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114441875	114441875	15999	1	T	G	G	56	56	SYT6	G	4	4
PTCHD2	57540	broad.mit.edu	36	1	11502066	11502066	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11502066C>A	uc001ash.2	+	c.1957C>A	c.(1957-1959)CAG>AAG	p.Q653K	PTCHD2_uc001asi.1_Missense_Mutation_p.Q653K	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	653	Cytoplasmic (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)										1	9.648397	9.58678	4	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11502066	11502066	13187	1	C	A	A	25	25	PTCHD2	A	3	3
VPS13D	55187	broad.mit.edu	36	1	12345754	12345754	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:12345754G>C	uc001atv.1	+	c.10312G>C	c.(10312-10314)GGT>CGT	p.G3438R	VPS13D_uc001atw.1_Missense_Mutation_p.G3413R|VPS13D_uc001atx.1_Missense_Mutation_p.G2625R	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3437					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)										0.185185	7.357312	9.870092	5	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12345754	12345754	17759	1	G	C	C	47	47	VPS13D	C	3	3
PRDM2	7799	broad.mit.edu	36	1	13980848	13980849	+	Missense_Mutation	DNP	AT	GA	GA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:13980848_13980849AT>GA	uc001avi.1	+	c.3971_3972AT>GA	c.(3970-3972)AAT>AGA	p.N1324R	PRDM2_uc001avg.1_Intron|PRDM2_uc001avh.1_Missense_Mutation_p.N1324R|PRDM2_uc001avj.1_Intron|PRDM2_uc001avk.1_Missense_Mutation_p.N1123R|PRDM2_uc009voe.1_Intron|PRDM2_uc009vof.1_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	1324					regulation of transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)										0.470588	17.891028	17.904187	8	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	13980848	13980849	12900	1	AT	GA	GA	4	4	PRDM2	GA	4	4
NUDT17	200035	broad.mit.edu	36	1	144298046	144298046	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:144298046G>T	uc001eoe.1	-	c.887C>A	c.(886-888)ACA>AAA	p.T296K		NM_001012758	NP_001012776	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety	296							hydrolase activity|metal ion binding				0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.5	9.159178	9.159178	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144298046	144298046	11139	1	G	T	T	48	48	NUDT17	T	3	3
PDZK1	5174	broad.mit.edu	36	1	144458592	144458593	+	Missense_Mutation	DNP	CA	TG	TG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:144458592_144458593CA>TG	uc001eon.1	+	c.192_193CA>TG	c.(190-195)GACAAA>GATGAA	p.K65E	PDZK1_uc001eoo.1_Missense_Mutation_p.K65E	NM_002614	NP_002605	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	65	PDZ 1.				carnitine transport|cell proliferation|drug transport|positive regulation of ion transmembrane transport	brush border membrane|cytoplasm	PDZ domain binding|transporter activity				0	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)											0.25	8.86184	10.001743	5	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	144458592	144458593	12128	1	CA	TG	TG	17	17	PDZK1	TG	2	2
FLG	2312	broad.mit.edu	36	1	150545480	150545480	+	Missense_Mutation	SNP	T	C	C	rs11582087	unknown	TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150545480T>C	uc001ezu.1	-	c.8506A>G	c.(8506-8508)AGT>GGT	p.S2836G		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2836	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.228261	26.196112	32.474797	21	71	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150545480	150545480	6160	1	T	C	C	56	56	FLG	C	4	4
CRTC2	200186	broad.mit.edu	36	1	152187398	152187398	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152187398A>C	uc009woo.1	-	c.1893T>G	c.(1891-1893)ATT>ATG	p.I631M	DENND4B_uc001fdd.1_5'Flank|CRTC2_uc001fde.2_Non-coding_Transcript|CRTC2_uc001fdf.2_Missense_Mutation_p.I167M	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	631					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)											0.428571	6.522328	6.553584	3	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152187398	152187398	4039	1	A	C	C	5	5	CRTC2	C	4	4
DCST2	127579	broad.mit.edu	36	1	153270672	153270673	+	Splice_Site_DNP	DNP	AC	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153270672_153270673AC>CT	uc001fgm.1	-	c.e4_splice_site			DCST2_uc009wpb.1_Splice_Site_DNP|DCST1_uc001fgn.1_5'Flank	NM_144622	NP_653223			DC-STAMP domain containing 2							integral to membrane				ovary(2)|central_nervous_system(1)	3	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)											0.217391	9.366593	12.834596	10	36	AA		KEEP	---	---	---	---	capture			Splice_Site_DNP	DNP	153270672	153270673	4474	1	AC	CT	CT	6	6	DCST2	CT	5	4
RXFP4	339403	broad.mit.edu	36	1	154178429	154178430	+	Missense_Mutation	DNP	CA	AC	AC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154178429_154178430CA>AC	uc001fmp.1	+	c.305_306CA>AC	c.(304-306)GCA>GAC	p.A102D		NM_181885	NP_871001	Q8TDU9	RL3R2_HUMAN	relaxin 3 receptor 2	102	Extracellular (Potential).					integral to membrane|plasma membrane	angiotensin type II receptor activity				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)													0.25	7.014865	8.402993	6	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	154178429	154178430	14242	1	CA	AC	AC	25	25	RXFP4	AC	3	3
CCT3	7203	broad.mit.edu	36	1	154547491	154547491	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154547491T>C	uc001fol.1	-	c.1275A>G	c.(1273-1275)AAA>AAG	p.K425K	CCT3_uc001fom.1_Silent_p.K424K|CCT3_uc001fon.1_Silent_p.K387K	NM_005998	NP_005989	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 isoform a	425					'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)	1	Hepatocellular(266;0.158)													0.245283	15.006938	18.183937	13	40	TT		KEEP	---	---	---	---	capture			Silent	SNP	154547491	154547491	3081	1	T	C	C	52	52	CCT3	C	4	4
AGMAT	79814	broad.mit.edu	36	1	15773914	15773914	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:15773914T>A	uc001awv.1	-	c.910A>T	c.(910-912)ATC>TTC	p.I304F	DNAJC16_uc001awu.2_Non-coding_Transcript	NM_024758	NP_079034	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	304					putrescine biosynthetic process|spermidine biosynthetic process	mitochondrion	agmatinase activity|metal ion binding				0		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		NSCLC(126;1678 1780 25805 43508 49531)								0.230769	7.81856	9.566652	6	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15773914	15773914	388	1	T	A	A	50	50	AGMAT	A	4	4
OLFML2B	25903	broad.mit.edu	36	1	160234675	160234675	+	Silent	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:160234675G>C	uc001gbu.1	-	c.1038C>G	c.(1036-1038)ACC>ACG	p.T346T		NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	346											0	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)											0.3	8.427681	9.152754	6	14	GG		KEEP	---	---	---	---	capture			Silent	SNP	160234675	160234675	11263	1	G	C	C	43	43	OLFML2B	C	3	3
UHMK1	127933	broad.mit.edu	36	1	160734417	160734417	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:160734417G>T	uc001gcc.1	+	c.3G>T	c.(1-3)ATG>ATT	p.M1I	UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Missense_Mutation_p.M1I	NM_175866	NP_787062	Q8TAS1	UHMK1_HUMAN	kinase interacting stathmin	1					cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)							266				0.8	8.593679	9.005762	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	160734417	160734417	17524	1	G	T	T	47	47	UHMK1	T	3	3
SPEN	23013	broad.mit.edu	36	1	16134681	16134681	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16134681C>T	uc001axk.1	+	c.9359C>T	c.(9358-9360)CCT>CTT	p.P3120L		NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	3120					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)						551				0.6	19.252736	19.341289	6	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16134681	16134681	15550	1	C	T	T	24	24	SPEN	T	2	2
ARHGEF19	128272	broad.mit.edu	36	1	16407109	16407109	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16407109C>T	uc001ayc.1	-	c.611G>A	c.(610-612)CGG>CAG	p.R204Q	ARHGEF19_uc009voo.1_5'Flank|ARHGEF19_uc001ayb.1_5'Flank	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	204					regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)										0.75	6.525627	6.745525	3	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16407109	16407109	916	1	C	T	T	23	23	ARHGEF19	T	1	1
ARHGEF19	128272	broad.mit.edu	36	1	16407113	16407113	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16407113T>C	uc001ayc.1	-	c.607A>G	c.(607-609)ACC>GCC	p.T203A	ARHGEF19_uc009voo.1_5'Flank|ARHGEF19_uc001ayb.1_5'Flank	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	203					regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)										0.75	6.835263	7.048121	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16407113	16407113	916	1	T	C	C	58	58	ARHGEF19	C	4	4
ARHGEF19	128272	broad.mit.edu	36	1	16407115	16407115	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16407115A>G	uc001ayc.1	-	c.605T>C	c.(604-606)ATG>ACG	p.M202T	ARHGEF19_uc009voo.1_5'Flank|ARHGEF19_uc001ayb.1_5'Flank	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	202					regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)										0.75	7.525682	7.750241	3	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16407115	16407115	916	1	A	G	G	8	8	ARHGEF19	G	4	4
NADK	65220	broad.mit.edu	36	1	1675996	1675996	+	Silent	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1675996C>A	uc001aie.1	-	c.1125G>T	c.(1123-1125)GGG>GGT	p.G375G	NADK_uc009vkw.1_Silent_p.G230G|NADK_uc001aic.1_Silent_p.G230G|NADK_uc001aid.2_Silent_p.G230G|NADK_uc009vkx.1_Silent_p.G108G	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	230					ATP metabolic process|NAD metabolic process|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|NAD+ kinase activity|protein binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)										0.396755	689.776417	696.134061	269	409	CC		KEEP	---	---	---	---	capture			Silent	SNP	1675996	1675996	10533	1	C	A	A	30	30	NADK	A	3	3
PADI4	23569	broad.mit.edu	36	1	17530106	17530106	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:17530106G>A	uc001baj.1	+	c.148G>A	c.(148-150)GTG>ATG	p.V50M	PADI4_uc009vpc.1_Missense_Mutation_p.V50M	NM_012387	NP_036519	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	50					chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)									0.454545	15.174948	15.194532	5	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17530106	17530106	11796	1	G	A	A	40	40	PADI4	A	1	1
TDRD5	163589	broad.mit.edu	36	1	177926695	177926695	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:177926695A>G	uc001gng.1	+	c.3102A>G	c.(3100-3102)GAA>GAG	p.E1034E	TDRD5_uc001gnf.1_Silent_p.E980E|TDRD5_uc001gnh.1_Silent_p.E535E	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	980					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.588235	19.420979	19.532215	10	7	AA		KEEP	---	---	---	---	capture			Silent	SNP	177926695	177926695	16260	1	A	G	G	3	3	TDRD5	G	4	4
ARHGEF10L	55160	broad.mit.edu	36	1	17812173	17812173	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:17812173T>C	uc001ban.1	+	c.643T>C	c.(643-645)TAC>CAC	p.Y215H	ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.1_Intron|ARHGEF10L_uc001bap.1_Intron|ARHGEF10L_uc001baq.1_5'Flank	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)	215					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)										0.5	13.409158	13.409158	7	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17812173	17812173	909	1	T	C	C	49	49	ARHGEF10L	C	4	4
C1orf26	54823	broad.mit.edu	36	1	183507077	183507077	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:183507077G>A	uc001grg.2	+	c.e17_splice_site			C1orf26_uc001grh.2_Splice_Site_SNP	NM_001105518	NP_060143			hypothetical protein LOC54823												0														0.5	6.417842	6.417842	3	3	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	183507077	183507077	2109	1	G	A	A	35	35	C1orf26	A	5	2
HMCN1	83872	broad.mit.edu	36	1	183970794	183970794	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:183970794A>G	uc001grq.1	+	c.260A>G	c.(259-261)CAT>CGT	p.H87R		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	87	VWFA.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.428571	8.522236	8.553674	3	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	183970794	183970794	7511	1	A	G	G	8	8	HMCN1	G	4	4
HMCN1	83872	broad.mit.edu	36	1	184373397	184373397	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184373397G>A	uc001grq.1	+	c.13727G>A	c.(13726-13728)CGA>CAA	p.R4576Q	HMCN1_uc001grs.1_Missense_Mutation_p.R145Q	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	4576	TSP type-1 1.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.72973	180.155777	183.674795	54	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184373397	184373397	7511	1	G	A	A	37	37	HMCN1	A	1	1
ASPM	259266	broad.mit.edu	36	1	195339907	195339907	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:195339907C>T	uc001gtu.1	-	c.5097G>A	c.(5095-5097)TTG>TTA	p.L1699L	ASPM_uc001gtv.1_Intron|ASPM_uc001gtw.2_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1699					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.333333	8.819714	9.274729	6	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	195339907	195339907	1075	1	C	T	T	25	25	ASPM	T	2	2
CACNA1S	779	broad.mit.edu	36	1	199319026	199319027	+	Missense_Mutation	DNP	TC	GT	GT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:199319026_199319027TC>GT	uc001gvv.1	-	c.1279_1280GA>AC	c.(1279-1281)GAC>ACC	p.D427T		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	427	II.|Cytoplasmic (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.159574	11.663793	22.082133	15	79	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	199319026	199319027	2663	1	TC	GT	GT	58	58	CACNA1S	GT	4	4
SLC26A9	115019	broad.mit.edu	36	1	204158927	204158927	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:204158927T>G	uc001hdp.1	-	c.1679A>C	c.(1678-1680)AAA>ACA	p.K560T	SLC26A9_uc001hdo.1_Missense_Mutation_p.K228T|SLC26A9_uc001hdq.1_Missense_Mutation_p.K560T	NM_134325	NP_443166	Q7LBE3	S26A9_HUMAN	solute carrier family 26, member 9 isoform b	560	STAS.					integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)	1	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)											0.454545	10.566169	10.586417	5	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	204158927	204158927	15021	1	T	G	G	64	64	SLC26A9	G	4	4
FAIM3	9214	broad.mit.edu	36	1	205152981	205152981	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205152981T>C	uc001hey.1	-	c.403A>G	c.(403-405)ATG>GTG	p.M135V		NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a	135	Extracellular (Potential).				anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)											OREG0014185	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.131222	51.145549	80.341458	29	192	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205152981	205152981	5574	1	T	C	C	52	52	FAIM3	C	4	4
TMEM206	55248	broad.mit.edu	36	1	210627030	210627030	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:210627030A>C	uc001hjc.2	-	c.169T>G	c.(169-171)TTC>GTC	p.F57V		NM_018252	NP_060722	Q9H813	TM206_HUMAN	transmembrane protein 206	57	Cytoplasmic (Potential).					integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)										0.454545	10.866038	10.886438	5	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	210627030	210627030	16666	1	A	C	C	3	3	TMEM206	C	4	4
USH2A	7399	broad.mit.edu	36	1	214565506	214565506	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:214565506G>T	uc001hku.1	-	c.907C>A	c.(907-909)CGT>AGT	p.R303S	USH2A_uc001hkv.1_Missense_Mutation_p.R303S	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	303	Laminin N-terminal.|Extracellular (Potential).		R -> C (in USH2A).|R -> S (in USH2A).		maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.444444	6.381406	6.407754	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	214565506	214565506	17598	1	G	T	T	39	39	USH2A	T	3	3
WNT3A	89780	broad.mit.edu	36	1	226313394	226313395	+	Missense_Mutation	DNP	CC	GG	GG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:226313394_226313395CC>GG	uc001hrp.1	+	c.664_665CC>GG	c.(664-666)CCC>GGC	p.P222G	WNT3A_uc001hrq.1_Missense_Mutation_p.P222G	NM_033131	NP_149122	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family,	222					axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of heart induction by canonical Wnt receptor signaling pathway|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)												0.857143	12.341986	12.694201	6	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	226313394	226313395	17963	1	CC	GG	GG	18	18	WNT3A	GG	3	3
SIPA1L2	57568	broad.mit.edu	36	1	230647983	230647983	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:230647983G>T	uc001hvg.1	-	c.3268C>A	c.(3268-3270)CTG>ATG	p.L1090M	SIPA1L2_uc001hvf.1_Missense_Mutation_p.L164M	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1090					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)												0.8	16.892938	17.721347	8	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	230647983	230647983	14825	1	G	T	T	34	34	SIPA1L2	T	3	3
MTR	4548	broad.mit.edu	36	1	235038674	235038674	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235038674C>T	uc001hyi.2	+	c.387C>T	c.(385-387)GCC>GCT	p.A129A	MTR_uc009xgj.1_5'Flank	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	129	Hcy-binding.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)									0.945205	1247.603621	1287.431859	345	20	CC		KEEP	---	---	---	---	capture			Silent	SNP	235038674	235038674	10351	1	C	T	T	23	23	MTR	T	1	1
ZP4	57829	broad.mit.edu	36	1	236115151	236115151	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:236115151G>A	uc001hym.1	-	c.1248C>T	c.(1246-1248)CGC>CGT	p.R416R		NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	416	ZP.|Extracellular (Potential).				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(1)	1	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			NSCLC(166;160 2029 11600 18754 19936)								0.333333	9.123276	9.344044	3	6	GG		KEEP	---	---	---	---	capture			Silent	SNP	236115151	236115151	18822	1	G	A	A	34	34	ZP4	A	2	2
CHRM3	1131	broad.mit.edu	36	1	238138554	238138556	+	Missense_Mutation	TNP	GAG	AGA	AGA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:238138554_238138556GAG>AGA	uc001hyp.1	+	c.1180_1182GAG>AGA	c.(1180-1182)GAG>AGA	p.E394R	CHRM3_uc009xgk.1_Missense_Mutation_p.E394R	NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	394	Cytoplasmic (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)									0.909091	22.750505	24.468711	10	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	238138554	238138556	3512	1	GAG	AGA	AGA	41	41	CHRM3	AGA	2	2
MYOM3	127294	broad.mit.edu	36	1	24289141	24289141	+	Splice_Site_SNP	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24289141C>G	uc001bin.2	-	c.e13_splice_site			MYOM3_uc001bim.2_Splice_Site_SNP|MYOM3_uc001bio.2_Splice_Site_SNP|MYOM3_uc001bip.1_Splice_Site_SNP	NM_152372	NP_689585			myomesin family, member 3											ovary(1)	1		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)										0.2	11.76573	13.855108	5	20	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	24289141	24289141	10488	1	C	G	G	18	18	MYOM3	G	5	3
PDIK1L	149420	broad.mit.edu	36	1	26321474	26321474	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:26321474C>T	uc001blj.2	+	c.845C>T	c.(844-846)GCA>GTA	p.A282V	PDIK1L_uc009vsb.1_Missense_Mutation_p.A282V	NM_152835	NP_690048	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	282	Protein kinase.				protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity				0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)						46				0.204082	9.902311	13.920784	10	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26321474	26321474	12094	1	C	T	T	25	25	PDIK1L	T	2	2
GPR3	2827	broad.mit.edu	36	1	27592978	27592978	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:27592978C>A	uc001bod.1	+	c.89C>A	c.(88-90)CCC>CAC	p.P30H	GPR3_uc009vsx.1_Missense_Mutation_p.P30H	NM_005281	NP_005272	P46089	GPR3_HUMAN	G protein-coupled receptor 3	30	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to plasma membrane					0		Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.81e-26)|Colorectal(126;1.24e-08)|KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;4.45e-06)|Lung(427;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|LUSC - Lung squamous cell carcinoma(448;0.008)|READ - Rectum adenocarcinoma(331;0.0419)										0.6	6.320061	6.362849	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27592978	27592978	6961	1	C	A	A	22	22	GPR3	A	3	3
TXLNA	200081	broad.mit.edu	36	1	32433098	32433098	+	Silent	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:32433098C>A	uc001bui.1	+	c.1356C>A	c.(1354-1356)GTC>GTA	p.V452V	TXLNA_uc001buj.1_Silent_p.V452V	NM_175852	NP_787048	P40222	TXLNA_HUMAN	taxilin	452	Potential.				cell proliferation|exocytosis	cytoplasm|extracellular region	cytokine activity|high molecular weight B cell growth factor receptor binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)												0.142857	9.906361	15.921031	7	42	CC		KEEP	---	---	---	---	capture			Silent	SNP	32433098	32433098	17343	1	C	A	A	30	30	TXLNA	A	3	3
CSMD2	114784	broad.mit.edu	36	1	33931175	33931175	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33931175A>G	uc001bxm.1	-	c.3994T>C	c.(3994-3996)TAT>CAT	p.Y1332H	CSMD2_uc001bxn.1_Missense_Mutation_p.Y1292H|CSMD2_uc001bxo.1_Missense_Mutation_p.Y205H	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1292	CUB 8.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.166667	8.992573	11.51445	4	20	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33931175	33931175	4086	1	A	G	G	15	15	CSMD2	G	4	4
DFFB	1677	broad.mit.edu	36	1	3774438	3774438	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3774438A>C	uc001alc.1	+	c.471A>C	c.(469-471)AGA>AGC	p.R157S	DFFB_uc001ale.1_Non-coding_Transcript|DFFB_uc009vlp.1_Non-coding_Transcript|DFFB_uc001alb.1_Non-coding_Transcript|DFFB_uc009vlq.1_Non-coding_Transcript|DFFB_uc009vlr.1_Missense_Mutation_p.R108S|DFFB_uc001ald.1_Missense_Mutation_p.R93S	NM_004402	NP_004393	O76075	DFFB_HUMAN	DNA fragmentation factor, 40 kD, beta	157					apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)						1253				1	10.65736	10.596175	4	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3774438	3774438	4632	1	A	C	C	12	12	DFFB	C	4	4
DFFB	1677	broad.mit.edu	36	1	3774440	3774440	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3774440A>T	uc001alc.1	+	c.473A>T	c.(472-474)TAC>TTC	p.Y158F	DFFB_uc001ale.1_Non-coding_Transcript|DFFB_uc009vlp.1_Non-coding_Transcript|DFFB_uc001alb.1_Non-coding_Transcript|DFFB_uc009vlq.1_Non-coding_Transcript|DFFB_uc009vlr.1_Missense_Mutation_p.Y109F|DFFB_uc001ald.1_Missense_Mutation_p.Y94F	NM_004402	NP_004393	O76075	DFFB_HUMAN	DNA fragmentation factor, 40 kD, beta	158					apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)						1253				1	7.738133	7.619315	3	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3774440	3774440	4632	1	A	T	T	14	14	DFFB	T	4	4
ZNF684	127396	broad.mit.edu	36	1	40779961	40779961	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:40779961G>T	uc001cft.1	+	c.230G>T	c.(229-231)AGC>ATC	p.S77I		NM_152373	NP_689586	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	77	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)											0.111111	6.883612	16.304524	7	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40779961	40779961	18686	1	G	T	T	34	34	ZNF684	T	3	3
PLK3	1263	broad.mit.edu	36	1	45043808	45043808	+	Silent	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:45043808T>G	uc001cmn.1	+	c.1812T>G	c.(1810-1812)ACT>ACG	p.T604T	PLK3_uc001cmo.1_Non-coding_Transcript	NM_004073	NP_004064	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	604	POLO box 2.				protein phosphorylation	membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)									186				0.263158	7.95962	8.930069	5	14	TT		KEEP	---	---	---	---	capture			Silent	SNP	45043808	45043808	12523	1	T	G	G	56	56	PLK3	G	4	4
RNF11	26994	broad.mit.edu	36	1	51475097	51475097	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:51475097C>T	uc001csi.2	+	c.81C>T	c.(79-81)GGC>GGT	p.G27G		NM_014372	NP_055187	Q9Y3C5	RNF11_HUMAN	ring finger protein 11	27					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	DNA binding|protein binding|zinc ion binding				0														0.3	7.022677	7.379364	3	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	51475097	51475097	13901	1	C	T	T	27	27	RNF11	T	1	1
GLIS1	148979	broad.mit.edu	36	1	53832862	53832863	+	Missense_Mutation	DNP	AC	TT	TT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53832862_53832863AC>TT	uc001cvr.1	-	c.301_302GT>AA	c.(301-303)GTA>AAA	p.V101K		NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1	101					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|specific RNA polymerase II transcription factor activity|zinc ion binding				0														1	9.952446	9.891026	4	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	53832862	53832863	6713	1	AC	TT	TT	14	14	GLIS1	TT	4	4
DHCR24	1718	broad.mit.edu	36	1	55109674	55109674	+	Silent	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:55109674G>T	uc001cyc.1	-	c.813C>A	c.(811-813)CTC>CTA	p.L271L		NM_014762	NP_055577	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase precursor	271					anti-apoptosis|apoptosis|cell cycle arrest|cholesterol biosynthetic process|negative regulation of caspase activity|neuroprotection|oxidation-reduction process|response to oxidative stress|skin development	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus	delta24-sterol reductase activity|enzyme binding|flavin adenine dinucleotide binding|peptide antigen binding			pancreas(1)	1						Pancreas(39;516 1021 24601 30715 32780)								0.933333	62.690631	66.455801	28	2	GG		KEEP	---	---	---	---	capture			Silent	SNP	55109674	55109674	4655	1	G	T	T	33	33	DHCR24	T	3	3
DHCR24	1718	broad.mit.edu	36	1	55109676	55109678	+	Missense_Mutation	TNP	GCA	TAT	TAT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:55109676_55109678GCA>TAT	uc001cyc.1	-	c.809_811TGC>ATA	c.(808-813)CTGCTC>CATATC	p.270_271LL>HI		NM_014762	NP_055577	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase precursor	270_271					anti-apoptosis|apoptosis|cell cycle arrest|cholesterol biosynthetic process|negative regulation of caspase activity|neuroprotection|oxidation-reduction process|response to oxidative stress|skin development	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus	delta24-sterol reductase activity|enzyme binding|flavin adenine dinucleotide binding|peptide antigen binding			pancreas(1)	1						Pancreas(39;516 1021 24601 30715 32780)								0.954545	47.142637	49.551366	21	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	55109676	55109678	4655	1	GCA	TAT	TAT	34	34	DHCR24	TAT	3	3
C8B	732	broad.mit.edu	36	1	57171643	57171643	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:57171643G>A	uc001cyp.1	-	c.1505C>T	c.(1504-1506)TCC>TTC	p.S502F		NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	502	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4														0.696429	124.03347	125.963685	39	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57171643	57171643	2526	1	G	A	A	41	41	C8B	A	2	2
SH3GLB1	51100	broad.mit.edu	36	1	86980604	86980604	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:86980604C>A	uc001dly.1	+	c.974C>A	c.(973-975)TCC>TAC	p.S325Y	SH3GLB1_uc001dlw.1_Missense_Mutation_p.S296Y|SH3GLB1_uc001dlx.1_Missense_Mutation_p.S317Y|SH3GLB1_uc001dlz.1_Missense_Mutation_p.S196Y	NM_016009	NP_057093	Q9Y371	SHLB1_HUMAN	SH3-containing protein SH3GLB1	296					anti-apoptosis|filopodium assembly|signal transduction	Golgi membrane|mitochondrial outer membrane	cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding				0		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)										0.150376	24.799295	40.433096	20	113	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86980604	86980604	14745	1	C	A	A	30	30	SH3GLB1	A	3	3
GFI1	2672	broad.mit.edu	36	1	92719145	92719145	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:92719145A>G	uc001dou.2	-	c.387T>C	c.(385-387)GGT>GGC	p.G129G	GFI1_uc001dov.2_Silent_p.G129G|GFI1_uc001dow.2_Silent_p.G129G	NM_001127215	NP_001120687	Q99684	GFI1_HUMAN	growth factor independent 1	129					negative regulation of calcidiol 1-monooxygenase activity|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of vitamin D biosynthetic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|transcription, DNA-dependent|viral reproduction	nucleus	promoter binding|protein binding|zinc ion binding			large_intestine(1)	1		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)										0.8	8.097872	8.503213	4	1	AA		KEEP	---	---	---	---	capture			Silent	SNP	92719145	92719145	6607	1	A	G	G	2	2	GFI1	G	4	4
ABCA4	24	broad.mit.edu	36	1	94269188	94269188	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:94269188G>T	uc001dqh.1	-	c.4205C>A	c.(4204-4206)GCT>GAT	p.A1402D		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1402	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|central_nervous_system(2)|breast(1)	7		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)										0.6	11.935533	12.020342	6	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94269188	94269188	35	1	G	T	T	34	34	ABCA4	T	3	3
SNPH	9751	broad.mit.edu	36	20	1229311	1229311	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:1229311C>T	uc002wet.1	+	c.396C>T	c.(394-396)CAC>CAT	p.H132H	SNPH_uc002wes.1_Silent_p.H88H	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin	88	Potential.				synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2														0.962963	54.321962	56.544976	26	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	1229311	1229311	15350	20	C	T	T	18	18	SNPH	T	2	2
SNPH	9751	broad.mit.edu	36	20	1229313	1229313	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:1229313T>C	uc002wet.1	+	c.398T>C	c.(397-399)CTG>CCG	p.L133P	SNPH_uc002wes.1_Missense_Mutation_p.L89P	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin	89	Potential.				synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2														0.875	13.519793	14.584832	7	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1229313	1229313	15350	20	T	C	C	55	55	SNPH	C	4	4
SIRPD	128646	broad.mit.edu	36	20	1480543	1480543	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:1480543C>T	uc002wfi.1	-	c.215G>A	c.(214-216)CGG>CAG	p.R72Q		NM_178460	NP_848555	Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	72	Ig-like V-type.					extracellular region				ovary(1)|kidney(1)|skin(1)	3														0.411765	20.819174	20.935268	7	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1480543	1480543	14830	20	C	T	T	23	23	SIRPD	T	1	1
NINL	22981	broad.mit.edu	36	20	25420142	25420142	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:25420142G>A	uc002wux.1	-	c.1330C>T	c.(1330-1332)CGG>TGG	p.R444W	NINL_uc010gdn.1_Missense_Mutation_p.R444W|NINL_uc010gdo.1_Missense_Mutation_p.R227W	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	444					G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.148148	8.488866	11.691464	4	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25420142	25420142	10821	20	G	A	A	39	39	NINL	A	1	1
SOX12	6666	broad.mit.edu	36	20	255401	255401	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:255401C>G	uc002wdh.1	+	c.833C>G	c.(832-834)CCT>CGT	p.P278R		NM_006943	NP_008874	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	278					cell fate commitment|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|RNA polymerase II transcription factor activity				0		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)											0.444444	8.490994	8.516032	4	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	255401	255401	15443	20	C	G	G	24	24	SOX12	G	3	3
ASXL1	171023	broad.mit.edu	36	20	30488352	30488352	+	Silent	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30488352C>G	uc002wxs.1	+	c.4176C>G	c.(4174-4176)CCC>CCG	p.P1392P	ASXL1_uc010gea.1_Silent_p.P1392P|ASXL1_uc010geb.1_Silent_p.P1283P	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1	1392					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(131)|large_intestine(6)|central_nervous_system(2)|ovary(1)	140														0.45	19.262539	19.306915	9	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	30488352	30488352	1085	20	C	G	G	22	22	ASXL1	G	3	3
SPAG4	6676	broad.mit.edu	36	20	33672067	33672067	+	Silent	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33672067C>G	uc002xdb.1	+	c.1125C>G	c.(1123-1125)ACC>ACG	p.T375T		NM_003116	NP_003107	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	375	SUN.				spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity				0	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)											0.888889	16.642912	17.91288	8	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	33672067	33672067	15483	20	C	G	G	24	24	SPAG4	G	3	3
LPIN3	64900	broad.mit.edu	36	20	39414725	39414725	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39414725C>A	uc010ggh.1	+	c.1432C>A	c.(1432-1434)CCA>ACA	p.P478T	LPIN3_uc002xjx.1_Missense_Mutation_p.P477T	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	477					fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)												1	7.836779	7.717831	3	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39414725	39414725	9293	20	C	A	A	22	22	LPIN3	A	3	3
GDAP1L1	78997	broad.mit.edu	36	20	42326614	42326614	+	Splice_Site_SNP	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:42326614G>C	uc002xlq.1	+	c.e5_splice_site			GDAP1L1_uc002xlp.1_Missense_Mutation_p.G254A	NM_024034	NP_076939			ganglioside-induced differentiation-associated											large_intestine(1)	1		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)											0.171429	8.944094	16.139172	12	58	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	42326614	42326614	6575	20	G	C	C	44	44	GDAP1L1	C	5	3
NEURL2	140825	broad.mit.edu	36	20	43952790	43952790	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43952790A>G	uc002xqg.1	-	c.248T>C	c.(247-249)CTC>CCC	p.L83P	CTSA_uc002xqh.1_5'Flank|CTSA_uc002xqj.2_5'Flank|CTSA_uc002xqi.1_5'Flank|CTSA_uc002xqk.2_5'Flank	NM_080749	NP_542787	Q9BR09	NEUL2_HUMAN	neuralized-like protein 2	83	NHR.				intracellular signal transduction						0		Myeloproliferative disorder(115;0.0122)												0.9	19.759656	21.247928	9	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43952790	43952790	10746	20	A	G	G	11	11	NEURL2	G	4	4
SALL4	57167	broad.mit.edu	36	20	49840157	49840158	+	Missense_Mutation	DNP	CA	TG	TG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49840157_49840158CA>TG	uc002xwh.2	-	c.2271_2272TG>CA	c.(2269-2274)GATGGC>GACAGC	p.G758S	SALL4_uc010gii.1_Intron|SALL4_uc002xwi.2_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	758					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.466667	13.911368	13.926628	7	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	49840157	49840158	14293	20	CA	TG	TG	21	21	SALL4	TG	2	2
DOK5	55816	broad.mit.edu	36	20	52660455	52660456	+	Missense_Mutation	DNP	GT	TG	TG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:52660455_52660456GT>TG	uc002xwy.1	+	c.721_722GT>TG	c.(721-723)GTG>TGG	p.V241W	DOK5_uc010gin.1_Missense_Mutation_p.V133W|DOK5_uc002xwz.1_Missense_Mutation_p.V103W	NM_018431	NP_060901	Q9P104	DOK5_HUMAN	docking protein 5	241							insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)											0.3125	7.457737	7.965557	5	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	52660455	52660456	4884	20	GT	TG	TG	48	48	DOK5	TG	3	3
PCK1	5105	broad.mit.edu	36	20	55572716	55572717	+	Missense_Mutation	DNP	GA	TG	TG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:55572716_55572717GA>TG	uc002xyn.2	+	c.1047_1048GA>TG	c.(1045-1050)AAGACC>AATGCC	p.349_350KT>NA		NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	349_350					gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity				0	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)											0.241379	9.095558	10.881963	7	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	55572716	55572717	12001	20	GA	TG	TG	33	33	PCK1	TG	3	3
SS18L1	26039	broad.mit.edu	36	20	60181190	60181190	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60181190A>T	uc002ycb.1	+	c.974A>T	c.(973-975)CAG>CTG	p.Q325L	SS18L1_uc002ybz.1_Non-coding_Transcript|SS18L1_uc002yca.1_Non-coding_Transcript|SS18L1_uc002ycc.1_Non-coding_Transcript	NM_198935	NP_945173	O75177	CREST_HUMAN	SS18-like protein 1	325	Gln-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore	transcription activator activity			ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)							359				0.5	7.58863	7.58863	4	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60181190	60181190	15691	20	A	T	T	7	7	SS18L1	T	4	4
ARFGAP1	55738	broad.mit.edu	36	20	61378428	61378428	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61378428G>C	uc002yel.1	+	c.322G>C	c.(322-324)GCG>CCG	p.A108P	ARFGAP1_uc002yem.1_Missense_Mutation_p.A108P|ARFGAP1_uc002yen.1_Missense_Mutation_p.A108P	NM_175609	NP_783202	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating	108	Arf-GAP.				COPI coating of Golgi vesicle|protein transport|regulation of ARF GTPase activity|retrograde vesicle-mediated transport, Golgi to ER	cytosol|Golgi-associated vesicle membrane	ARF GTPase activator activity|zinc ion binding			pancreas(1)	1	all_cancers(38;1.59e-09)													0.666667	8.090164	8.234881	4	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61378428	61378428	860	20	G	C	C	38	38	ARFGAP1	C	3	3
CYYR1	116159	broad.mit.edu	36	21	26860544	26860545	+	Missense_Mutation	DNP	GA	TT	TT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:26860544_26860545GA>TT	uc002yme.2	-	c.87_88TC>AA	c.(85-90)GCTCAG>GCAAAG	p.Q30K	CYYR1_uc002ymd.1_Missense_Mutation_p.Q30K	NM_052954	NP_443186	Q96J86	CYYR1_HUMAN	cysteine and tyrosine-rich 1 protein precursor	30	Extracellular (Potential).					integral to membrane					0														0.333333	11.33439	11.782014	6	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	26860544	26860545	4376	21	GA	TT	TT	45	45	CYYR1	TT	3	3
ADAMTS1	9510	broad.mit.edu	36	21	27138477	27138477	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:27138477T>A	uc002ymf.1	-	c.668A>T	c.(667-669)GAG>GTG	p.E223V		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	223					integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)								OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.8	7.692503	8.098132	4	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27138477	27138477	256	21	T	A	A	54	54	ADAMTS1	A	4	4
ADAMTS5	11096	broad.mit.edu	36	21	27218390	27218390	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:27218390G>A	uc002ymg.1	-	c.2646C>T	c.(2644-2646)GGC>GGT	p.G882G		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	882	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						Esophageal Squamous(53;683 1080 10100 14424 45938)								0.217391	10.303652	13.725891	10	36	GG		KEEP	---	---	---	---	capture			Silent	SNP	27218390	27218390	270	21	G	A	A	42	42	ADAMTS5	A	2	2
SIM2	6493	broad.mit.edu	36	21	37025226	37025226	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37025226G>A	uc002yvr.1	+	c.754G>A	c.(754-756)GTG>ATG	p.V252M	SIM2_uc002yvq.1_Missense_Mutation_p.V252M	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	252	PAS 2.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1														0.5	6.350256	6.350254	2	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37025226	37025226	14819	21	G	A	A	44	44	SIM2	A	2	2
DYRK1A	1859	broad.mit.edu	36	21	37774959	37774959	+	Silent	SNP	C	T	T	rs1049773	unknown	TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37774959C>T	uc002ywk.1	+	c.477C>T	c.(475-477)TAC>TAT	p.Y159Y	DYRK1A_uc002ywh.1_Silent_p.Y121Y|DYRK1A_uc002ywi.1_Silent_p.Y159Y|DYRK1A_uc002ywj.1_Silent_p.Y150Y|DYRK1A_uc002ywm.1_Silent_p.Y159Y|DYRK1A_uc002ywl.1_Silent_p.Y159Y	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	159	Protein kinase.				nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(1)	1						Melanoma(114;464 1602 31203 43785 45765)				141				0.217391	11.162834	12.857265	5	18	CC		KEEP	---	---	---	---	capture			Silent	SNP	37774959	37774959	5040	21	C	T	T	19	19	DYRK1A	T	1	1
PRDM15	63977	broad.mit.edu	36	21	42094483	42094485	+	Missense_Mutation	TNP	TCT	GTG	GTG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:42094483_42094485TCT>GTG	uc002yzq.1	-	c.4508_4510AGA>CAC	c.(4507-4512)CAGATG>CCACTG	p.1503_1504QM>PL	PRDM15_uc002yzo.1_Missense_Mutation_p.1174_1175QM>PL|PRDM15_uc002yzp.1_Missense_Mutation_p.1194_1195QM>PL|PRDM15_uc002yzr.1_Missense_Mutation_p.1194_1195QM>PL	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	1503_1504					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.857143	14.159789	14.998711	6	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	42094483	42094485	12898	21	TCT	GTG	GTG	50	50	PRDM15	GTG	4	4
SLC37A1	54020	broad.mit.edu	36	21	42852257	42852258	+	Missense_Mutation	DNP	TT	CG	CG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:42852257_42852258TT>CG	uc002zbi.1	+	c.970_971TT>CG	c.(970-972)TTG>CGG	p.L324R	SLC37A1_uc002zbj.1_Missense_Mutation_p.L324R	NM_018964	NP_061837	P57057	GLPT_HUMAN	solute carrier family 37 member 1	324	Helical; (Potential).				carbohydrate transport|transmembrane transport	integral to membrane					0														0.909091	23.185509	24.681415	10	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	42852257	42852258	15094	21	TT	CG	CG	56	56	SLC37A1	CG	4	4
SLC37A1	54020	broad.mit.edu	36	21	42852260	42852260	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42852260A>G	uc002zbi.1	+	c.973A>G	c.(973-975)AAA>GAA	p.K325E	SLC37A1_uc002zbj.1_Missense_Mutation_p.K325E	NM_018964	NP_061837	P57057	GLPT_HUMAN	solute carrier family 37 member 1	325					carbohydrate transport|transmembrane transport	integral to membrane					0														0.875	14.419159	15.494449	7	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42852260	42852260	15094	21	A	G	G	9	9	SLC37A1	G	4	4
PDXK	8566	broad.mit.edu	36	21	43986007	43986007	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43986007T>A	uc002zdm.2	+	c.174T>A	c.(172-174)AAT>AAA	p.N58K	PDXK_uc010gpj.1_Missense_Mutation_p.N58K|PDXK_uc002zdn.2_Missense_Mutation_p.N58K|PDXK_uc002zdq.2_5'UTR	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase	58					cell proliferation|pyridoxal phosphate biosynthetic process|pyridoxine biosynthetic process	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)									0.428571	11.131017	11.196133	6	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43986007	43986007	12118	21	T	A	A	52	52	PDXK	A	4	4
C21orf29	54084	broad.mit.edu	36	21	44770039	44770039	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44770039T>G	uc002zfe.1	-	c.1261A>C	c.(1261-1263)ACA>CCA	p.T421P	C21orf29_uc010gpv.1_Missense_Mutation_p.T353P	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29	421	EAR 3.				cell adhesion	extracellular region	structural molecule activity				0														0.5	8.797057	8.797057	4	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44770039	44770039	2204	21	T	G	G	59	59	C21orf29	G	4	4
C21orf58	54058	broad.mit.edu	36	21	46567001	46567002	+	Missense_Mutation	DNP	GA	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46567001_46567002GA>CT	uc002zjf.1	-	c.79_80TC>AG	c.(79-81)TCA>AGA	p.S27R	PCNT_uc002zji.2_5'Flank|PCNT_uc002zjj.1_5'Flank|C21orf58_uc002zja.2_5'Flank|C21orf58_uc010gqj.1_Non-coding_Transcript|C21orf58_uc002zjg.1_Non-coding_Transcript	NM_058180	NP_478060	P58505	CU058_HUMAN	hypothetical protein LOC54058	27										pancreas(1)	1	Breast(49;0.112)			Colorectal(79;0.239)										0.8	8.896158	9.309755	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	46567001	46567002	2209	21	GA	CT	CT	45	45	C21orf58	CT	3	3
CCDC116	164592	broad.mit.edu	36	22	20319272	20319272	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:20319272A>G	uc002zve.1	+	c.920A>G	c.(919-921)CAC>CGC	p.H307R		NM_152612	NP_689825	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	307										ovary(1)	1	Colorectal(54;0.105)													0.4	7.392046	7.480703	4	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20319272	20319272	2873	22	A	G	G	6	6	CCDC116	G	4	4
PPIL2	23759	broad.mit.edu	36	22	20356640	20356640	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:20356640G>T	uc002zvh.2	+	c.213G>T	c.(211-213)AAG>AAT	p.K71N	PPIL2_uc010gtj.1_Missense_Mutation_p.K71N|PPIL2_uc002zvi.2_Missense_Mutation_p.K71N|PPIL2_uc002zvg.2_Missense_Mutation_p.K71N	NM_148176	NP_680481	Q13356	PPIL2_HUMAN	peptidylprolyl isomerase-like 2 isoform b	71	U-box.				blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-protein ligase activity			ovary(2)	2	Colorectal(54;0.105)													0.290366	589.741917	618.774625	214	523	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20356640	20356640	12762	22	G	T	T	33	33	PPIL2	T	3	3
HPS4	89781	broad.mit.edu	36	22	25183877	25183877	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:25183877G>T	uc003acl.1	-	c.1903C>A	c.(1903-1905)CTG>ATG	p.L635M	HPS4_uc003ach.1_Missense_Mutation_p.L370M|HPS4_uc003aci.1_Missense_Mutation_p.L630M|HPS4_uc003acj.1_Missense_Mutation_p.L499M|HPS4_uc003ack.1_Missense_Mutation_p.L426M|HPS4_uc003acn.1_Missense_Mutation_p.L481M	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	635					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														0.145228	177.889486	265.380879	105	618	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25183877	25183877	7633	22	G	T	T	35	35	HPS4	T	3	3
KREMEN1	83999	broad.mit.edu	36	22	27863608	27863608	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:27863608T>G	uc003aek.1	+	c.910T>G	c.(910-912)TAT>GAT	p.Y304D	KREMEN1_uc003ael.1_Missense_Mutation_p.Y304D	NM_001039570	NP_001034659	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1	302	Extracellular (Potential).|CUB.				cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(1)|lung(1)	2														0.75	7.123739	7.347093	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27863608	27863608	8757	22	T	G	G	57	57	KREMEN1	G	4	4
CCDC157	550631	broad.mit.edu	36	22	29096593	29096593	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29096593G>T	uc003ahn.1	+	c.546G>T	c.(544-546)AAG>AAT	p.K182N		NM_001017437	NP_001017437	Q569K6	CC157_HUMAN	hypothetical protein LOC550631	233										central_nervous_system(1)	1														0.375	9.426017	9.652069	6	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29096593	29096593	2911	22	G	T	T	35	35	CCDC157	T	3	3
DEPDC5	9681	broad.mit.edu	36	22	30623631	30623631	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:30623631T>A	uc003alt.1	+	c.4340T>A	c.(4339-4341)CTG>CAG	p.L1447Q	DEPDC5_uc003als.1_Missense_Mutation_p.L1425Q|DEPDC5_uc003alu.1_Missense_Mutation_p.L874Q|DEPDC5_uc003alv.1_Non-coding_Transcript|DEPDC5_uc003alw.1_Missense_Mutation_p.L723Q|DEPDC5_uc010gwk.1_Missense_Mutation_p.L451Q	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	1425					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8														0.354839	14.962599	15.560069	11	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30623631	30623631	4621	22	T	A	A	55	55	DEPDC5	A	4	4
CARD10	29775	broad.mit.edu	36	22	36236373	36236373	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36236373A>G	uc003asx.1	-	c.701T>C	c.(700-702)GTG>GCG	p.V234A	CARD10_uc003ast.1_Non-coding_Transcript|CARD10_uc003asw.1_5'Flank|CARD10_uc003asy.1_Missense_Mutation_p.V234A	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	234	Potential.				activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			ovary(1)|kidney(1)	2	Melanoma(58;0.0574)									672				0.666667	9.093648	9.239173	4	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36236373	36236373	2763	22	A	G	G	6	6	CARD10	G	4	4
TAB1	10454	broad.mit.edu	36	22	38147835	38147835	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38147835G>A	uc003axr.1	+	c.1062G>A	c.(1060-1062)CTG>CTA	p.L354L	TAB1_uc003axt.1_Silent_p.L278L|TAB1_uc003axu.1_Silent_p.L278L	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7	278	PP2C-like.				activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane	catalytic activity|protein binding				0										336				0.845238	477.919099	497.038572	142	26	GG		KEEP	---	---	---	---	capture			Silent	SNP	38147835	38147835	16016	22	G	A	A	47	47	TAB1	A	2	2
FAM109B	150368	broad.mit.edu	36	22	40803927	40803927	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40803927T>A	uc003bbz.1	+	c.684T>A	c.(682-684)CAT>CAA	p.H228Q	FAM109B_uc010gyt.1_Missense_Mutation_p.H228Q|C22orf32_uc003bca.1_5'Flank	NM_001002034	NP_001002034	Q6ICB4	SESQ2_HUMAN	hypothetical protein LOC150368	228				H->A: Loss of OCRL-binding.		clathrin-coated vesicle|early endosome|Golgi apparatus|recycling endosome					0														0.75	6.620729	6.84443	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40803927	40803927	5592	22	T	A	A	51	51	FAM109B	A	4	4
PKDREJ	10343	broad.mit.edu	36	22	45037071	45037072	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:45037071_45037072GG>AT	uc003bhh.1	-	c.812_813CC>AT	c.(811-813)CCC>CAT	p.P271H		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	271	Extracellular (Potential).|REJ.				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)										0.8	9.218632	9.003785	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	45037071	45037072	12395	22	GG	AT	AT	39	39	PKDREJ	AT	1	1
CELSR1	9620	broad.mit.edu	36	22	45308348	45308348	+	Silent	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45308348C>A	uc003bhw.1	-	c.3384G>T	c.(3382-3384)CCG>CCT	p.P1128P		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1128	Extracellular (Potential).|Cadherin 9.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			pancreas(2)|skin(1)	3		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)										0.8	8.693555	9.105593	4	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	45308348	45308348	3354	22	C	A	A	23	23	CELSR1	A	3	3
CERK	64781	broad.mit.edu	36	22	45473998	45473998	+	Silent	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45473998T>G	uc003bia.1	-	c.819A>C	c.(817-819)TCA>TCC	p.S273S	CERK_uc010hae.1_Silent_p.S75S	NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase	273	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)										0.983193	300.069854	302.329078	117	2	TT		KEEP	---	---	---	---	capture			Silent	SNP	45473998	45473998	3400	22	T	G	G	55	55	CERK	G	4	4
TUBGCP6	85378	broad.mit.edu	36	22	49005112	49005112	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49005112C>A	uc003bkb.1	-	c.2020G>T	c.(2020-2022)GCT>TCT	p.A674S	TUBGCP6_uc010har.1_Missense_Mutation_p.A674S|TUBGCP6_uc010has.1_Non-coding_Transcript|TUBGCP6_uc003bka.1_5'Flank|TUBGCP6_uc010hat.1_5'UTR|TUBGCP6_uc003bkd.1_Missense_Mutation_p.A28S	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	674					G2/M transition of mitotic cell cycle|microtubule nucleation	cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)										1	24.673073	24.671087	9	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49005112	49005112	17325	22	C	A	A	27	27	TUBGCP6	A	3	3
TUBGCP6	85378	broad.mit.edu	36	22	49005114	49005115	+	Missense_Mutation	DNP	AT	GC	GC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:49005114_49005115AT>GC	uc003bkb.1	-	c.2017_2018AT>GC	c.(2017-2019)ATC>GCC	p.I673A	TUBGCP6_uc010har.1_Missense_Mutation_p.I673A|TUBGCP6_uc010has.1_Non-coding_Transcript|TUBGCP6_uc003bka.1_5'Flank|TUBGCP6_uc010hat.1_5'UTR|TUBGCP6_uc003bkd.1_Missense_Mutation_p.I27A	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	673					G2/M transition of mitotic cell cycle|microtubule nucleation	cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)										1	20.085814	20.081809	8	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	49005114	49005115	17325	22	AT	GC	GC	12	12	TUBGCP6	GC	4	4
TUBGCP6	85378	broad.mit.edu	36	22	49024465	49024465	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49024465G>C	uc003bkb.1	-	c.551C>G	c.(550-552)GCT>GGT	p.A184G	TUBGCP6_uc010har.1_Missense_Mutation_p.A184G|TUBGCP6_uc010has.1_Non-coding_Transcript|TUBGCP6_uc010hau.1_Missense_Mutation_p.A184G	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	184					G2/M transition of mitotic cell cycle|microtubule nucleation	cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)										0.5	7.389383	7.389383	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49024465	49024465	17325	22	G	C	C	34	34	TUBGCP6	C	3	3
SLC9A2	6549	broad.mit.edu	36	2	102667188	102667188	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102667188G>A	uc002tca.1	+	c.1386G>A	c.(1384-1386)ACG>ACA	p.T462T		NM_003048	NP_003039	Q9UBY0	SL9A2_HUMAN	solute carrier family 9 (sodium/hydrogen	462	Helical; Name=M13; (Potential).					integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			central_nervous_system(3)|breast(2)	5														0.278107	119.553418	127.043595	47	122	GG		KEEP	---	---	---	---	capture			Silent	SNP	102667188	102667188	15209	2	G	A	A	39	39	SLC9A2	A	1	1
IL1RN	3557	broad.mit.edu	36	2	113603625	113603625	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113603625A>C	uc002tiz.1	+	c.127A>C	c.(127-129)ATC>CTC	p.I43L	IL1RN_uc002tix.1_Non-coding_Transcript|IL1RN_uc002tiy.1_Missense_Mutation_p.I6L|IL1RN_uc002tja.1_Missense_Mutation_p.I22L|IL1RN_uc002tjb.1_Missense_Mutation_p.I40L	NM_173841	NP_776215	P18510	IL1RA_HUMAN	interleukin 1 receptor antagonist isoform 2	40					immune response|inflammatory response|response to glucocorticoid stimulus	centrosome|extracellular space|nucleus|plasma membrane	cytokine activity|interleukin-1 receptor antagonist activity			skin(1)	1					Anakinra(DB00026)					97				0.444444	6.784223	6.810267	4	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113603625	113603625	7966	2	A	C	C	4	4	IL1RN	C	4	4
DDX18	8886	broad.mit.edu	36	2	118298641	118298641	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:118298641G>T	uc002tlh.1	+	c.1093G>T	c.(1093-1095)GCC>TCC	p.A365S		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	365	Helicase ATP-binding.						ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4														0.120482	14.592955	26.317945	10	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118298641	118298641	4516	2	G	T	T	46	46	DDX18	T	3	3
DBI	1622	broad.mit.edu	36	2	119846358	119846358	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:119846358G>A	uc002tlw.1	+	c.309G>A	c.(307-309)GGG>GGA	p.G103G	DBI_uc002tlv.1_Silent_p.G86G|DBI_uc002tlx.1_Silent_p.G87G	NM_020548	NP_065438	P07108	ACBP_HUMAN	diazepam binding inhibitor isoform 1	86	ACB.				transport		benzodiazepine receptor binding|fatty-acyl-CoA binding				0														0.5	14.776956	14.776956	8	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	119846358	119846358	4422	2	G	A	A	41	41	DBI	A	2	2
PLEKHB2	55041	broad.mit.edu	36	2	131604796	131604796	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131604796C>A	uc002tsi.2	+	c.449C>A	c.(448-450)ACA>AAA	p.T150K	PLEKHB2_uc002tsj.2_Missense_Mutation_p.T109K|PLEKHB2_uc002tsg.2_Missense_Mutation_p.T109K|PLEKHB2_uc002tsf.2_Missense_Mutation_p.T109K|PLEKHB2_uc002tsh.2_Missense_Mutation_p.T109K	NM_001100623	NP_001094093	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B	109	PH.					membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)										0.4	6.483542	6.574646	4	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131604796	131604796	12491	2	C	A	A	17	17	PLEKHB2	A	3	3
CCNT2	905	broad.mit.edu	36	2	135427951	135427951	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:135427951A>C	uc002tuc.1	+	c.1456A>C	c.(1456-1458)ATA>CTA	p.I486L	CCNT2_uc002tub.1_Missense_Mutation_p.I486L|CCNT2_uc002tud.1_Missense_Mutation_p.I149L	NM_058241	NP_490595	O60583	CCNT2_HUMAN	cyclin T2 isoform b	486					cell cycle|cell division|interspecies interaction between organisms|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm				ovary(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.107)										0.5	8.393262	8.393262	4	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135427951	135427951	3062	2	A	C	C	4	4	CCNT2	C	4	4
LRP2	4036	broad.mit.edu	36	2	169791291	169791291	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169791291G>T	uc002ues.1	-	c.5281C>A	c.(5281-5283)CTT>ATT	p.L1761I		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1761	Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.193548	6.628067	9.358815	6	25	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	169791291	169791291	9329	2	G	T	T	35	35	LRP2	T	3	3
LRP2	4036	broad.mit.edu	36	2	169883538	169883538	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169883538G>T	uc002ues.1	-	c.290C>A	c.(289-291)TCA>TAA	p.S97*		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	97	LDL-receptor class A 2.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.183566	218.518777	272.3154	105	467	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	169883538	169883538	9329	2	G	T	T	45	45	LRP2	T	5	3
PRKRA	8575	broad.mit.edu	36	2	179023281	179023285	+	Missense_Mutation	ONP	ATCTT	TGACG	TGACG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179023281_179023285ATCTT>TGACG	uc002umf.1	-	c.165_169AAGAT>CGTCA	c.(163-171)GAAAGATCT>GACGTCACT	p.55_57ERS>DVT	PRKRA_uc002umd.1_Missense_Mutation_p.30_32ERS>DVT|PRKRA_uc002ume.1_Missense_Mutation_p.44_46ERS>DVT|PRKRA_uc002umg.1_5'UTR|DFNB59_uc002umi.2_5'Flank	NM_003690	NP_003681	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double	55_57	Sufficient for self-association and interaction with TARBP2.|DRBM 1.				immune response|negative regulation of cell proliferation|production of siRNA involved in RNA interference|response to virus	perinuclear region of cytoplasm	double-stranded RNA binding|enzyme activator activity|protein homodimerization activity			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			Melanoma(200;68 3001 23825 48764)								0.875	13.531581	14.584981	7	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	ONP	179023281	179023285	12967	2	ATCTT	TGACG	TGACG	12	12	PRKRA	TGACG	4	4
TTN	7273	broad.mit.edu	36	2	179340886	179340886	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179340886G>T	uc002umr.1	-	c.9316C>A	c.(9316-9318)CAG>AAG	p.Q3106K	TTN_uc002ums.1_Missense_Mutation_p.Q3060K|TTN_uc010frc.1_Missense_Mutation_p.Q3060K|TTN_uc010frd.1_Missense_Mutation_p.Q3060K|TTN_uc002unb.1_Missense_Mutation_p.Q3106K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3106										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				0.225806	7.192523	9.357598	7	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	179340886	179340886	17290	2	G	T	T	45	45	TTN	T	3	3
FAM171B	165215	broad.mit.edu	36	2	187334652	187334652	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:187334652A>T	uc002ups.1	+	c.1338A>T	c.(1336-1338)GAA>GAT	p.E446D	FAM171B_uc002upr.1_Missense_Mutation_p.K413N|FAM171B_uc002upt.2_5'Flank	NM_177454	NP_803237	Q6P995	F171B_HUMAN	KIAA1946	446	Cytoplasmic (Potential).					integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10														0.25	6.653337	7.802295	5	15	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	187334652	187334652	5697	2	A	T	T	1	1	FAM171B	T	4	4
OSR1	130497	broad.mit.edu	36	2	19416641	19416643	+	Missense_Mutation	TNP	CGA	AAG	AAG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:19416641_19416643CGA>AAG	uc002rdc.1	-	c.405_407TCG>CTT	c.(403-408)GGTCGC>GGCTTC	p.R136F		NM_145260	NP_660303	Q8TAX0	OSR1_HUMAN	odd-skipped related 1	136					heart development|mesangial cell development|mesonephric duct morphogenesis|metanephric cap mesenchymal cell proliferation involved in metanephros development|metanephric glomerulus vasculature development|metanephric interstitial cell development|metanephric mesenchymal cell differentiation|metanephric nephron tubule development|metanephric smooth muscle tissue development|middle ear morphogenesis|negative regulation of apoptosis|negative regulation of nephron tubule epithelial cell differentiation|odontogenesis|palate development|pattern specification involved in metanephros development|positive regulation of epithelial cell proliferation|positive regulation of gastrulation|positive regulation of gene expression|pronephros development|regulation of transcription, DNA-dependent|renal vesicle progenitor cell differentiation|specification of anterior mesonephric tubule identity|specification of posterior mesonephric tubule identity|stem cell differentiation|transcription, DNA-dependent|ureter urothelium development|ureteric bud development	nucleolus	nucleic acid binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)							p.R136H(GMS10-Tumor)	40				0.888889	17.586593	18.823783	8	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	19416641	19416643	11704	2	CGA	AAG	AAG	27	27	OSR1	AAG	3	3
MAP2	4133	broad.mit.edu	36	2	210283055	210283055	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:210283055C>T	uc002vde.1	+	c.4905C>T	c.(4903-4905)GCC>GCT	p.A1635A	MAP2_uc002vdd.1_Silent_p.A336A|MAP2_uc002vdf.1_Silent_p.A279A|MAP2_uc002vdg.1_Silent_p.A279A|MAP2_uc002vdh.1_Silent_p.A336A|MAP2_uc002vdi.1_Silent_p.A1631A	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	1635					negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|large_intestine(2)|pancreas(2)|central_nervous_system(1)	14		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	Pancreas(27;423 979 28787 29963)								0.236842	9.716981	12.165398	9	29	CC		KEEP	---	---	---	---	capture			Silent	SNP	210283055	210283055	9618	2	C	T	T	21	21	MAP2	T	2	2
TNS1	7145	broad.mit.edu	36	2	218391702	218391702	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:218391702C>G	uc002vgt.2	-	c.3286G>C	c.(3286-3288)GGA>CGA	p.G1096R	TNS1_uc002vgr.2_Missense_Mutation_p.G1083R|TNS1_uc002vgs.2_Missense_Mutation_p.G1075R	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	1096	Ser-rich.					cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)										0.380952	12.668482	12.937708	8	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	218391702	218391702	16884	2	C	G	G	22	22	TNS1	G	3	3
CTDSP1	58190	broad.mit.edu	36	2	218975160	218975160	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:218975160C>G	uc002vhy.1	+	c.299C>G	c.(298-300)ACC>AGC	p.T100S	CTDSP1_uc002vhx.1_Missense_Mutation_p.T99S|CTDSP1_uc002vhz.1_5'UTR|MIR26B_hsa-mir-26b|MI0000084_5'Flank	NM_021198	NP_067021	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	100	FCP1 homology.				protein dephosphorylation|regulation of transcription from RNA polymerase II promoter	nucleus	CTD phosphatase activity|metal ion binding|protein binding			ovary(1)	1		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.8	8.794227	9.205787	4	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	218975160	218975160	4162	2	C	G	G	18	18	CTDSP1	G	3	3
CTDSP1	58190	broad.mit.edu	36	2	218977339	218977339	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:218977339A>G	uc002vhy.1	+	c.733A>G	c.(733-735)AGC>GGC	p.S245G	CTDSP1_uc002vhx.1_Missense_Mutation_p.S244G|CTDSP1_uc002vhz.1_Missense_Mutation_p.S104G	NM_021198	NP_067021	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	245					protein dephosphorylation|regulation of transcription from RNA polymerase II promoter	nucleus	CTD phosphatase activity|metal ion binding|protein binding			ovary(1)	1		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.4	10.244966	10.375193	6	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	218977339	218977339	4162	2	A	G	G	7	7	CTDSP1	G	4	4
DNMT3A	1788	broad.mit.edu	36	2	25320606	25320606	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:25320606G>A	uc002rgc.1	-	c.1773C>T	c.(1771-1773)ACC>ACT	p.T591T	DNMT3A_uc002rgb.1_Silent_p.T402T|DNMT3A_uc002rgd.1_Silent_p.T591T|DNMT3A_uc010eyi.1_Non-coding_Transcript	NM_022552	NP_783328	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	591	ADD.				regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(107)|ovary(3)	110	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.444444	7.388902	7.414354	4	5	GG		KEEP	---	---	---	---	capture			Silent	SNP	25320606	25320606	4859	2	G	A	A	35	35	DNMT3A	A	2	2
GTF3C2	2976	broad.mit.edu	36	2	27403653	27403654	+	Missense_Mutation	DNP	AC	GG	GG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27403653_27403654AC>GG	uc002rju.1	-	c.2444_2445GT>CC	c.(2443-2445)GGT>GCC	p.G815A	MPV17_uc002rjt.1_5'Flank|GTF3C2_uc010eyy.1_Missense_Mutation_p.G259A|GTF3C2_uc002rjv.1_Missense_Mutation_p.G804A|GTF3C2_uc002rjw.1_Missense_Mutation_p.G804A	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	804					5S class rRNA transcription from RNA polymerase III type 1 promoter|tRNA transcription from RNA polymerase III promoter	transcription factor TFIIIC complex				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.25	13.783624	16.308881	11	33	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	27403653	27403654	7153	2	AC	GG	GG	2	2	GTF3C2	GG	4	4
STRN	6801	broad.mit.edu	36	2	36948478	36948478	+	Nonsense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:36948478A>C	uc002rpn.1	-	c.1530T>G	c.(1528-1530)TAT>TAG	p.Y510*	STRN_uc010ezx.1_Nonsense_Mutation_p.Y473*	NM_003162	NP_003153	O43815	STRN_HUMAN	striatin, calmodulin binding protein	510					dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(717;0.0129)|all_hematologic(82;0.21)												0.16	7.157015	12.689139	8	42	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	36948478	36948478	15849	2	A	C	C	16	16	STRN	C	5	4
CDKL4	344387	broad.mit.edu	36	2	39294101	39294101	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:39294101T>A	uc010fal.1	-	c.307A>T	c.(307-309)ATC>TTC	p.I103F	CDKL4_uc002rrm.1_Missense_Mutation_p.I103F	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	103	Protein kinase.				protein phosphorylation	cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)								219				0.511628	69.348631	69.353671	22	21	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39294101	39294101	3285	2	T	A	A	50	50	CDKL4	A	4	4
PREPL	9581	broad.mit.edu	36	2	44402081	44402081	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:44402081G>C	uc002ruf.1	-	c.2102C>G	c.(2101-2103)GCC>GGC	p.A701G	PREPL_uc002rug.1_Missense_Mutation_p.A635G|PREPL_uc002ruh.1_Missense_Mutation_p.A639G|PREPL_uc002rui.2_Missense_Mutation_p.A612G|PREPL_uc010fax.1_Missense_Mutation_p.A701G|PREPL_uc002ruk.1_Missense_Mutation_p.A701G|PREPL_uc002ruj.1_Missense_Mutation_p.A612G	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C	701					proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.5	10.363746	10.363746	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44402081	44402081	12918	2	G	C	C	42	42	PREPL	C	3	3
ADD2	119	broad.mit.edu	36	2	70785080	70785080	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:70785080T>A	uc002sgz.1	-	c.203A>T	c.(202-204)GAA>GTA	p.E68V	ADD2_uc010fds.1_Non-coding_Transcript|ADD2_uc002sgy.1_Missense_Mutation_p.E68V|ADD2_uc002sha.1_Missense_Mutation_p.E68V|ADD2_uc002sgx.2_Missense_Mutation_p.E68V|ADD2_uc010fdt.1_Missense_Mutation_p.E68V|ADD2_uc010fdu.1_Missense_Mutation_p.E84V|ADD2_uc002shc.1_Missense_Mutation_p.E68V|ADD2_uc002shd.1_Missense_Mutation_p.E68V	NM_001617	NP_001608	P35612	ADDB_HUMAN	adducin 2 isoform a	68					actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3														0.272727	7.923047	8.962137	6	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70785080	70785080	306	2	T	A	A	62	62	ADD2	A	4	4
ZNF638	27332	broad.mit.edu	36	2	71446270	71446270	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71446270T>C	uc002shx.1	+	c.1921T>C	c.(1921-1923)TCA>CCA	p.S641P	ZNF638_uc010fec.1_Missense_Mutation_p.S747P|ZNF638_uc002shw.2_Missense_Mutation_p.S641P|ZNF638_uc002shy.1_Missense_Mutation_p.S641P|ZNF638_uc002shz.1_Missense_Mutation_p.S641P|ZNF638_uc002sia.1_Missense_Mutation_p.S641P|ZNF638_uc002sib.1_Missense_Mutation_p.S641P|ZNF638_uc010fed.1_Non-coding_Transcript	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	641					RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)	3														0.384615	9.061999	9.216604	5	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71446270	71446270	18650	2	T	C	C	50	50	ZNF638	C	4	4
HK2	3099	broad.mit.edu	36	2	74967193	74967193	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74967193C>T	uc002snd.1	+	c.2104C>T	c.(2104-2106)CGG>TGG	p.R702W		NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2	702	Catalytic.				apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2														0.3	21.569109	22.638352	9	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74967193	74967193	7482	2	C	T	T	27	27	HK2	T	1	1
KIDINS220	57498	broad.mit.edu	36	2	8788936	8788936	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:8788936C>A	uc002qzc.1	-	c.4681G>T	c.(4681-4683)GAG>TAG	p.E1561*	KIDINS220_uc002qzb.1_Nonsense_Mutation_p.E415*|KIDINS220_uc002qzd.1_Nonsense_Mutation_p.E1462*	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	1561	Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)													0.162162	6.610817	14.728073	12	62	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	8788936	8788936	8582	2	C	A	A	29	29	KIDINS220	A	5	3
ASTL	431705	broad.mit.edu	36	2	96153465	96153465	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:96153465G>T	uc002svj.1	-	c.1147C>A	c.(1147-1149)CAG>AAG	p.Q383K		NM_001002036	NP_001002036	Q6HA08	ASTL_HUMAN	astacin-like metalloendopeptidase	383					proteolysis		metalloendopeptidase activity|zinc ion binding				0														0.316176	102.669702	106.762035	43	93	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96153465	96153465	1082	2	G	T	T	45	45	ASTL	T	3	3
LIPT1	51601	broad.mit.edu	36	2	99145053	99145053	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:99145053G>T	uc002szm.2	+	c.201G>T	c.(199-201)CAG>CAT	p.Q67H	MRPL30_uc002szl.1_Intron|LIPT1_uc002szn.2_Missense_Mutation_p.Q67H|LIPT1_uc002szo.2_Missense_Mutation_p.Q67H|LIPT1_uc002szp.2_Missense_Mutation_p.Q67H|LIPT1_uc002szq.2_Missense_Mutation_p.Q67H|MRPL30_uc002szr.2_Intron|LIPT1_uc010fio.1_Missense_Mutation_p.Q67H	NM_145198	NP_660200	Q9Y234	LIPT_HUMAN	lipoyltransferase 1	67					lipid metabolic process|protein lipoylation	mitochondrion	acyltransferase activity				0					Lipoic Acid(DB00166)	GBM(84;665 1268 21657 25485 30647)								0.133758	27.871513	48.317216	21	136	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99145053	99145053	9157	2	G	T	T	33	33	LIPT1	T	3	3
ZDHHC23	254887	broad.mit.edu	36	3	115155762	115155762	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:115155762G>T	uc003eau.1	+	c.687G>T	c.(685-687)ATG>ATT	p.M229I	ZDHHC23_uc003eav.1_Missense_Mutation_p.M223I	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23	229						integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2														0.333333	7.253455	7.630761	5	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115155762	115155762	18202	3	G	T	T	48	48	ZDHHC23	T	3	3
B4GALT4	8702	broad.mit.edu	36	3	120428421	120428421	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:120428421C>T	uc003ecg.1	-	c.411G>A	c.(409-411)CTG>CTA	p.L137L	B4GALT4_uc003ece.1_Silent_p.L137L|B4GALT4_uc003ecf.1_Non-coding_Transcript|B4GALT4_uc003ech.1_Silent_p.L137L|B4GALT4_uc003eci.1_Silent_p.L137L	NM_212543	NP_997708	O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	137	Lumenal (Potential).				membrane lipid metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding|N-acetyllactosamine synthase activity				0				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)									0.5	7.085991	7.085991	4	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	120428421	120428421	1294	3	C	T	T	29	29	B4GALT4	T	2	2
GPR156	165829	broad.mit.edu	36	3	121369746	121369746	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:121369746T>G	uc003edq.2	-	c.1268A>C	c.(1267-1269)CAG>CCG	p.Q423P		NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	423	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.19)										0.388889	12.212233	12.40871	7	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121369746	121369746	6936	3	T	G	G	55	55	GPR156	G	4	4
UMPS	7372	broad.mit.edu	36	3	125932035	125932035	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:125932035G>A	uc003ehl.2	+	c.27G>A	c.(25-27)GGG>GGA	p.G9G	UMPS_uc003ehm.2_Non-coding_Transcript|UMPS_uc003ehn.2_5'UTR	NM_000373	NP_000364	P11172	PYR5_HUMAN	uridine monophosphate synthase	9	OPRTase.				'de novo' pyrimidine base biosynthetic process|'de novo' UMP biosynthetic process|pyrimidine nucleoside biosynthetic process	cytosol|nucleus	orotate phosphoribosyltransferase activity|orotidine-5'-phosphate decarboxylase activity			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.146)										0.384615	7.542631	7.703163	5	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	125932035	125932035	17539	3	G	A	A	42	42	UMPS	A	2	2
ITGB5	3693	broad.mit.edu	36	3	125965990	125965990	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:125965990T>G	uc003eho.1	-	c.2242A>C	c.(2242-2244)ATC>CTC	p.I748L	ITGB5_uc010hrx.1_Non-coding_Transcript	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5	748	Cytoplasmic (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.163)										0.272727	8.730787	9.763921	6	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125965990	125965990	8202	3	T	G	G	51	51	ITGB5	G	4	4
ABTB1	80325	broad.mit.edu	36	3	128879349	128879350	+	Missense_Mutation	DNP	CT	GC	GC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:128879349_128879350CT>GC	uc003ejt.1	+	c.1002_1003CT>GC	c.(1000-1005)CTCTAC>CTGCAC	p.Y335H	ABTB1_uc003ejr.1_Missense_Mutation_p.Y193H|ABTB1_uc003ejs.1_Missense_Mutation_p.Y310H|ABTB1_uc003eju.1_Missense_Mutation_p.Y193H|ABTB1_uc010hsm.1_Missense_Mutation_p.Y62H	NM_172027	NP_742024	Q969K4	ABTB1_HUMAN	ankyrin repeat and BTB (POZ) domain containing 1	335	BTB 2.					cytoplasm|nucleolus|plasma membrane	translation elongation factor activity				0														0.75	6.320211	6.543742	3	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	128879349	128879350	103	3	CT	GC	GC	32	32	ABTB1	GC	3	3
MSL2	55167	broad.mit.edu	36	3	137352975	137352976	+	Missense_Mutation	DNP	GT	TC	TC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:137352975_137352976GT>TC	uc003eqx.1	-	c.1437_1438AC>GA	c.(1435-1440)CAACGC>CAGAGC	p.R480S		NM_018133	NP_060603	Q9HCI7	MSL2_HUMAN	ring finger protein 184 isoform 1	480					histone H4-K16 acetylation	MSL complex	zinc ion binding			central_nervous_system(1)	1														0.590909	26.147097	26.302009	13	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	137352975	137352976	10271	3	GT	TC	TC	40	40	MSL2	TC	3	3
ATR	545	broad.mit.edu	36	3	143764234	143764234	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:143764234A>T	uc003eux.2	-	c.700T>A	c.(700-702)TGT>AGT	p.C234S		NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	234					cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|breast(4)|ovary(3)|skin(2)|stomach(1)|central_nervous_system(1)|liver(1)	17										936				0.222222	7.09309	8.369911	4	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143764234	143764234	1223	3	A	T	T	5	5	ATR	T	4	4
C3orf20	84077	broad.mit.edu	36	3	14730534	14730534	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14730534G>T	uc003byy.1	+	c.1177G>T	c.(1177-1179)GTC>TTC	p.V393F	C3orf20_uc003byz.1_Missense_Mutation_p.V271F|C3orf20_uc003bza.1_Missense_Mutation_p.V271F|C3orf20_uc003bzb.1_5'UTR	NM_032137	NP_115513	Q8ND61	CC020_HUMAN	hypothetical protein LOC84077	393						cytoplasm|integral to membrane				ovary(3)	3														0.466667	12.301801	12.317789	7	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14730534	14730534	2306	3	G	T	T	40	40	C3orf20	T	3	3
SIAH2	6478	broad.mit.edu	36	3	151963062	151963062	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:151963062G>T	uc003eyi.1	-	c.265C>A	c.(265-267)CCT>ACT	p.P89T		NM_005067	NP_005058	O43255	SIAH2_HUMAN	seven in absentia homolog 2	89	RING-type.				apoptosis|axon guidance|cell cycle|negative regulation of canonical Wnt receptor signaling pathway|small GTPase mediated signal transduction|ubiquitin-dependent protein catabolic process	cytosol|nucleus	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)											0.947368	36.600674	38.859694	18	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151963062	151963062	14795	3	G	T	T	42	42	SIAH2	T	3	3
GHSR	2693	broad.mit.edu	36	3	173648438	173648438	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173648438C>T	uc003fib.1	-	c.460G>A	c.(460-462)GTG>ATG	p.V154M	GHSR_uc003fic.1_Missense_Mutation_p.V154M	NM_198407	NP_940799	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor isoform 1a	154	Cytoplasmic (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)								0.333333	6.443534	6.825826	5	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	173648438	173648438	6643	3	C	T	T	18	18	GHSR	T	2	2
TNFSF10	8743	broad.mit.edu	36	3	173712107	173712107	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173712107C>G	uc003fid.1	-	c.307G>C	c.(307-309)GTT>CTT	p.V103L	TNFSF10_uc003fie.1_Intron	NM_003810	NP_003801	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily,	103	Extracellular (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction	extracellular space|integral to plasma membrane|soluble fraction	cytokine activity|metal ion binding|tumor necrosis factor receptor binding			skin(1)	1	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)							52				0.272727	9.832232	10.863686	6	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	173712107	173712107	16842	3	C	G	G	20	20	TNFSF10	G	3	3
PIK3CA	5290	broad.mit.edu	36	3	180402008	180402008	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180402008C>T	uc003fjk.1	+	c.799C>T	c.(799-801)CTG>TTG	p.L267L		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	267					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.5	7.085521	7.085521	4	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	180402008	180402008	12337	3	C	T	T	32	32	PIK3CA	T	2	2
MUC4	4585	broad.mit.edu	36	3	196963542	196963542	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:196963542C>T	uc010hzt.1	-	c.15376G>A	c.(15376-15378)GCC>ACC	p.A5126T	MUC4_uc003fvo.1_Missense_Mutation_p.A1018T|MUC4_uc003fvp.1_Missense_Mutation_p.A967T|MUC4_uc010hzq.1_Missense_Mutation_p.A111T|MUC4_uc003fuz.1_Missense_Mutation_p.A852T|MUC4_uc003fva.1_Missense_Mutation_p.A734T|MUC4_uc003fvb.1_Missense_Mutation_p.A770T|MUC4_uc003fvd.1_Non-coding_Transcript|MUC4_uc003fve.1_Missense_Mutation_p.A770T|MUC4_uc003fvc.1_Non-coding_Transcript|MUC4_uc010hzr.1_Non-coding_Transcript|MUC4_uc003fvm.1_Missense_Mutation_p.A734T|MUC4_uc003fvg.1_Missense_Mutation_p.A818T|MUC4_uc003fvf.1_Non-coding_Transcript|MUC4_uc003fvh.1_Missense_Mutation_p.A818T|MUC4_uc010hzs.1_Missense_Mutation_p.A995T|MUC4_uc003fvi.1_Missense_Mutation_p.A734T|MUC4_uc003fvj.1_Missense_Mutation_p.A763T|MUC4_uc003fvk.1_Missense_Mutation_p.A943T|MUC4_uc003fvl.1_Missense_Mutation_p.A734T	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	2011					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)										0.5	7.184942	7.184942	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	196963542	196963542	10372	3	C	T	T	26	26	MUC4	T	2	2
SENP5	205564	broad.mit.edu	36	3	198097587	198097587	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:198097587C>T	uc003fwz.2	+	c.1138C>T	c.(1138-1140)CAT>TAT	p.H380Y		NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	380					cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			lung(1)	1	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		Ovarian(47;891 1095 11174 13858 51271)								0.333333	9.528665	9.979161	6	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	198097587	198097587	14535	3	C	T	T	17	17	SENP5	T	2	2
CNTN4	152330	broad.mit.edu	36	3	2942404	2942404	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:2942404G>A	uc003bpc.1	+	c.1299G>A	c.(1297-1299)GCG>GCA	p.A433A	CNTN4_uc003bpb.1_Silent_p.A105A|CNTN4_uc003bpd.1_Silent_p.A433A|CNTN4_uc003bpe.1_Silent_p.A105A|CNTN4_uc003bpf.1_Silent_p.A105A	NM_175607	NP_783302	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	433	Ig-like C2-type 5.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)										0.466667	39.340102	39.369345	14	16	GG		KEEP	---	---	---	---	capture			Silent	SNP	2942404	2942404	3781	3	G	A	A	40	40	CNTN4	A	1	1
CSRNP1	64651	broad.mit.edu	36	3	39159973	39159973	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:39159973G>T	uc003cjg.1	-	c.1347C>A	c.(1345-1347)TTC>TTA	p.F449L	CSRNP1_uc003cjh.1_Missense_Mutation_p.F449L	NM_033027	NP_149016	Q96S65	CSRN1_HUMAN	AXIN1 up-regulated 1	449					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(4)|skin(1)	5														0.239899	429.988974	479.007464	190	602	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39159973	39159973	4104	3	G	T	T	45	45	CSRNP1	T	3	3
C3orf39	84892	broad.mit.edu	36	3	43097883	43097884	+	Missense_Mutation	DNP	CA	AC	AC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:43097883_43097884CA>AC	uc003cmq.1	-	c.44_45TG>GT	c.(43-45)CTG>CGT	p.L15R	C3orf39_uc003cmr.1_Missense_Mutation_p.L15R|C3orf39_uc010hij.1_Missense_Mutation_p.L15R	NM_032806	NP_116195	Q8NAT1	AGO61_HUMAN	glycosyltransferase	15						extracellular region	transferase activity, transferring glycosyl groups			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0571)|Kidney(284;0.0718)										1	15.695753	15.687652	7	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	43097883	43097884	2322	3	CA	AC	AC	21	21	C3orf39	AC	3	3
PFKFB4	5210	broad.mit.edu	36	3	48548771	48548771	+	Silent	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48548771G>T	uc003ctv.1	-	c.762C>A	c.(760-762)CTC>CTA	p.L254L	PFKFB4_uc003ctw.1_Silent_p.L63L|PFKFB4_uc003ctx.1_Silent_p.L211L|PFKFB4_uc010hkb.1_Silent_p.L254L|PFKFB4_uc010hkc.1_Silent_p.L254L	NM_004567	NP_004558	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,	254	Fructose-2,6-bisphosphatase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)										0.652174	30.786994	31.248603	15	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	48548771	48548771	12185	3	G	T	T	33	33	PFKFB4	T	3	3
IMPDH2	3615	broad.mit.edu	36	3	49039445	49039445	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49039445C>T	uc003cvt.1	-	c.571G>A	c.(571-573)GGC>AGC	p.G191S		NM_000884	NP_000875	P12268	IMDH2_HUMAN	inosine monophosphate dehydrogenase 2	191	CBS 2.			AG -> RS (in Ref. 1; AAA36112).	GMP biosynthetic process|oxidation-reduction process|purine base metabolic process	cytosol	IMP dehydrogenase activity|metal ion binding|protein binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)									0.461538	12.235707	12.25355	6	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49039445	49039445	8028	3	C	T	T	24	24	IMPDH2	T	2	2
QARS	5859	broad.mit.edu	36	3	49111108	49111108	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49111108G>A	uc003cvx.1	-	c.1885C>T	c.(1885-1887)CGC>TGC	p.R629C	QARS_uc003cvy.1_Missense_Mutation_p.R484C	NM_005051	NP_005042	P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	629					glutaminyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|glutamine-tRNA ligase activity|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)									0.428571	6.421893	6.453262	3	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49111108	49111108	13329	3	G	A	A	38	38	QARS	A	1	1
USP19	10869	broad.mit.edu	36	3	49128584	49128584	+	Silent	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49128584T>A	uc003cvz.2	-	c.1371A>T	c.(1369-1371)CCA>CCT	p.P457P	USP19_uc003cwa.1_Silent_p.P162P|USP19_uc003cwb.1_Silent_p.P442P|USP19_uc003cwc.1_Silent_p.P112P|USP19_uc003cwd.1_Silent_p.P356P	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	356	CS 2.|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)										0.333333	8.192935	8.489676	4	8	TT		KEEP	---	---	---	---	capture			Silent	SNP	49128584	49128584	17613	3	T	A	A	55	55	USP19	A	4	4
CCDC71	64925	broad.mit.edu	36	3	49175690	49175691	+	Missense_Mutation	DNP	TT	GC	GC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49175690_49175691TT>GC	uc003cwg.2	-	c.955_956AA>GC	c.(955-957)AAG>GCG	p.K319A	CCDC71_uc010hks.1_Missense_Mutation_p.K319A	NM_022903	NP_075054	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	319	Potential.									ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)										0.75	7.754981	7.948982	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	49175690	49175691	2967	3	TT	GC	GC	56	56	CCDC71	GC	4	4
KLHDC8B	200942	broad.mit.edu	36	3	49186807	49186807	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49186807A>T	uc003cwh.1	+	c.508A>T	c.(508-510)ACC>TCC	p.T170S	KLHDC8B_uc003cwi.1_Missense_Mutation_p.T43S	NM_173546	NP_775817	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	170	Kelch 4.					cytoplasm					0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)										0.714286	9.761512	10.046322	5	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49186807	49186807	8675	3	A	T	T	6	6	KLHDC8B	T	4	4
ITIH1	3697	broad.mit.edu	36	3	52800854	52800854	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52800854T>G	uc003dfs.2	+	c.2623T>G	c.(2623-2625)TAC>GAC	p.Y875D	ITIH1_uc010hmn.1_Non-coding_Transcript|ITIH1_uc003dft.2_Missense_Mutation_p.L466R|ITIH1_uc010hmo.1_Missense_Mutation_p.Y429D|ITIH1_uc003dfu.2_Missense_Mutation_p.Y241D|ITIH3_uc003dfv.2_5'Flank	NM_002215	NP_002206	P19827	ITIH1_HUMAN	inter-alpha (globulin) inhibitor H1	875	Hyaluronan-binding.				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)										0.416667	8.357055	8.432835	5	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52800854	52800854	8207	3	T	G	G	53	53	ITIH1	G	4	4
FOXP1	27086	broad.mit.edu	36	3	71119876	71119876	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:71119876G>A	uc003dol.1	-	c.1105C>T	c.(1105-1107)CTG>TTG	p.L369L	FOXP1_uc003dom.1_Silent_p.L293L|FOXP1_uc003don.1_Non-coding_Transcript|FOXP1_uc003doo.1_Silent_p.L369L|FOXP1_uc003dop.1_Silent_p.L369L|FOXP1_uc003doq.1_Silent_p.L368L|FOXP1_uc003doi.1_Silent_p.L269L|FOXP1_uc003doj.1_Silent_p.L269L|FOXP1_uc003dok.1_Silent_p.L182L|FOXP1_uc003dor.1_Silent_p.L147L	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	369	Leucine-zipper.				cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization 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|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)						261				0.555556	31.549404	31.59758	10	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	71119876	71119876	6272	3	G	A	A	35	35	FOXP1	A	2	2
CPOX	1371	broad.mit.edu	36	3	99783032	99783032	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99783032T>A	uc003dsx.1	-	c.1186A>T	c.(1186-1188)AAT>TAT	p.N396Y		NM_000097	NP_000088	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	396	Important for dimerization.			Missing: Loss for dimerization.	oxidation-reduction process	mitochondrial intermembrane space	coproporphyrinogen oxidase activity|protein homodimerization activity				0						Esophageal Squamous(75;7 1223 22300 43648 48951)								0.333333	6.892399	7.189416	4	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99783032	99783032	3959	3	T	A	A	61	61	CPOX	A	4	4
FAT4	79633	broad.mit.edu	36	4	126631331	126631331	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:126631331T>A	uc003ifj.2	+	c.13904T>A	c.(13903-13905)ATC>AAC	p.I4635N	FAT4_uc003ifh.2_Missense_Mutation_p.I4578N|FAT4_uc003ifi.1_Missense_Mutation_p.I2112N	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4	4635	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.277778	7.156425	7.96535	5	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	126631331	126631331	5928	4	T	A	A	50	50	FAT4	A	4	4
DCHS2	54798	broad.mit.edu	36	4	155461330	155461330	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155461330C>T	uc003inw.1	-	c.3306G>A	c.(3304-3306)ACG>ACA	p.T1102T		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1102	Cadherin 9.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)										0.285714	11.096617	11.672063	4	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	155461330	155461330	4459	4	C	T	T	31	31	DCHS2	T	1	1
FGFBP2	83888	broad.mit.edu	36	4	15573537	15573537	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:15573537G>A	uc003gon.1	-	c.314C>T	c.(313-315)GCG>GTG	p.A105V	FGFBP2_uc010ieb.1_Missense_Mutation_p.A105V	NM_031950	NP_114156	Q9BYJ0	FGFP2_HUMAN	killer-specific secretory protein of 37 kDa	105						extracellular space	growth factor binding				0														0.384615	40.215601	40.670417	15	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15573537	15573537	6098	4	G	A	A	38	38	FGFBP2	A	1	1
FGG	2266	broad.mit.edu	36	4	155749251	155749251	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155749251C>T	uc003iok.1	-	c.692G>A	c.(691-693)AGA>AAA	p.R231K	FGG_uc003iog.1_Missense_Mutation_p.R223K|FGG_uc003ioh.1_Missense_Mutation_p.R231K|FGG_uc010ipx.1_Missense_Mutation_p.R51K|FGG_uc010ipy.1_5'UTR|FGG_uc003ioi.1_5'UTR|FGG_uc003ioj.1_Missense_Mutation_p.R223K	NM_021870	NP_068656	P02679	FIBG_HUMAN	fibrinogen, gamma chain isoform gamma-B	223	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)									0.227273	6.753683	8.267765	5	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	155749251	155749251	6107	4	C	T	T	32	32	FGG	T	2	2
C4orf41	60684	broad.mit.edu	36	4	184852794	184852794	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:184852794G>C	uc003ivx.1	+	c.2552G>C	c.(2551-2553)AGA>ACA	p.R851T	C4orf41_uc003ivw.1_Missense_Mutation_p.R851T|C4orf41_uc010isc.1_Missense_Mutation_p.R195T|C4orf41_uc003ivy.1_Missense_Mutation_p.R457T	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	851											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)										0.6	7.022304	7.065408	3	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184852794	184852794	2365	4	G	C	C	33	33	C4orf41	C	3	3
TBC1D19	55296	broad.mit.edu	36	4	26359142	26359142	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:26359142C>T	uc003gsf.2	+	c.1331C>T	c.(1330-1332)TCA>TTA	p.S444L	TBC1D19_uc010iew.1_Missense_Mutation_p.S444L	NM_018317	NP_060787	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	444	Rab-GAP TBC.					intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)												0.25	24.182257	26.211492	9	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26359142	26359142	16129	4	C	T	T	29	29	TBC1D19	T	2	2
PCDH7	5099	broad.mit.edu	36	4	30334030	30334030	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:30334030G>T	uc010iez.1	+	c.1747G>T	c.(1747-1749)GCT>TCT	p.A583S	PCDH7_uc003gsj.1_Missense_Mutation_p.A630S|PCDH7_uc003gsk.1_Missense_Mutation_p.A630S	NM_032457	NP_115833	O60245	PCDH7_HUMAN	protocadherin 7 isoform c precursor	630	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4														0.220183	341.705599	396.793212	168	595	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30334030	30334030	11936	4	G	T	T	42	42	PCDH7	T	3	3
C4orf19	55286	broad.mit.edu	36	4	37268729	37268729	+	Silent	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:37268729A>C	uc003gsw.2	+	c.657A>C	c.(655-657)GGA>GGC	p.G219G	C4orf19_uc003gsy.2_Silent_p.G219G	NM_001104629	NP_060772	Q8IY42	CD019_HUMAN	hypothetical protein LOC55286	219											0														0.636364	15.715706	15.893012	7	4	AA		KEEP	---	---	---	---	capture			Silent	SNP	37268729	37268729	2348	4	A	C	C	9	9	C4orf19	C	4	4
GRXCR1	389207	broad.mit.edu	36	4	42727226	42727226	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:42727226G>A	uc003gwt.1	+	c.785G>A	c.(784-786)CGA>CAA	p.R262Q		NM_001080476	NP_001073945	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	262					cell redox homeostasis|inner ear receptor stereocilium organization|sensory perception of sound|vestibular receptor cell development	kinocilium|stereocilium	electron carrier activity|protein disulfide oxidoreductase activity			ovary(1)	1														0.861111	101.533788	106.065203	31	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42727226	42727226	7092	4	G	A	A	37	37	GRXCR1	A	1	1
PIGG	54872	broad.mit.edu	36	4	510917	510920	+	Nonsense_Mutation	ONP	CCAA	AAGC	AAGC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:510917_510920CCAA>AAGC	uc003gak.2	+	c.2159_2162CCAA>AAGC	c.(2158-2163)TCCAAG>TAAGCG	p.720_721SK>*A	PIGG_uc003gaj.2_Nonsense_Mutation_p.712_713SK>*A|PIGG_uc010ibf.1_Nonsense_Mutation_p.587_588SK>*A|PIGG_uc003gal.2_Nonsense_Mutation_p.631_632SK>*A	NM_001127178	NP_001120650	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	720_721	Helical; (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			ovary(1)|central_nervous_system(1)	2														1	10.657932	10.596775	4	0	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	ONP	510917	510920	12312	4	CCAA	AAGC	AAGC	30	30	PIGG	AAGC	5	3
TMPRSS11F	389208	broad.mit.edu	36	4	68607670	68607670	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:68607670C>A	uc003hdt.1	-	c.1127G>T	c.(1126-1128)GGA>GTA	p.G376V	LOC550112_uc003hdl.2_Intron	NM_207407	NP_997290	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	376	Peptidase S1.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1														0.333333	7.455246	7.831652	5	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68607670	68607670	16784	4	C	A	A	30	30	TMPRSS11F	A	3	3
KIAA0232	9778	broad.mit.edu	36	4	6915905	6915906	+	Missense_Mutation	DNP	TG	AA	AA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:6915905_6915906TG>AA	uc003gjr.2	+	c.2895_2896TG>AA	c.(2893-2898)GATGTT>GAAATT	p.965_966DV>EI	KIAA0232_uc003gjq.2_Missense_Mutation_p.965_966DV>EI	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	965_966							ATP binding			ovary(2)	2														0.224138	14.910495	19.011115	13	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	6915905	6915906	8470	4	TG	AA	AA	51	51	KIAA0232	AA	4	4
CXCL6	6372	broad.mit.edu	36	4	74921798	74921798	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74921798A>T	uc003hhf.1	+	c.257A>T	c.(256-258)AAC>ATC	p.N86I		NM_002993	NP_002984	P80162	CXCL6_HUMAN	chemokine (C-X-C motif) ligand 6 (granulocyte	86					cell-cell signaling|chemotaxis|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity|heparin binding				0	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)											0.275862	10.357297	11.694202	8	21	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74921798	74921798	4248	4	A	T	T	2	2	CXCL6	T	4	4
MRPS18C	51023	broad.mit.edu	36	4	84596349	84596349	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:84596349A>C	uc003hor.2	+	c.95A>C	c.(94-96)CAC>CCC	p.H32P	HELQ_uc003hom.1_5'Flank|HELQ_uc010ikb.1_5'Flank|HELQ_uc003hol.2_5'Flank|HELQ_uc010ikc.1_5'Flank|HELQ_uc003hon.1_5'Flank|HELQ_uc003hoo.1_5'Flank|HELQ_uc003hop.1_5'Flank|HELQ_uc003hoq.1_5'Flank	NM_016067	NP_057151	Q9Y3D5	RT18C_HUMAN	mitochondrial ribosomal protein S18C	32					translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0		Hepatocellular(203;0.114)												0.818182	18.457637	19.496756	9	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84596349	84596349	10223	4	A	C	C	6	6	MRPS18C	C	4	4
WDFY3	23001	broad.mit.edu	36	4	85990127	85990127	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:85990127G>A	uc003hpd.1	-	c.256C>T	c.(256-258)CGA>TGA	p.R86*	WDFY3_uc003hpf.1_Nonsense_Mutation_p.R86*	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	86						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)										0.308824	54.745108	56.96325	21	47	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	85990127	85990127	17842	4	G	A	A	40	40	WDFY3	A	5	1
SLC12A7	10723	broad.mit.edu	36	5	1128533	1128533	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1128533G>A	uc003jbu.1	-	c.1920C>T	c.(1918-1920)TCC>TCT	p.S640S		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	640	Helical; (Potential).				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			large_intestine(1)	1	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)									0.133333	11.763214	19.592535	8	52	GG		KEEP	---	---	---	---	capture			Silent	SNP	1128533	1128533	14883	5	G	A	A	39	39	SLC12A7	A	1	1
REEP2	51308	broad.mit.edu	36	5	137802798	137802798	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137802798T>G	uc003lda.1	+	c.2T>G	c.(1-3)ATG>AGG	p.M1R	REEP2_uc003lcz.1_Missense_Mutation_p.M1R	NM_016606	NP_057690	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	1	Helical; (Potential).					integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)											1	9.847935	9.786295	4	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	137802798	137802798	13674	5	T	G	G	51	51	REEP2	G	4	4
TMCO6	55374	broad.mit.edu	36	5	139999611	139999611	+	Silent	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:139999611G>C	uc003lgm.1	+	c.189G>C	c.(187-189)GGG>GGC	p.G63G	TMCO6_uc003lgl.1_Silent_p.G63G|TMCO6_uc010jft.1_5'UTR|TMCO6_uc003lgn.1_5'Flank|TMCO6_uc003lgo.1_5'Flank	NM_018502	NP_060972	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	63	Potential.|Arg-rich.				protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.75	6.485723	6.648943	3	1	GG		KEEP	---	---	---	---	capture			Silent	SNP	139999611	139999611	16530	5	G	C	C	43	43	TMCO6	C	3	3
PCDHA1	56147	broad.mit.edu	36	5	140146510	140146511	+	Missense_Mutation	DNP	CG	AC	AC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140146510_140146511CG>AC	uc003lhb.1	+	c.451_452CG>AC	c.(451-453)CGT>ACT	p.R151T	PCDHA1_uc003lha.1_Missense_Mutation_p.R151T|PCDHA1_uc003lgz.1_Missense_Mutation_p.R151T	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	151	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.833333	11.374385	11.993005	5	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	140146510	140146511	11939	5	CG	AC	AC	27	27	PCDHA1	AC	3	3
PCDHA2	56146	broad.mit.edu	36	5	140154807	140154809	+	Missense_Mutation	TNP	AGG	CCA	CCA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140154807_140154809AGG>CCA	uc003lhd.1	+	c.74_76AGG>CCA	c.(73-78)GAGGTG>GCCATG	p.25_26EV>AM	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.25_26EV>AM	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	25_26	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.75	6.502413	6.650248	3	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	140154807	140154809	11944	5	AGG	CCA	CCA	11	11	PCDHA2	CCA	4	4
PCDHA6	56142	broad.mit.edu	36	5	140189362	140189362	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140189362A>T	uc003lho.1	+	c.1502A>T	c.(1501-1503)GAG>GTG	p.E501V	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lhn.1_Missense_Mutation_p.E501V|PCDHA6_uc003lhm.1_Missense_Mutation_p.E501V	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	501	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.526316	17.517406	17.527564	10	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140189362	140189362	11948	5	A	T	T	11	11	PCDHA6	T	4	4
PCDHA8	56140	broad.mit.edu	36	5	140202654	140202654	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140202654C>A	uc003lhs.1	+	c.1564C>A	c.(1564-1566)CCG>ACG	p.P522T	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.P522T	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	522	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.75	6.421091	6.644564	3	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140202654	140202654	11950	5	C	A	A	26	26	PCDHA8	A	3	3
PCDHB15	56121	broad.mit.edu	36	5	140605635	140605635	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140605635G>A	uc003lje.1	+	c.305G>A	c.(304-306)TGT>TAT	p.C102Y		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	102	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.341463	41.240147	42.149487	14	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140605635	140605635	11960	5	G	A	A	48	48	PCDHB15	A	2	2
NDST1	3340	broad.mit.edu	36	5	149887768	149887768	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149887768C>T	uc003lsk.2	+	c.723C>T	c.(721-723)GCC>GCT	p.A241A	NDST1_uc003lsl.2_Silent_p.A241A|NDST1_uc003lsm.1_Silent_p.A241A	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	241	Heparan sulfate N-deacetylase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.333333	6.35094	6.497076	2	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	149887768	149887768	10654	5	C	T	T	21	21	NDST1	T	2	2
GALNT10	55568	broad.mit.edu	36	5	153772742	153772742	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:153772742C>G	uc003lvh.1	+	c.1487C>G	c.(1486-1488)GCC>GGC	p.A496G	GALNT10_uc010jic.1_Non-coding_Transcript|GALNT10_uc010jid.1_Missense_Mutation_p.A337G|GALNT10_uc003lvj.1_Missense_Mutation_p.A167G	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a	496	Lumenal (Potential).|Ricin B-type lectin.					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)											0.363636	6.487225	6.670766	4	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153772742	153772742	6472	5	C	G	G	26	26	GALNT10	G	3	3
ATP10B	23120	broad.mit.edu	36	5	159950674	159950674	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:159950674C>A	uc003lym.1	-	c.3615G>T	c.(3613-3615)CAG>CAT	p.Q1205H	ATP10B_uc010jit.1_Missense_Mutation_p.Q455H	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1205	Helical; (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(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.210526	9.388926	10.862524	4	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159950674	159950674	1136	5	C	A	A	32	32	ATP10B	A	3	3
GABRA6	2559	broad.mit.edu	36	5	161049827	161049827	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161049827A>G	uc003lyu.2	+	c.716A>G	c.(715-717)AAG>AGG	p.K239R	GABRA6_uc003lyv.2_Missense_Mutation_p.K10R	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	239	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|large_intestine(1)|central_nervous_system(1)	9	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)						TCGA Ovarian(5;0.080)			0.204082	9.091491	13.121706	10	39	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	161049827	161049827	6416	5	A	G	G	3	3	GABRA6	G	4	4
SLIT3	6586	broad.mit.edu	36	5	168176942	168176942	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168176942G>C	uc010jjg.1	-	c.734C>G	c.(733-735)CCT>CGT	p.P245R	SLIT3_uc003mab.1_Missense_Mutation_p.P245R|SLIT3_uc003mac.1_Missense_Mutation_p.P42R|SLIT3_uc010jji.1_Missense_Mutation_p.P245R	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	245	LRRCT 1.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			Ovarian(29;311 847 10864 17279 24903)								0.236842	10.833324	13.264883	9	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	168176942	168176942	15239	5	G	C	C	35	35	SLIT3	C	3	3
SLC34A1	6569	broad.mit.edu	36	5	176745670	176745670	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176745670C>T	uc003mgk.2	+	c.186C>T	c.(184-186)TGC>TGT	p.C62C		NM_003052	NP_003043	Q06495	NPT2A_HUMAN	solute carrier family 34 (sodium phosphate),	62	Cytoplasmic (Potential).				phosphate ion homeostasis|response to cadmium ion|response to lead ion|response to mercury ion|sodium ion transport	brush border membrane|integral to plasma membrane	protein binding|sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)											1	45.453238	45.45323	17	0	CC		KEEP	---	---	---	---	capture			Silent	SNP	176745670	176745670	15064	5	C	T	T	26	26	SLC34A1	T	2	2
SLC34A1	6569	broad.mit.edu	36	5	176745672	176745672	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176745672C>T	uc003mgk.2	+	c.188C>T	c.(187-189)CCC>CTC	p.P63L		NM_003052	NP_003043	Q06495	NPT2A_HUMAN	solute carrier family 34 (sodium phosphate),	63	Cytoplasmic (Potential).				phosphate ion homeostasis|response to cadmium ion|response to lead ion|response to mercury ion|sodium ion transport	brush border membrane|integral to plasma membrane	protein binding|sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)											1	44.244056	44.244048	17	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176745672	176745672	15064	5	C	T	T	22	22	SLC34A1	T	2	2
SLC34A1	6569	broad.mit.edu	36	5	176745674	176745674	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176745674T>C	uc003mgk.2	+	c.190T>C	c.(190-192)TGT>CGT	p.C64R		NM_003052	NP_003043	Q06495	NPT2A_HUMAN	solute carrier family 34 (sodium phosphate),	64	Cytoplasmic (Potential).				phosphate ion homeostasis|response to cadmium ion|response to lead ion|response to mercury ion|sodium ion transport	brush border membrane|integral to plasma membrane	protein binding|sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)											1	31.283424	31.283171	12	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176745674	176745674	15064	5	T	C	C	55	55	SLC34A1	C	4	4
SLC34A1	6569	broad.mit.edu	36	5	176745678	176745678	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176745678G>T	uc003mgk.2	+	c.194G>T	c.(193-195)GGG>GTG	p.G65V		NM_003052	NP_003043	Q06495	NPT2A_HUMAN	solute carrier family 34 (sodium phosphate),	65	Cytoplasmic (Potential).				phosphate ion homeostasis|response to cadmium ion|response to lead ion|response to mercury ion|sodium ion transport	brush border membrane|integral to plasma membrane	protein binding|sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)											0.857143	12.420746	12.990835	6	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176745678	176745678	15064	5	G	T	T	43	43	SLC34A1	T	3	3
DBN1	1627	broad.mit.edu	36	5	176827780	176827780	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176827780T>C	uc003mgx.2	-	c.196A>G	c.(196-198)ATG>GTG	p.M66V	DBN1_uc003mgy.2_Missense_Mutation_p.M64V|DBN1_uc010jkn.1_5'UTR|DBN1_uc003mgz.1_Missense_Mutation_p.M1V	NM_080881	NP_543157	Q16643	DREB_HUMAN	drebrin 1 isoform b	64	ADF-H.				actin filament organization|regulation of dendrite development|regulation of neuronal synaptic plasticity	actomyosin|cytoplasm|dendrite	actin binding|profilin binding			breast(3)	3	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)						p.M66V(EN-Tumor)	168				0.363636	7.187059	7.370739	4	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176827780	176827780	4423	5	T	C	C	50	50	DBN1	C	4	4
N4BP3	23138	broad.mit.edu	36	5	177479503	177479505	+	Missense_Mutation	TNP	CGG	GCT	GCT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:177479503_177479505CGG>GCT	uc003mik.1	+	c.313_315CGG>GCT	c.(313-315)CGG>GCT	p.R105A	N4BP3_uc003mil.1_5'Flank	NM_015111	NP_055926	O15049	N4BP3_HUMAN	Nedd4 binding protein 3	105						cytoplasmic vesicle membrane					0	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	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)											0.833333	12.020166	12.597588	5	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	177479503	177479505	10508	5	CGG	GCT	GCT	19	19	N4BP3	GCT	3	3
ZNF454	285676	broad.mit.edu	36	5	178324752	178324752	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178324752G>C	uc003mjo.1	+	c.741G>C	c.(739-741)AAG>AAC	p.K247N	ZNF454_uc010jkz.1_Missense_Mutation_p.K247N	NM_182594	NP_872400	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	247	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|lung(1)	2	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)										0.238095	6.856249	8.182428	5	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	178324752	178324752	18516	5	G	C	C	35	35	ZNF454	C	3	3
PLEKHG4B	153478	broad.mit.edu	36	5	226026	226027	+	Missense_Mutation	DNP	AC	GG	GG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:226026_226027AC>GG	uc003jak.2	+	c.2997_2998AC>GG	c.(2995-3000)GAACAG>GAGGAG	p.Q1000E		NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G	1000	PH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)										0.833333	11.774439	12.397282	5	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	226026	226027	12498	5	AC	GG	GG	2	2	PLEKHG4B	GG	4	4
SDHA	6389	broad.mit.edu	36	5	309508	309508	+	Silent	SNP	C	T	T	rs3211499	unknown	TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:309508C>T	uc003jao.2	+	c.1968C>T	c.(1966-1968)ACC>ACT	p.T656T	SDHA_uc003jap.2_Silent_p.T575T|SDHA_uc003jaq.2_Silent_p.T431T|SDHA_uc003jar.2_Silent_p.T250T	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,	656					nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)									0.235294	9.592042	10.681098	4	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	309508	309508	14448	5	C	T	T	23	23	SDHA	T	1	1
PDZD2	23037	broad.mit.edu	36	5	32124362	32124362	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:32124362C>A	uc003jhl.1	+	c.5051C>A	c.(5050-5052)ACT>AAT	p.T1684N	PDZD2_uc003jhm.1_Missense_Mutation_p.T1684N	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1684					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|large_intestine(1)	7														0.5	15.010552	15.010552	7	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32124362	32124362	12122	5	C	A	A	20	20	PDZD2	A	3	3
NIPBL	25836	broad.mit.edu	36	5	36997362	36997362	+	Nonsense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:36997362T>A	uc003jkl.2	+	c.378T>A	c.(376-378)TAT>TAA	p.Y126*	NIPBL_uc003jkk.2_Nonsense_Mutation_p.Y126*|NIPBL_uc003jkm.1_Nonsense_Mutation_p.Y5*	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	126					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding|transcription repressor activity			ovary(3)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	8	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)						p.Y126Y(ESS1-Tumor)	934				0.166667	11.025166	14.822493	6	30	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	36997362	36997362	10829	5	T	A	A	49	49	NIPBL	A	5	4
TNPO1	3842	broad.mit.edu	36	5	72225018	72225018	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:72225018C>T	uc003kck.2	+	c.1955C>T	c.(1954-1956)GCT>GTT	p.A652V	TNPO1_uc003kch.2_Missense_Mutation_p.A644V|TNPO1_uc003kci.2_Missense_Mutation_p.A644V|TNPO1_uc003kcg.2_Missense_Mutation_p.A644V	NM_002270	NP_694858	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	652					interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)										0.25	6.454092	7.602449	5	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72225018	72225018	16876	5	C	T	T	28	28	TNPO1	T	2	2
PDE8B	8622	broad.mit.edu	36	5	76744796	76744796	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:76744796C>A	uc003kfa.1	+	c.1817C>A	c.(1816-1818)GCC>GAC	p.A606D	PDE8B_uc003kfb.1_Missense_Mutation_p.A586D|PDE8B_uc003kfc.1_Missense_Mutation_p.A551D|PDE8B_uc003kfd.1_Missense_Mutation_p.A559D|PDE8B_uc003kfe.1_Missense_Mutation_p.A509D	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1	606	Catalytic (By similarity).				cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)										0.160465	94.437222	141.693382	69	361	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76744796	76744796	12075	5	C	A	A	26	26	PDE8B	A	3	3
LHFPL2	10184	broad.mit.edu	36	5	77841543	77841546	+	Missense_Mutation	ONP	GCCC	TAAA	TAAA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:77841543_77841546GCCC>TAAA	uc003kfo.1	-	c.247_250GGGC>TTTA	c.(247-252)GGGCCC>TTTACC	p.83_84GP>FT		NM_005779	NP_005770	Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	83_84						integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)										1	40.71993	40.719922	17	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	ONP	77841543	77841546	9091	5	GCCC	TAAA	TAAA	42	42	LHFPL2	TAAA	3	3
ZDHHC11	79844	broad.mit.edu	36	5	867894	867894	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:867894G>A	uc003jbi.1	-	c.1163C>T	c.(1162-1164)CCG>CTG	p.P388L	ZDHHC11_uc010itc.1_Non-coding_Transcript|ZDHHC11_uc003jbj.1_Non-coding_Transcript	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	388						integral to membrane	acyltransferase activity|zinc ion binding			pancreas(1)	1			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)											0.333333	34.988514	35.87388	12	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	867894	867894	18189	5	G	A	A	39	39	ZDHHC11	A	1	1
RFX6	222546	broad.mit.edu	36	6	117305735	117305735	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117305735T>G	uc003pxm.1	+	c.307T>G	c.(307-309)TAC>GAC	p.Y103D		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	103					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	promoter binding|protein binding|transcription activator activity			ovary(1)|pancreas(1)	2														0.4	6.587859	6.677604	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117305735	117305735	13739	6	T	G	G	49	49	RFX6	G	4	4
MAN1A1	4121	broad.mit.edu	36	6	119711607	119711607	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:119711607C>T	uc003pym.1	-	c.323G>A	c.(322-324)GGG>GAG	p.G108E	MAN1A1_uc010kei.1_Missense_Mutation_p.G108E	NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	108	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		Ovarian(136;8 1825 12608 33541 47587)								0.714286	10.467512	10.759366	5	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119711607	119711607	9593	6	C	T	T	22	22	MAN1A1	T	2	2
HIVEP2	3097	broad.mit.edu	36	6	143135573	143135573	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:143135573A>C	uc003qjd.1	-	c.1996T>G	c.(1996-1998)TCT>GCT	p.S666A		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	666					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		Esophageal Squamous(107;843 1510 13293 16805 42198)								0.294118	7.359412	8.011309	5	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143135573	143135573	7478	6	A	C	C	9	9	HIVEP2	C	4	4
HIVEP2	3097	broad.mit.edu	36	6	143135943	143135943	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:143135943T>C	uc003qjd.1	-	c.1626A>G	c.(1624-1626)AGA>AGG	p.R542R		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	542					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		Esophageal Squamous(107;843 1510 13293 16805 42198)								0.277778	7.053043	7.865207	5	13	TT		KEEP	---	---	---	---	capture			Silent	SNP	143135943	143135943	7478	6	T	C	C	62	62	HIVEP2	C	4	4
TIAM2	26230	broad.mit.edu	36	6	155492236	155492237	+	Missense_Mutation	DNP	AG	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:155492236_155492237AG>CT	uc003qqb.1	+	c.187_188AG>CT	c.(187-189)AGC>CTC	p.S63L	TIAM2_uc003qqd.1_Missense_Mutation_p.S63L|TIAM2_uc003qqe.1_Missense_Mutation_p.S63L	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	63					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)										0.318182	10.095845	10.754694	7	15	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	155492236	155492237	16419	6	AG	CT	CT	3	3	TIAM2	CT	4	4
PDCD2	5134	broad.mit.edu	36	6	170734713	170734713	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:170734713G>T	uc003qxw.1	-	c.331C>A	c.(331-333)CCA>ACA	p.P111T	PDCD2_uc003qxv.1_Missense_Mutation_p.P78T|PDCD2_uc003qxx.1_Missense_Mutation_p.P111T|PDCD2_uc003qxy.1_Missense_Mutation_p.P78T|PDCD2_uc003qxz.1_Missense_Mutation_p.P111T|PDCD2_uc003qya.1_Missense_Mutation_p.P78T|PDCD2_uc003qyb.1_Intron	NM_002598	NP_002589	Q16342	PDCD2_HUMAN	programmed cell death 2 isoform 1	111					apoptosis	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding				0		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		Colon(60;1476 1726 39478)								0.307692	6.685408	7.120062	4	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170734713	170734713	12040	6	G	T	T	42	42	PDCD2	T	3	3
SCGN	10590	broad.mit.edu	36	6	25777725	25777725	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:25777725G>A	uc003nfb.1	+	c.344G>A	c.(343-345)CGC>CAC	p.R115H	SCGN_uc010jpz.1_Missense_Mutation_p.A25T	NM_006998	NP_008929	O76038	SEGN_HUMAN	secretagogin precursor	115	EF-hand 3.					extracellular region|transport vesicle membrane	calcium ion binding			ovary(2)|pancreas(1)	3														0.765027	475.474685	487.245252	140	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25777725	25777725	14385	6	G	A	A	38	38	SCGN	A	1	1
MYLK4	340156	broad.mit.edu	36	6	2620347	2620347	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:2620347C>A	uc003mty.2	-	c.1052G>T	c.(1051-1053)AGT>ATT	p.S351I	MYLK4_uc003mtx.2_Missense_Mutation_p.S66I	NM_001012418	NP_001012418	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	351	Protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)								535				0.362573	173.885369	176.73364	62	109	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2620347	2620347	10454	6	C	A	A	20	20	MYLK4	A	3	3
ZKSCAN4	387032	broad.mit.edu	36	6	28327443	28327443	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:28327443C>G	uc003nks.1	-	c.295G>C	c.(295-297)GAG>CAG	p.E99Q		NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	99	SCAN box.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.8	8.594834	9.006627	4	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28327443	28327443	18280	6	C	G	G	30	30	ZKSCAN4	G	3	3
ZKSCAN4	387032	broad.mit.edu	36	6	28327445	28327445	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:28327445A>T	uc003nks.1	-	c.293T>A	c.(292-294)CTG>CAG	p.L98Q		NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	98	SCAN box.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.666667	8.696175	8.843362	4	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28327445	28327445	18280	6	A	T	T	7	7	ZKSCAN4	T	4	4
TRIM26	7726	broad.mit.edu	36	6	30274264	30274264	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30274264T>C	uc003npr.1	-	c.455A>G	c.(454-456)CAC>CGC	p.H152R	TRIM26_uc003nps.1_Missense_Mutation_p.H152R|TRIM26_uc010jry.1_5'UTR|TRIM26_uc003npt.1_Missense_Mutation_p.H152R	NM_003449	NP_003440	Q12899	TRI26_HUMAN	tripartite motif-containing 26	152							DNA binding|zinc ion binding			ovary(2)|lung(1)	3														0.444444	9.396093	9.420554	4	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30274264	30274264	17044	6	T	C	C	59	59	TRIM26	C	4	4
MICB	4277	broad.mit.edu	36	6	31581478	31581478	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31581478A>G	uc003ntn.2	+	c.176A>G	c.(175-177)TAT>TGT	p.Y59C	MICB_uc003nto.2_Missense_Mutation_p.Y59C	NM_005931	NP_005922	Q29980	MICB_HUMAN	MHC class I polypeptide-related sequence B	59	Extracellular (Potential).				antigen processing and presentation|cytolysis|gamma-delta T cell activation|immune response|immune response-activating cell surface receptor signaling pathway|interspecies interaction between organisms|negative regulation of defense response to virus by host|response to heat|response to oxidative stress|response to retinoic acid	integral to plasma membrane|MHC class I protein complex	natural killer cell lectin-like receptor binding				0														0.461538	18.147893	18.164564	6	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31581478	31581478	9965	6	A	G	G	16	16	MICB	G	4	4
ZBTB12	221527	broad.mit.edu	36	6	31976274	31976274	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31976274A>C	uc003nyd.1	-	c.788T>G	c.(787-789)GTG>GGG	p.V263G	C2_uc003nyc.1_Intron|EHMT2_uc003nxz.1_5'Flank|EHMT2_uc003nya.1_5'Flank|EHMT2_uc003nyb.1_5'Flank|ZBTB12_uc010jtj.1_Missense_Mutation_p.V263G	NM_181842	NP_862825	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	263	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.333333	6.521841	6.743329	3	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31976274	31976274	18111	6	A	C	C	6	6	ZBTB12	C	4	4
DOM3Z	1797	broad.mit.edu	36	6	32045773	32045773	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32045773G>C	uc003nyo.1	-	c.1051C>G	c.(1051-1053)CAT>GAT	p.H351D	DOM3Z_uc003nyp.1_Missense_Mutation_p.H351D|DOM3Z_uc003nyq.1_Missense_Mutation_p.H92D|DOM3Z_uc003nyr.1_Missense_Mutation_p.H351D|DOM3Z_uc003nys.1_3'UTR|STK19_uc003nyt.1_5'Flank|STK19_uc010jtm.1_5'Flank|STK19_uc003nyv.1_5'Flank|STK19_uc003nyw.1_5'Flank|STK19_uc010jtn.1_5'Flank	NM_005510	NP_005501	O77932	DOM3Z_HUMAN	DOM-3 homolog Z	351							identical protein binding|metal ion binding|nucleotide binding				0										1				0.4	6.383712	6.474654	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32045773	32045773	4889	6	G	C	C	45	45	DOM3Z	C	3	3
TBC1D22B	55633	broad.mit.edu	36	6	37389632	37389632	+	Silent	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:37389632C>A	uc003onn.1	+	c.1152C>A	c.(1150-1152)GTC>GTA	p.V384V	TBC1D22B_uc010jwt.1_Non-coding_Transcript|TBC1D22B_uc003ono.1_Silent_p.V42V|TBC1D22B_uc003onp.1_Silent_p.V42V	NM_017772	NP_060242	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	384	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)											0.5	18.055167	18.055167	9	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	37389632	37389632	16134	6	C	A	A	29	29	TBC1D22B	A	3	3
FAM50B	26240	broad.mit.edu	36	6	3795548	3795549	+	Silent	DNP	GC	AT	AT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:3795548_3795549GC>AT	uc003mvu.1	+	c.504_505GC>AT	c.(502-507)GAGCTG>GAATTG	p.168_169EL>EL	FAM50B_uc010jnp.1_Silent_p.168_169EL>EL	NM_012135	NP_036267	Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	168_169						nucleus				pancreas(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)												0.8	8.634535	9.009621	4	1	GG		KEEP	---	---	---	---	capture			Silent	DNP	3795548	3795549	5800	6	GC	AT	AT	34	34	FAM50B	AT	2	2
NCR2	9436	broad.mit.edu	36	6	41412006	41412007	+	Missense_Mutation	DNP	GA	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41412006_41412007GA>AG	uc003oqh.2	+	c.256_257GA>AG	c.(256-258)GAC>AGC	p.D86S	NCR2_uc003oqi.2_Missense_Mutation_p.D86S|NCR2_uc003oqj.2_Missense_Mutation_p.D86S	NM_004828	NP_004819	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	86	Extracellular (Potential).|Ig-like.				cellular defense response	integral to plasma membrane	transmembrane receptor activity			ovary(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)													0.857143	12.88778	13.396635	6	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	41412006	41412007	10637	6	GA	AG	AG	37	37	NCR2	AG	1	1
MRPS10	55173	broad.mit.edu	36	6	42284627	42284627	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:42284627A>G	uc003osa.2	-	c.469T>C	c.(469-471)TTG>CTG	p.L157L		NM_018141	NP_060611	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	157					translation	actin cytoskeleton|mitochondrion|ribosome	structural constituent of ribosome				0	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)											0.363636	13.171629	13.539888	8	14	AA		KEEP	---	---	---	---	capture			Silent	SNP	42284627	42284627	10214	6	A	G	G	3	3	MRPS10	G	4	4
ZNF318	24149	broad.mit.edu	36	6	43417838	43417839	+	Missense_Mutation	DNP	AA	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43417838_43417839AA>CT	uc003oux.1	-	c.3365_3366TT>AG	c.(3364-3366)GTT>GAG	p.V1122E	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1122					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(2)|breast(2)|central_nervous_system(1)	5			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)											0.181818	8.165175	12.372635	8	36	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	43417838	43417839	18428	6	AA	CT	CT	9	9	ZNF318	CT	4	4
DLK2	65989	broad.mit.edu	36	6	43526574	43526574	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43526574G>A	uc003ova.1	-	c.833C>T	c.(832-834)GCC>GTC	p.A278V	DLK2_uc003ovb.1_Missense_Mutation_p.A278V	NM_023932	NP_996262	Q6UY11	DLK2_HUMAN	EGF-like-domain, multiple 9	278	Extracellular (Potential).					integral to membrane	calcium ion binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)											0.944444	35.608692	36.525342	17	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43526574	43526574	4745	6	G	A	A	42	42	DLK2	A	2	2
DLK2	65989	broad.mit.edu	36	6	43526576	43526577	+	Missense_Mutation	DNP	TG	CA	CA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43526576_43526577TG>CA	uc003ova.1	-	c.830_831CA>TG	c.(829-831)CCA>CTG	p.P277L	DLK2_uc003ovb.1_Missense_Mutation_p.P277L	NM_023932	NP_996262	Q6UY11	DLK2_HUMAN	EGF-like-domain, multiple 9	277	Extracellular (Potential).					integral to membrane	calcium ion binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)											0.909091	22.02238	22.979375	10	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	43526576	43526577	4745	6	TG	CA	CA	55	55	DLK2	CA	4	4
POLH	5429	broad.mit.edu	36	6	43690127	43690128	+	Missense_Mutation	DNP	CC	TT	TT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43690127_43690128CC>TT	uc003ovq.2	+	c.1997_1998CC>TT	c.(1996-1998)CCC>CTT	p.P666L	POLH_uc010jyu.1_Missense_Mutation_p.P542L|POLH_uc003ovr.2_Missense_Mutation_p.P567L	NM_006502	NP_006493	Q9Y253	POLH_HUMAN	polymerase (DNA directed), eta	666					DNA replication|DNA synthesis involved in DNA repair|regulation of DNA repair|response to UV-C	cytoplasm|nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			breast(2)	2	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)											0.470588	14.580179	14.593911	8	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	43690127	43690128	12630	6	CC	TT	TT	22	22	POLH	TT	2	2
HTR1B	3351	broad.mit.edu	36	6	78229144	78229144	+	Nonsense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:78229144G>C	uc003pil.1	-	c.696C>G	c.(694-696)TAC>TAG	p.Y232*		NM_000863	NP_000854	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B	232	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cAMP biosynthetic process|synaptic transmission	integral to plasma membrane	protein binding|serotonin receptor activity				0		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Dexfenfluramine(DB01191)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Pindolol(DB00960)|Propranolol(DB00571)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Venlafaxine(DB00285)|Zolmitriptan(DB00315)									1	67.715329	67.715329	26	0	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	78229144	78229144	7737	6	G	C	C	40	40	HTR1B	C	5	3
HTR1B	3351	broad.mit.edu	36	6	78229147	78229148	+	Missense_Mutation	DNP	GA	CC	CC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:78229147_78229148GA>CC	uc003pil.1	-	c.692_693TC>GG	c.(691-693)ATC>AGG	p.I231R		NM_000863	NP_000854	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B	231	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cAMP biosynthetic process|synaptic transmission	integral to plasma membrane	protein binding|serotonin receptor activity				0		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Dexfenfluramine(DB01191)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Pindolol(DB00960)|Propranolol(DB00571)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Venlafaxine(DB00285)|Zolmitriptan(DB00315)									1	36.988165	36.988133	15	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	78229147	78229148	7737	6	GA	CC	CC	33	33	HTR1B	CC	3	3
TXNDC5	81567	broad.mit.edu	36	6	7828382	7828382	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7828382T>G	uc003mxv.1	-	c.1293A>C	c.(1291-1293)GAA>GAC	p.E431D	TXNDC5_uc003mxw.1_Missense_Mutation_p.E388D|TXNDC5_uc010jnz.1_Missense_Mutation_p.E323D	NM_030810	NP_110437	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 1	431	Prevents secretion from ER (Potential).				anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					Ovarian(119;1430 1625 3928 26125 34589)								0.666667	12.036359	12.255708	6	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7828382	7828382	17355	6	T	G	G	60	60	TXNDC5	G	4	4
TPBG	7162	broad.mit.edu	36	6	83132280	83132280	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:83132280C>A	uc003pjn.2	+	c.883C>A	c.(883-885)CCC>ACC	p.P295T	TPBG_uc010kbj.1_Missense_Mutation_p.P295T|TPBG_uc003pjo.1_Missense_Mutation_p.P295T|TPBG_uc010kbk.1_Missense_Mutation_p.P295T	NM_006670	NP_006661	Q13641	TPBG_HUMAN	trophoblast glycoprotein	295	Extracellular (Potential).|LRRCT.				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)										1	11.483541	11.451973	5	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83132280	83132280	16938	6	C	A	A	30	30	TPBG	A	3	3
TPBG	7162	broad.mit.edu	36	6	83132282	83132282	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:83132282C>T	uc003pjn.2	+	c.885C>T	c.(883-885)CCC>CCT	p.P295P	TPBG_uc010kbj.1_Silent_p.P295P|TPBG_uc003pjo.1_Silent_p.P295P|TPBG_uc010kbk.1_Silent_p.P295P	NM_006670	NP_006661	Q13641	TPBG_HUMAN	trophoblast glycoprotein	295	Extracellular (Potential).|LRRCT.				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)										1	22.35587	22.353857	9	0	CC		KEEP	---	---	---	---	capture			Silent	SNP	83132282	83132282	16938	6	C	T	T	24	24	TPBG	T	2	2
TPBG	7162	broad.mit.edu	36	6	83132284	83132285	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:83132284_83132285GG>TT	uc003pjn.2	+	c.887_888GG>TT	c.(886-888)TGG>TTT	p.W296F	TPBG_uc010kbj.1_Missense_Mutation_p.W296F|TPBG_uc003pjo.1_Missense_Mutation_p.W296F|TPBG_uc010kbk.1_Missense_Mutation_p.W296F	NM_006670	NP_006661	Q13641	TPBG_HUMAN	trophoblast glycoprotein	296	Extracellular (Potential).|LRRCT.				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)										1	28.309221	28.308718	11	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	83132284	83132285	16938	6	GG	TT	TT	47	47	TPBG	TT	3	3
LRCH4	4034	broad.mit.edu	36	7	100013999	100013999	+	Silent	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100013999C>G	uc003uvj.1	-	c.807G>C	c.(805-807)CTG>CTC	p.L269L	LRCH4_uc010lgz.1_Non-coding_Transcript|LRCH4_uc003uvi.1_Non-coding_Transcript	NM_002319	NP_002310	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH)	269					nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.333333	6.989165	7.287798	4	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	100013999	100013999	9308	7	C	G	G	21	21	LRCH4	G	3	3
SLC26A5	375611	broad.mit.edu	36	7	102819323	102819323	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102819323T>C	uc003vbz.1	-	c.1215A>G	c.(1213-1215)GGA>GGG	p.G405G	SLC26A5_uc003vbt.1_Silent_p.G405G|SLC26A5_uc003vbu.1_Silent_p.G405G|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.1_Non-coding_Transcript|SLC26A5_uc003vbx.1_Silent_p.G405G|SLC26A5_uc003vby.1_Non-coding_Transcript|SLC26A5_uc010liy.1_Non-coding_Transcript	NM_198999	NP_945350	P58743	S26A5_HUMAN	prestin isoform a	405	Extracellular (Potential).				regulation of cell shape|sensory perception of sound	integral to membrane	motor activity|secondary active sulfate transmembrane transporter activity			ovary(1)	1														0.24	6.721599	8.283434	6	19	TT		KEEP	---	---	---	---	capture			Silent	SNP	102819323	102819323	15017	7	T	C	C	62	62	SLC26A5	C	4	4
RELN	5649	broad.mit.edu	36	7	102928471	102928471	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102928471G>A	uc003vca.1	-	c.8624C>T	c.(8623-8625)CCG>CTG	p.P2875L	RELN_uc010liz.1_Missense_Mutation_p.P2875L	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2875	EGF-like 7.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.365854	44.314017	44.962741	15	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102928471	102928471	13689	7	G	A	A	39	39	RELN	A	1	1
PUS7	54517	broad.mit.edu	36	7	104910045	104910045	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:104910045G>T	uc010lji.1	-	c.1017C>A	c.(1015-1017)AAC>AAA	p.N339K	PUS7_uc003vcx.1_Missense_Mutation_p.N333K|PUS7_uc003vcy.1_Missense_Mutation_p.N333K|PUS7_uc003vcz.1_Missense_Mutation_p.N333K	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog	333					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						Colon(138;2387 3051 17860)								0.111111	11.121129	27.2888	12	96	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104910045	104910045	13291	7	G	T	T	44	44	PUS7	T	3	3
NRCAM	4897	broad.mit.edu	36	7	107610515	107610515	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:107610515G>C	uc003vfb.1	-	c.2390C>G	c.(2389-2391)TCT>TGT	p.S797C	NRCAM_uc003vfc.1_Missense_Mutation_p.S781C|NRCAM_uc003vfd.1_Missense_Mutation_p.S773C|NRCAM_uc003vfe.1_Missense_Mutation_p.S773C	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A	797	Fibronectin type-III 2.|Extracellular (Potential).				angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5														0.238095	6.353494	7.682053	5	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107610515	107610515	11049	7	G	C	C	33	33	NRCAM	C	3	3
PTPRZ1	5803	broad.mit.edu	36	7	121411323	121411323	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:121411323C>A	uc003vjy.1	+	c.844C>A	c.(844-846)CAA>AAA	p.Q282K	PTPRZ1_uc003vjz.1_Missense_Mutation_p.Q282K	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	282	Extracellular (Potential).|Alpha-carbonic anhydrase.				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9														0.159292	73.37805	98.355059	36	190	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121411323	121411323	13272	7	C	A	A	17	17	PTPRZ1	A	3	3
FLNC	2318	broad.mit.edu	36	7	128268743	128268743	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:128268743G>A	uc003vnz.2	+	c.e13_splice_site			FLNC_uc003voa.2_Splice_Site_SNP	NM_001458	NP_001449			gamma filamin isoform a						cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)	10										892				0.444444	7.287079	7.312711	4	5	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	128268743	128268743	6177	7	G	A	A	35	35	FLNC	A	5	2
SMO	6608	broad.mit.edu	36	7	128632315	128632316	+	Missense_Mutation	DNP	CC	GG	GG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128632315_128632316CC>GG	uc003vor.1	+	c.573_574CC>GG	c.(571-576)GGCCAG>GGGGAG	p.Q192E	SMO_uc003vos.2_5'Flank	NM_005631	NP_005622	Q99835	SMO_HUMAN	smoothened	192	Extracellular (Potential).				adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|negative regulation of gene-specific transcription from RNA polymerase II promoter|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis	cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(18)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1)	36										232				0.266667	7.172714	7.928944	4	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	128632315	128632316	15300	7	CC	GG	GG	26	26	SMO	GG	3	3
CPA2	1358	broad.mit.edu	36	7	129696867	129696867	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:129696867T>C	uc003vpq.1	+	c.270T>C	c.(268-270)ATT>ATC	p.I90I		NM_001869	NP_001860	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic) precursor	92					proteolysis|vacuolar protein catabolic process	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)													0.44	19.889907	19.972529	11	14	TT		KEEP	---	---	---	---	capture			Silent	SNP	129696867	129696867	3928	7	T	C	C	63	63	CPA2	C	4	4
LRGUK	136332	broad.mit.edu	36	7	133478400	133478401	+	Missense_Mutation	DNP	CT	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:133478400_133478401CT>AG	uc003vrm.1	+	c.533_534CT>AG	c.(532-534)GCT>GAG	p.A178E		NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain	178	LRR 3.						ATP binding|kinase activity			lung(2)|kidney(1)|skin(1)	4										973				0.170732	7.694943	11.911488	7	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	133478400	133478401	9316	7	CT	AG	AG	28	28	LRGUK	AG	3	3
FASTK	10922	broad.mit.edu	36	7	150407639	150407639	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150407639G>C	uc003wix.1	-	c.386C>G	c.(385-387)CCA>CGA	p.P129R	FASTK_uc003wiw.1_Intron|FASTK_uc003wiy.1_Intron|FASTK_uc003wiz.1_Missense_Mutation_p.P129R|FASTK_uc003wja.1_Missense_Mutation_p.P95R	NM_006712	NP_006703	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase isoform 1	129					apoptosis|induction of apoptosis by extracellular signals|protein phosphorylation|regulation of RNA splicing		ATP binding|Fas-activated serine/threonine kinase activity|protein binding			lung(2)|stomach(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)						113				0.8	7.898314	8.300976	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150407639	150407639	5920	7	G	C	C	47	47	FASTK	C	3	3
ANKMY2	57037	broad.mit.edu	36	7	16622049	16622049	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:16622049G>T	uc003sti.1	-	c.376C>A	c.(376-378)CAT>AAT	p.H126N	ANKMY2_uc010ktz.1_Non-coding_Transcript	NM_020319	NP_064715	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	126						cilium	zinc ion binding			central_nervous_system(1)	1	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)										0.178571	9.861104	12.582484	5	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16622049	16622049	638	7	G	T	T	48	48	ANKMY2	T	3	3
SP8	221833	broad.mit.edu	36	7	20791346	20791346	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:20791346C>T	uc003suz.1	-	c.615G>A	c.(613-615)TCG>TCA	p.S205S	SP8_uc003suy.1_Silent_p.S187S|SP8_uc010kuj.1_Silent_p.S187S	NM_182700	NP_945194	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor isoform 1	187					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1														0.987805	287.597204	288.546716	81	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	20791346	20791346	15470	7	C	T	T	19	19	SP8	T	1	1
IL6	3569	broad.mit.edu	36	7	22735721	22735721	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:22735721C>T	uc003svj.2	+	c.388C>T	c.(388-390)CAG>TAG	p.Q130*		NM_000600	NP_000591	P05231	IL6_HUMAN	interleukin 6	130					acute-phase response|cellular response to hydrogen peroxide|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|defense response to virus|endocrine pancreas development|glucagon secretion|hepatic immune response|humoral immune response|interleukin-6-mediated signaling pathway|monocyte chemotaxis|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of chemokine biosynthetic process|negative regulation of collagen biosynthetic process|negative regulation of fat cell differentiation|negative regulation of lipid storage|neuron projection development|neutrophil apoptosis|neutrophil mediated immunity|platelet activation|positive regulation of acute inflammatory response|positive regulation of anti-apoptosis|positive regulation of B cell activation|positive regulation of chemokine production|positive regulation of gene-specific transcription|positive regulation of immunoglobulin secretion|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of osteoblast differentiation|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of smooth muscle cell proliferation|positive regulation of T cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of translation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of angiogenesis|regulation of vascular endothelial growth factor production|response to glucocorticoid stimulus|response to peptidoglycan	extracellular space|interleukin-6 receptor complex	cytokine activity|growth factor activity|interleukin-6 receptor binding				0					Arsenic trioxide(DB01169)|Bicalutamide(DB01128)|Ginseng(DB01404)|Simvastatin(DB00641)	Esophageal Squamous(47;342 1214 13936 33513)								0.333333	8.21798	8.673842	6	12	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	22735721	22735721	8002	7	C	T	T	21	21	IL6	T	5	2
CARD11	84433	broad.mit.edu	36	7	2932916	2932916	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:2932916T>G	uc003smv.2	-	c.1790A>C	c.(1789-1791)GAC>GCC	p.D597A		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	597					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|central_nervous_system(1)	48		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)						1492				0.294118	7.456162	8.109666	5	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2932916	2932916	2764	7	T	G	G	58	58	CARD11	G	4	4
INMT	11185	broad.mit.edu	36	7	30759974	30759974	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:30759974T>C	uc003tbs.1	+	c.257T>C	c.(256-258)TTT>TCT	p.F86S	FAM188B_uc010kwe.1_5'UTR|INMT_uc010kwc.1_Non-coding_Transcript|INMT_uc010kwd.1_Missense_Mutation_p.F85S	NM_006774	NP_006765	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	86	S-adenosyl-L-methionine binding.					cytoplasm	amine N-methyltransferase activity				0														0.896552	55.990221	60.121323	26	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30759974	30759974	8046	7	T	C	C	64	64	INMT	C	4	4
INMT	11185	broad.mit.edu	36	7	30759978	30759978	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:30759978C>T	uc003tbs.1	+	c.261C>T	c.(259-261)ACC>ACT	p.T87T	FAM188B_uc010kwe.1_5'UTR|INMT_uc010kwc.1_Non-coding_Transcript|INMT_uc010kwd.1_Silent_p.T86T	NM_006774	NP_006765	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	87	S-adenosyl-L-methionine binding.					cytoplasm	amine N-methyltransferase activity				0														0.95	39.428251	41.47876	19	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	30759978	30759978	8046	7	C	T	T	23	23	INMT	T	1	1
EEPD1	80820	broad.mit.edu	36	7	36305296	36305296	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:36305296G>A	uc003tfa.1	+	c.1666G>A	c.(1666-1668)GTG>ATG	p.V556M		NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family	556					DNA repair|protein secretion	integral to membrane	DNA binding				0														0.347826	12.572652	13.051578	8	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36305296	36305296	5119	7	G	A	A	44	44	EEPD1	A	2	2
DDX56	54606	broad.mit.edu	36	7	44578850	44578850	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:44578850C>A	uc003tlg.1	-	c.402G>T	c.(400-402)AAG>AAT	p.K134N	DDX56_uc003tle.1_Non-coding_Transcript|DDX56_uc003tlf.1_Missense_Mutation_p.K70N|DDX56_uc003tlh.1_Non-coding_Transcript|DDX56_uc010kyg.1_Missense_Mutation_p.K134N|DDX56_uc010kyh.1_Non-coding_Transcript	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 56	134	Helicase ATP-binding.				rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding				0														0.825	219.977753	227.940214	66	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44578850	44578850	4545	7	C	A	A	28	28	DDX56	A	3	3
FKBP6	8468	broad.mit.edu	36	7	72392657	72392657	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72392657A>G	uc003tya.2	+	c.670A>G	c.(670-672)AAC>GAC	p.N224D	FKBP6_uc003twz.2_Missense_Mutation_p.N194D|FKBP6_uc010lbe.1_Non-coding_Transcript	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	224	TPR 2.				protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.222222	9.283665	11.848676	8	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72392657	72392657	6150	7	A	G	G	9	9	FKBP6	G	4	4
POM121C	100101267	broad.mit.edu	36	7	74891283	74891285	+	Missense_Mutation	TNP	GGC	CTG	CTG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:74891283_74891285GGC>CTG	uc003udk.2	-	c.1031_1033GCC>CAG	c.(1030-1035)AGCCTG>ACAGTG	p.344_345SL>TV		NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like	586_587	Pore side (Potential).				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0														1	11.280738	11.2491	5	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	74891283	74891285	12668	7	GGC	CTG	CTG	35	35	POM121C	CTG	3	3
AKAP9	10142	broad.mit.edu	36	7	91546865	91546865	+	Silent	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:91546865A>T	uc003ulh.1	+	c.7518A>T	c.(7516-7518)ATA>ATT	p.I2506I	AKAP9_uc003ulf.1_Silent_p.I2486I|AKAP9_uc003ulg.1_Silent_p.I2494I|AKAP9_uc003uli.1_Silent_p.I2117I|AKAP9_uc003ulj.2_Silent_p.I264I	NM_147171	NP_671700	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 (Protein kinase A-anchoring protein 9) (PRKA9) (A-kinase anchor protein 450 kDa) (AKAP 450) (A-kinase anchor protein 350 kDa) (AKAP 350) (hgAKAP 350) (AKAP 120-like protein) (Protein hyperion) (Protein yotiao) (Centrosome- and Golgi-localized PKN-associated protein) (CG-NAP).	2506	Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)							807				0.277778	7.960463	8.766229	5	13	AA		KEEP	---	---	---	---	capture			Silent	SNP	91546865	91546865	462	7	A	T	T	13	13	AKAP9	T	4	4
TRRAP	8295	broad.mit.edu	36	7	98440726	98440727	+	Missense_Mutation	DNP	CA	GT	GT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:98440726_98440727CA>GT	uc003upp.1	+	c.10530_10531CA>GT	c.(10528-10533)AACACC>AAGTCC	p.3510_3511NT>KS	TRRAP_uc003upq.1_Missense_Mutation_p.3481_3482NT>KS|TRRAP_uc003upr.1_Missense_Mutation_p.3216_3217NT>KS	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3510_3511					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)							1847				0.875	13.242071	14.274433	7	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	98440726	98440727	17152	7	CA	GT	GT	17	17	TRRAP	GT	3	3
TRRAP	8295	broad.mit.edu	36	7	98443973	98443973	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98443973C>T	uc003upp.1	+	c.10749C>T	c.(10747-10749)CTC>CTT	p.L3583L	TRRAP_uc003upq.1_Silent_p.L3554L|TRRAP_uc003upr.1_Silent_p.L3289L	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3583	PI3K/PI4K.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)							1847				0.295455	17.31559	18.99239	13	31	CC		KEEP	---	---	---	---	capture			Silent	SNP	98443973	98443973	17152	7	C	T	T	31	31	TRRAP	T	1	1
SMURF1	57154	broad.mit.edu	36	7	98481347	98481347	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98481347T>A	uc003upu.1	-	c.1244A>T	c.(1243-1245)CAG>CTG	p.Q415L	SMURF1_uc003upv.1_Missense_Mutation_p.Q389L	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform	415					BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			ovary(1)	1	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)							444				0.263158	7.056014	8.029754	5	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98481347	98481347	15319	7	T	A	A	55	55	SMURF1	A	4	4
UBR5	51366	broad.mit.edu	36	8	103408036	103408037	+	Missense_Mutation	DNP	TT	CA	CA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:103408036_103408037TT>CA	uc003ykr.1	-	c.1512_1513AA>TG	c.(1510-1515)AAAATG>AATGTG	p.504_505KM>NV	UBR5_uc003yks.1_Missense_Mutation_p.504_505KM>NV	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	504_505					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(5)|ovary(3)|large_intestine(3)|kidney(1)|central_nervous_system(1)	13	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			Ovarian(131;96 1741 5634 7352 27489)				1024				0.4	14.880684	15.059184	8	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	103408036	103408037	17463	8	TT	CA	CA	52	52	UBR5	CA	4	4
OXR1	55074	broad.mit.edu	36	8	107792195	107792196	+	Splice_Site_DNP	DNP	GT	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:107792195_107792196GT>AG	uc003ymh.1	+	c.e8_splice_site			OXR1_uc010mcg.1_Intron|OXR1_uc003ymj.1_Splice_Site_DNP|OXR1_uc010mch.1_Splice_Site_DNP	NM_181354	NP_851999			oxidation resistance 1 isoform 2						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)											0.52381	21.896979	21.906056	11	10	GG		KEEP	---	---	---	---	capture			Splice_Site_DNP	DNP	107792195	107792196	11747	8	GT	AG	AG	44	44	OXR1	AG	5	2
FAM91A1	157769	broad.mit.edu	36	8	124868778	124868778	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:124868778T>G	uc003yqv.1	+	c.1175T>G	c.(1174-1176)ATG>AGG	p.M392R		NM_144963	NP_659400	Q658Y4	F91A1_HUMAN	hypothetical protein LOC157769	392										ovary(1)|central_nervous_system(1)	2	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)											0.342105	34.259843	35.09851	13	25	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124868778	124868778	5887	8	T	G	G	51	51	FAM91A1	G	4	4
RNF139	11236	broad.mit.edu	36	8	125556579	125556580	+	Missense_Mutation	DNP	GC	CA	CA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:125556579_125556580GC>CA	uc003yrc.1	+	c.48_49GC>CA	c.(46-51)CAGCAG>CACAAG	p.16_17QQ>HK		NM_007218	NP_009149	Q8WU17	RN139_HUMAN	ring finger protein 139	16_17					regulation of protein ubiquitination	endoplasmic reticulum membrane|integral to membrane	ligase activity|protein binding|receptor activity|zinc ion binding			kidney(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)											0.8	7.617633	7.997939	4	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	125556579	125556580	13919	8	GC	CA	CA	34	34	RNF139	CA	3	3
RNF139	11236	broad.mit.edu	36	8	125556584	125556585	+	Missense_Mutation	DNP	TC	CG	CG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:125556584_125556585TC>CG	uc003yrc.1	+	c.53_54TC>CG	c.(52-54)GTC>GCG	p.V18A		NM_007218	NP_009149	Q8WU17	RN139_HUMAN	ring finger protein 139	18				V -> I (in Ref. 1; AAC39930/AAC39931).	regulation of protein ubiquitination	endoplasmic reticulum membrane|integral to membrane	ligase activity|protein binding|receptor activity|zinc ion binding			kidney(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)											0.95	44.212877	45.966383	19	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	125556584	125556585	13919	8	TC	CG	CG	58	58	RNF139	CG	4	4
NSMCE2	286053	broad.mit.edu	36	8	126439154	126439154	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:126439154G>T	uc003yrw.1	+	c.538G>T	c.(538-540)GTG>TTG	p.V180L		NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog	180	SP-RING-type.				DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)											0.25	6.919179	8.302899	6	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	126439154	126439154	11081	8	G	T	T	36	36	NSMCE2	T	3	3
FAM84B	157638	broad.mit.edu	36	8	127638367	127638367	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:127638367C>T	uc003yrz.1	-	c.450G>A	c.(448-450)GTG>GTA	p.V150V	FAM84B_uc010mdo.1_Silent_p.V150V	NM_174911	NP_777571	Q96KN1	FA84B_HUMAN	family with sequence similarity 84, member B	150						cytoplasm|plasma membrane	protein binding				0	Ovarian(5;9.43e-05)|Esophageal squamous(12;0.0012)|Hepatocellular(40;0.128)|Myeloproliferative disorder(2;0.135)		STAD - Stomach adenocarcinoma(47;0.000556)|Colorectal(2;0.0102)|Lung(2;0.0136)|READ - Rectum adenocarcinoma(2;0.0723)											0.714286	15.977149	16.265987	5	2	CC		KEEP	---	---	---	---	capture			Silent	SNP	127638367	127638367	5868	8	C	T	T	29	29	FAM84B	T	2	2
EEF1D	1936	broad.mit.edu	36	8	144743228	144743229	+	Missense_Mutation	DNP	TC	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144743228_144743229TC>CT	uc003yyq.1	-	c.316_317GA>AG	c.(316-318)GAC>AGC	p.D106S	EEF1D_uc003yyp.1_Missense_Mutation_p.D56S|EEF1D_uc003yyr.1_Missense_Mutation_p.D56S|EEF1D_uc003yys.1_Intron|EEF1D_uc003yyt.1_Missense_Mutation_p.D56S|EEF1D_uc003yyu.1_Intron|EEF1D_uc003yyv.1_Intron	NM_032378	NP_115754	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	Error:Variant_position_missing_in_P29692_after_alignment					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)							610				0.9	17.561881	19.019787	9	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	144743228	144743229	5113	8	TC	CT	CT	58	58	EEF1D	CT	4	4
EEF1D	1936	broad.mit.edu	36	8	144743234	144743234	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144743234T>A	uc003yyq.1	-	c.311A>T	c.(310-312)CAG>CTG	p.Q104L	EEF1D_uc003yyp.1_Missense_Mutation_p.Q54L|EEF1D_uc003yyr.1_Missense_Mutation_p.Q54L|EEF1D_uc003yys.1_Intron|EEF1D_uc003yyt.1_Missense_Mutation_p.Q54L|EEF1D_uc003yyu.1_Intron|EEF1D_uc003yyv.1_Intron	NM_032378	NP_115754	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	Error:Variant_position_missing_in_P29692_after_alignment					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)							610				0.972222	84.776973	86.9719	35	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144743234	144743234	5113	8	T	A	A	55	55	EEF1D	A	4	4
MAF1	84232	broad.mit.edu	36	8	145233489	145233491	+	Missense	Complex_substitution	ANC	GNA	GNA			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:145233489A>G	uc003zbc.1	+	c.544A>G	c.(544-546)AGC>GGC	p.S182G	SHARPIN_uc003zba.1_5'Flank|SHARPIN_uc003zbb.1_5'Flank|KIAA1875_uc003zbd.2_5'Flank|KIAA1875_uc010mfq.1_5'Flank	NM_032272	NP_115648	Q9H063	MAF1_HUMAN	MAF1 protein	182					negative regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulator activity				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.1e-42)|Epithelial(56;1.23e-40)|all cancers(56;4.84e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)											0.9	20.741091	22.24941	9	1	AA		KEEP	---	---	---	---	capture			Missense	Complex_substitution	145233489	145233491	9533	8	ANC	GNA	GNA	15	15	MAF1	GNA	5	5
ZNF517	340385	broad.mit.edu	36	8	146004018	146004018	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:146004018A>G	uc003zed.1	+	c.913A>G	c.(913-915)AAC>GAC	p.N305D	ZNF517_uc010mgd.1_Missense_Mutation_p.N211D|ZNF517_uc003zee.1_Non-coding_Transcript|ZNF517_uc003zef.1_Intron	NM_213605	NP_998770	Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	305	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)											0.875	14.10584	14.693339	7	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	146004018	146004018	18555	8	A	G	G	5	5	ZNF517	G	4	4
PSD3	23362	broad.mit.edu	36	8	18773980	18773980	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:18773980G>C	uc003wza.1	-	c.674C>G	c.(673-675)ACT>AGT	p.T225S		NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	225					regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)										0.285714	9.024842	9.902685	6	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18773980	18773980	13101	8	G	C	C	36	36	PSD3	C	3	3
DPYSL2	1808	broad.mit.edu	36	8	26548265	26548265	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:26548265G>A	uc003xfa.2	+	c.1058G>A	c.(1057-1059)TGC>TAC	p.C353Y	DPYSL2_uc010luk.1_Non-coding_Transcript|DPYSL2_uc003xfb.1_Missense_Mutation_p.C248Y	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	248					axon guidance|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)										0.122137	15.705138	34.04801	16	115	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26548265	26548265	4931	8	G	A	A	46	46	DPYSL2	A	2	2
INTS9	55756	broad.mit.edu	36	8	28681603	28681603	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:28681603G>A	uc003xha.1	-	c.1956C>T	c.(1954-1956)CTC>CTT	p.L652L	INTS9_uc010lvc.1_Non-coding_Transcript	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1	652					snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)										1	7.537178	7.418269	3	0	GG		KEEP	---	---	---	---	capture			Silent	SNP	28681603	28681603	8086	8	G	A	A	45	45	INTS9	A	2	2
XKR4	114786	broad.mit.edu	36	8	56178283	56178283	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:56178283C>T	uc003xsf.1	+	c.681C>T	c.(679-681)GCC>GCT	p.A227A		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	227						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)											0.555556	9.25917	9.281762	5	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	56178283	56178283	18014	8	C	T	T	21	21	XKR4	T	2	2
DEFA1B	728358	broad.mit.edu	36	8	6861022	6861022	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:6861022T>C	uc003wqz.1	-	c.185A>G	c.(184-186)AAA>AGA	p.K62R		NM_005217	NP_005208	P59665	DEF1_HUMAN	defensin, alpha 3 preproprotein	62					chemotaxis|defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism|response to virus	extracellular space					0														0.217391	26.32893	29.713314	10	36	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6861022	6861022	4560	8	T	C	C	64	64	DEFA1B	C	4	4
SLCO5A1	81796	broad.mit.edu	36	8	70830315	70830315	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:70830315C>T	uc003xyl.1	-	c.1156G>A	c.(1156-1158)GTT>ATT	p.V386I	SLCO5A1_uc010lzb.1_Missense_Mutation_p.V386I|SLCO5A1_uc003xyk.1_Missense_Mutation_p.V386I|SLCO5A1_uc010lzc.1_Missense_Mutation_p.V386I	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	386	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)	3	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)											0.314815	40.742518	42.398003	17	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70830315	70830315	15228	8	C	T	T	17	17	SLCO5A1	T	2	2
HEY1	23462	broad.mit.edu	36	8	80841856	80841856	+	Silent	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:80841856C>T	uc003ybl.1	-	c.192G>A	c.(190-192)CGG>CGA	p.R64R	HEY1_uc010lzq.1_5'Flank|HEY1_uc003ybm.1_Silent_p.R64R	NM_001040708	NP_001035798	Q9Y5J3	HEY1_HUMAN	hairy/enhancer-of-split related with YRPW motif	64	Helix-loop-helix motif.|Transcriptional repression and interaction with NCOR1 and SIN3A (By similarity).				angiogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|nervous system development|Notch signaling pathway|organ morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			lung(1)	1	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)											0.384615	9.161967	9.316653	5	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	80841856	80841856	7361	8	C	T	T	30	30	HEY1	T	2	2
ABCA1	19	broad.mit.edu	36	9	106614763	106614763	+	Silent	SNP	G	C	C			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:106614763G>C	uc004bcl.1	-	c.3963C>G	c.(3961-3963)GGC>GGG	p.G1321G		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1321					Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol binding|cholesterol transporter activity|phospholipid binding|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|ovary(4)|central_nervous_system(1)|pancreas(1)	10				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.955817	2223.061426	2282.018617	649	30	GG		KEEP	---	---	---	---	capture			Silent	SNP	106614763	106614763	29	9	G	C	C	34	34	ABCA1	C	3	3
ALAD	210	broad.mit.edu	36	9	115191879	115191879	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115191879A>G	uc004bhl.2	-	c.708T>C	c.(706-708)CCT>CCC	p.P236P	ALAD_uc004bhm.2_Silent_p.P216P	NM_001003945	NP_001003945	P13716	HEM2_HUMAN	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24).	207					heme biosynthetic process|protein homooligomerization	cytosol	identical protein binding|lead ion binding|porphobilinogen synthase activity|zinc ion binding				0					Aminolevulinic acid(DB00855)									0.242424	10.165425	12.182418	8	25	AA		KEEP	---	---	---	---	capture			Silent	SNP	115191879	115191879	486	9	A	G	G	3	3	ALAD	G	4	4
C9orf43	257169	broad.mit.edu	36	9	115223230	115223230	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115223230G>A	uc004bho.2	+	c.372G>A	c.(370-372)ACG>ACA	p.T124T	C9orf43_uc004bhp.1_Silent_p.T124T	NM_152786	NP_689999	Q8TAL5	CI043_HUMAN	hypothetical protein LOC257169	124											0														0.865772	893.014179	931.681285	258	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	115223230	115223230	2598	9	G	A	A	38	38	C9orf43	A	1	1
KIF12	113220	broad.mit.edu	36	9	115896554	115896554	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115896554A>G	uc004bif.1	-	c.708T>C	c.(706-708)TCT>TCC	p.S236S	KIF12_uc004big.1_Non-coding_Transcript	NM_138424	NP_612433	Q96FN5	KIF12_HUMAN	kinesin family member 12	369					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0														0.375	9.624779	9.733834	3	5	AA		KEEP	---	---	---	---	capture			Silent	SNP	115896554	115896554	8584	9	A	G	G	11	11	KIF12	G	4	4
ASTN2	23245	broad.mit.edu	36	9	119016751	119016751	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:119016751T>G	uc004bjs.1	-	c.722A>C	c.(721-723)CAG>CCG	p.Q241P	ASTN2_uc004bjr.1_Missense_Mutation_p.Q241P|ASTN2_uc004bjt.1_Missense_Mutation_p.Q241P	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	241	Cytoplasmic (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.333333	7.35485	7.731458	5	10	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119016751	119016751	1084	9	T	G	G	55	55	ASTN2	G	4	4
SCAI	286205	broad.mit.edu	36	9	126831807	126831807	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:126831807T>A	uc004bpd.1	-	c.332A>T	c.(331-333)CAG>CTG	p.Q111L	SCAI_uc004bpe.1_Missense_Mutation_p.Q88L|SCAI_uc010mwu.1_Non-coding_Transcript	NM_173690	NP_775961	Q8N9R8	SCAI_HUMAN	hypothetical protein LOC286205 isoform 1	88	Required for interaction with MKL1 (By similarity).|Necessary to inhibit MKL1-induced SRF transcriptional activity (By similarity).				negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5														0.5	8.49403	8.49403	4	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	126831807	126831807	14350	9	T	A	A	55	55	SCAI	A	4	4
HSPA5	3309	broad.mit.edu	36	9	127042787	127042787	+	Silent	SNP	A	G	G			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:127042787A>G	uc004bpn.1	-	c.343T>C	c.(343-345)TTG>CTG	p.L115L		NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5	115					anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|negative regulation of caspase activity|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			ovary(3)	3					Antihemophilic Factor(DB00025)						Prostate(1;0.17)			0.185185	10.33842	15.35977	10	44	AA		KEEP	---	---	---	---	capture			Silent	SNP	127042787	127042787	7713	9	A	G	G	3	3	HSPA5	G	4	4
NUP188	23511	broad.mit.edu	36	9	130803774	130803774	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:130803774T>C	uc004bws.1	+	c.3989T>C	c.(3988-3990)CTG>CCG	p.L1330P	NUP188_uc004bwu.2_Missense_Mutation_p.L673P	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1330					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|kidney(1)|breast(1)	6														0.388889	12.403593	12.603094	7	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130803774	130803774	11163	9	T	C	C	55	55	NUP188	C	4	4
BRD3	8019	broad.mit.edu	36	9	135903127	135903128	+	Missense_Mutation	DNP	CC	GA	GA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135903127_135903128CC>GA	uc004cew.1	-	c.984_985GG>TC	c.(982-987)GCGGCC>GCTCCC	p.A329P	BRD3_uc004cex.1_Missense_Mutation_p.A329P	NM_007371	NP_031397	Q15059	BRD3_HUMAN	bromodomain containing protein 3	329	Bromo 2.					nucleus	protein binding		BRD3/C15orf55(3)	stomach(4)|midline_organs(3)|kidney(1)	8				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)						497				0.75	12.738462	13.189104	6	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	135903127	135903128	1534	9	CC	GA	GA	26	26	BRD3	GA	3	3
FAM154A	158297	broad.mit.edu	36	9	18940842	18940842	+	Nonsense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:18940842A>T	uc003zni.1	-	c.132T>A	c.(130-132)TAT>TAA	p.Y44*	FAM154A_uc010mip.1_5'UTR	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297	44										pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)										0.25641	12.100154	14.229265	10	29	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	18940842	18940842	5661	9	A	T	T	12	12	FAM154A	T	5	4
DMRTA1	63951	broad.mit.edu	36	9	22437635	22437635	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:22437635G>T	uc003zpp.1	+	c.571G>T	c.(571-573)GGG>TGG	p.G191W		NM_022160	NP_071443	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	191					cell differentiation|regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)	1		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)										0.933333	28.402886	29.668796	14	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22437635	22437635	4768	9	G	T	T	43	43	DMRTA1	T	3	3
TAF1L	138474	broad.mit.edu	36	9	32622101	32622101	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:32622101T>C	uc003zrg.1	-	c.3477A>G	c.(3475-3477)GCA>GCG	p.A1159A		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1159					male meiosis|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding|transcription activator activity			lung(8)|large_intestine(3)|central_nervous_system(3)|skin(2)|ovary(2)|breast(1)|pancreas(1)	20			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)						234				0.190476	14.486062	18.243609	8	34	TT		KEEP	---	---	---	---	capture			Silent	SNP	32622101	32622101	16044	9	T	C	C	51	51	TAF1L	C	4	4
PIGO	84720	broad.mit.edu	36	9	35080538	35080538	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35080538C>G	uc003zwd.1	-	c.2779G>C	c.(2779-2781)GGT>CGT	p.G927R	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.1_Missense_Mutation_p.G510R|PIGO_uc003zwf.1_Missense_Mutation_p.G510R|PIGO_uc003zwg.1_Missense_Mutation_p.G490R	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	927				PFTVPWQAVSAWALMATQTFYSTGHQPVFPAIHWHAAFVGF PEGHGSCTWLPALLVGANTFASHLLFAVGCPLLLLWPFLCE SQGL -> KYLSSDSLKDNSDVSSAPLVFKEVLLLMFLSLT EGPMPHTTRKVFLVSSLLPAIAKQIDPSCWFPGFMERRDKE SSKTPCGNAASS (in Ref. 8).	C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)											0.888889	16.644151	17.914553	8	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35080538	35080538	12318	9	C	G	G	22	22	PIGO	G	3	3
UNC13B	10497	broad.mit.edu	36	9	35393803	35393803	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35393803T>C	uc003zwr.1	+	c.4606T>C	c.(4606-4608)TAC>CAC	p.Y1536H	UNC13B_uc003zwq.1_Missense_Mutation_p.Y1517H|ATP8B5P_uc010mkn.1_5'Flank|ATP8B5P_uc010mko.1_5'Flank|ATP8B5P_uc010mkp.1_5'Flank|ATP8B5P_uc003zwu.2_5'Flank	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like	1517	C2 3.				excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)	4	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)											0.25	10.631579	12.704859	9	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35393803	35393803	17543	9	T	C	C	61	61	UNC13B	C	4	4
RUSC2	9853	broad.mit.edu	36	9	35550333	35550333	+	Silent	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35550333G>A	uc003zww.1	+	c.3696G>A	c.(3694-3696)GTG>GTA	p.V1232V	RUSC2_uc010mkq.1_Non-coding_Transcript|RUSC2_uc003zwx.2_Silent_p.V1232V	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1232						cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)											0.75	6.320211	6.543742	3	1	GG		KEEP	---	---	---	---	capture			Silent	SNP	35550333	35550333	14231	9	G	A	A	47	47	RUSC2	A	2	2
EXOSC3	51010	broad.mit.edu	36	9	37775005	37775005	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:37775005C>T	uc004aal.2	-	c.37G>A	c.(37-39)GCG>ACG	p.A13T	EXOSC3_uc010mly.1_Missense_Mutation_p.A13T|EXOSC3_uc004aam.2_Missense_Mutation_p.A13T	NM_016042	NP_057126	Q9NQT5	EXOS3_HUMAN	exosome component 3 isoform 1	13					CUT catabolic process|DNA deamination|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|isotype switching|rRNA processing	cytoplasmic exosome (RNase complex)|cytosol|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5'-exoribonuclease activity|protein binding|RNA binding			breast(2)	2				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)										0.4	6.482993	6.574213	4	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37775005	37775005	5509	9	C	T	T	27	27	EXOSC3	T	1	1
DOCK8	81704	broad.mit.edu	36	9	416939	416940	+	Missense_Mutation	DNP	AG	GC	GC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:416939_416940AG>GC	uc003zgf.1	+	c.4296_4297AG>GC	c.(4294-4299)GAAGCA>GAGCCA	p.A1433P	DOCK8_uc003zgi.1_Missense_Mutation_p.A1365P|DOCK8_uc010mgu.1_Missense_Mutation_p.A735P|DOCK8_uc010mgv.1_Missense_Mutation_p.A1333P|DOCK8_uc003zgk.1_Missense_Mutation_p.A891P	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1433	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)										0.545455	13.341453	13.360463	6	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	416939	416940	4877	9	AG	GC	GC	3	3	DOCK8	GC	4	4
FOXB2	442425	broad.mit.edu	36	9	78824761	78824761	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:78824761C>G	uc004ako.1	+	c.371C>G	c.(370-372)ACC>AGC	p.T124S		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	124					brain development|embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|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				0														0.833333	10.388043	10.892576	5	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78824761	78824761	6235	9	C	G	G	18	18	FOXB2	G	3	3
VPS13A	23230	broad.mit.edu	36	9	79144252	79144252	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:79144252G>T	uc004akr.1	+	c.6379G>T	c.(6379-6381)GGA>TGA	p.G2127*	VPS13A_uc004akp.2_Nonsense_Mutation_p.G2127*|VPS13A_uc004akq.2_Nonsense_Mutation_p.G2127*|VPS13A_uc004aks.1_Nonsense_Mutation_p.G2088*	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2127					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7														1	8.341988	8.223534	3	0	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	79144252	79144252	17756	9	G	T	T	43	43	VPS13A	T	5	3
PTPRD	5789	broad.mit.edu	36	9	8328977	8328977	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:8328977G>A	uc003zkk.1	-	c.5324C>T	c.(5323-5325)GCT>GTT	p.A1775V	PTPRD_uc003zkp.1_Missense_Mutation_p.A1369V|PTPRD_uc003zkq.1_Missense_Mutation_p.A1368V|PTPRD_uc003zkr.1_Missense_Mutation_p.A1359V|PTPRD_uc003zks.1_Missense_Mutation_p.A1368V|PTPRD_uc003zkl.1_Missense_Mutation_p.A1766V|PTPRD_uc003zkm.1_Missense_Mutation_p.A1762V|PTPRD_uc003zko.1_Missense_Mutation_p.A1365V|PTPRD_uc003zkn.1_Missense_Mutation_p.A1364V	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1775	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				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)			0.179487	12.300671	16.073521	7	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8328977	8328977	13256	9	G	A	A	34	34	PTPRD	A	2	2
HABP4	22927	broad.mit.edu	36	9	98290258	98290258	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:98290258C>T	uc010msg.1	+	c.1066C>T	c.(1066-1068)CAG>TAG	p.Q356*	HABP4_uc010msh.1_Nonsense_Mutation_p.Q251*	NM_014282	NP_055097	Q5JVS0	HABP4_HUMAN	hyaluronan binding protein 4	356					platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)												0.346154	15.847864	16.399741	9	17	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	98290258	98290258	7221	9	C	T	T	21	21	HABP4	T	5	2
TIMM8A	1678	broad.mit.edu	36	X	100490290	100490290	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100490290A>C	uc004ehd.1	-	c.19T>G	c.(19-21)TCC>GCC	p.S7A		NM_004085	NP_004076	O60220	TIM8A_HUMAN	translocase of inner mitochondrial membrane 8	7					nervous system development|protein import into mitochondrial inner membrane|transmembrane transport	mitochondrial inner membrane|mitochondrial intermembrane space protein transporter complex	protein binding				0														0.444444	7.187925	7.21347	4	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100490290	100490290	16443	23	A	C	C	9	9	TIMM8A	C	4	4
NXF2B	728343	broad.mit.edu	36	X	101502210	101502210	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:101502210T>C	uc004ejb.2	-	c.1849A>G	c.(1849-1851)ATC>GTC	p.I617V	NXF2B_uc004eiz.2_3'UTR|NXF2_uc004eiy.2_Missense_Mutation_p.I617V|NXF2B_uc004eja.2_Missense_Mutation_p.I617V	NM_001099686	NP_071336	Q9GZY0	NXF2_HUMAN	nuclear RNA export factor 2B	617	TAP-C.				mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|RNA binding			ovary(1)	1														0.15625	9.654326	13.264225	5	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101502210	101502210	11189	23	T	C	C	50	50	NXF2B	C	4	4
PAK3	5063	broad.mit.edu	36	X	110277758	110277758	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:110277758G>T	uc010npv.1	+	c.522G>T	c.(520-522)ATG>ATT	p.M174I	PAK3_uc010npt.1_Missense_Mutation_p.M138I|PAK3_uc010npu.1_Missense_Mutation_p.M138I|PAK3_uc004eoy.1_5'UTR|PAK3_uc004eoz.2_Missense_Mutation_p.M138I|PAK3_uc010npw.1_Missense_Mutation_p.M159I|PAK3_uc004epa.2_Missense_Mutation_p.M153I	NM_001128168	NP_001121640	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform b	153	Linker.				multicellular organismal development|protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding	p.M138I(1)		lung(5)|ovary(3)|large_intestine(1)	9										137	TSP Lung(19;0.15)			0.24	6.919051	8.48223	6	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110277758	110277758	11818	23	G	T	T	45	45	PAK3	T	3	3
SLC25A5	292	broad.mit.edu	36	X	118488427	118488427	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118488427C>G	uc004erh.2	+	c.662C>G	c.(661-663)ACT>AGT	p.T221S		NM_001152	NP_001143	P05141	ADT2_HUMAN	solute carrier family 25, member 5	221	Helical; Name=5; (By similarity).|Solcar 3.				chromosome segregation|energy reserve metabolic process|interspecies interaction between organisms|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane|mitochondrial nucleoid|MMXD complex	adenine transmembrane transporter activity|protein binding			ovary(1)	1					Clodronate(DB00720)									0.444444	10.996983	11.021373	4	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118488427	118488427	15009	23	C	G	G	20	20	SLC25A5	G	3	3
UPF3B	65109	broad.mit.edu	36	X	118852954	118852954	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118852954T>C	uc004erz.1	-	c.1367A>G	c.(1366-1368)GAT>GGT	p.D456G	UPF3B_uc004esa.1_Missense_Mutation_p.D443G	NM_080632	NP_542199	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B	456					mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|termination of RNA polymerase II transcription	cytosol|exon-exon junction complex|nucleoplasm	mRNA binding|nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(2)|kidney(1)	3														0.3125	7.051795	7.563054	5	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118852954	118852954	17566	23	T	C	C	50	50	UPF3B	C	4	4
GRIA3	2892	broad.mit.edu	36	X	122426517	122426517	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122426517G>T	uc004etq.2	+	c.2197G>T	c.(2197-2199)GCC>TCC	p.A733S	GRIA3_uc004etr.2_Missense_Mutation_p.A733S|GRIA3_uc004ets.2_Non-coding_Transcript	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	733	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|pancreas(1)	4					L-Glutamic Acid(DB00142)					217				0.17	68.25366	88.844625	34	166	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122426517	122426517	7047	23	G	T	T	38	38	GRIA3	T	3	3
ODZ1	10178	broad.mit.edu	36	X	123342639	123342639	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:123342639T>C	uc010nqy.1	-	c.7627A>G	c.(7627-7629)ACA>GCA	p.T2543A	ODZ1_uc004euj.1_Missense_Mutation_p.T2536A	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1	2536	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				0.25	7.920927	8.601609	3	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123342639	123342639	11239	23	T	C	C	60	60	ODZ1	C	4	4
IGSF1	3547	broad.mit.edu	36	X	130243482	130243482	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:130243482T>A	uc004ewd.1	-	c.1364A>T	c.(1363-1365)GAA>GTA	p.E455V	IGSF1_uc004ewf.1_Missense_Mutation_p.E435V|IGSF1_uc010nri.1_Missense_Mutation_p.E444V|IGSF1_uc004ewe.2_Missense_Mutation_p.E444V	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	455	Extracellular (Potential).|Ig-like C2-type 5.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5														0.272727	8.229063	9.26408	6	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130243482	130243482	7897	23	T	A	A	62	62	IGSF1	A	4	4
MAGEA8	4107	broad.mit.edu	36	X	148773769	148773769	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:148773769C>G	uc004fdw.1	+	c.65C>G	c.(64-66)GCA>GGA	p.A22G	MAGEA8_uc010ntd.1_Missense_Mutation_p.A22G	NM_005364	NP_005355	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	22											0	Acute lymphoblastic leukemia(192;6.56e-05)													0.6	8.225131	8.26893	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148773769	148773769	9550	23	C	G	G	25	25	MAGEA8	G	3	3
MECP2	4204	broad.mit.edu	36	X	152949906	152949906	+	Silent	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152949906T>C	uc004fjw.2	-	c.603A>G	c.(601-603)GGA>GGG	p.G201G	MECP2_uc004fjv.2_Silent_p.G189G	NM_001110792	NP_001104262	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 2	189	A.T hook 1.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity|transcription repressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.8	8.347323	8.612145	4	1	TT		KEEP	---	---	---	---	capture			Silent	SNP	152949906	152949906	9812	23	T	C	C	58	58	MECP2	C	4	4
OPN1LW	5956	broad.mit.edu	36	X	153071757	153071757	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153071757C>T	uc004fjz.2	+	c.560C>T	c.(559-561)CCC>CTC	p.P187L		NM_020061	NP_064445	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	187	Helical; Name=4; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity				0	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.347826	24.633198	25.596592	16	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153071757	153071757	11283	23	C	T	T	22	22	OPN1LW	T	2	2
FLNA	2316	broad.mit.edu	36	X	153234767	153234767	+	Splice_Site_SNP	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153234767C>A	uc004fkk.2	-	c.e38_splice_site			FLNA_uc004fki.2_Splice_Site_SNP|FLNA_uc010nuu.1_Splice_Site_SNP	NM_001110556	NP_001104026			filamin A, alpha isoform 2						actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.75	6.372245	6.54781	3	1	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	153234767	153234767	6175	23	C	A	A	24	24	FLNA	A	5	3
FLNA	2316	broad.mit.edu	36	X	153239164	153239164	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153239164T>G	uc004fkk.2	-	c.4777A>C	c.(4777-4779)AAG>CAG	p.K1593Q	FLNA_uc010nuu.1_Missense_Mutation_p.K1593Q	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1593	Interaction with furin (By similarity).|Filamin 14.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.714286	11.771329	12.06034	5	2	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153239164	153239164	6175	23	T	G	G	62	62	FLNA	G	4	4
FLNA	2316	broad.mit.edu	36	X	153239166	153239166	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153239166T>C	uc004fkk.2	-	c.4775A>G	c.(4774-4776)AAG>AGG	p.K1592R	FLNA_uc010nuu.1_Missense_Mutation_p.K1592R	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1592	Interaction with furin (By similarity).|Filamin 14.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.8	8.694348	9.107263	4	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153239166	153239166	6175	23	T	C	C	56	56	FLNA	C	4	4
RPS6KA3	6197	broad.mit.edu	36	X	20103216	20103216	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:20103216T>C	uc004czu.1	-	c.1214A>G	c.(1213-1215)CAT>CGT	p.H405R	RPS6KA3_uc004czv.1_Missense_Mutation_p.H393R	NM_004586	NP_004577	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	405					axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of caspase activity|nerve growth factor receptor signaling pathway|protein phosphorylation|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|ovary(1)|stomach(1)|breast(1)	7										144				0.307692	6.686885	7.120595	4	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20103216	20103216	14132	23	T	C	C	51	51	RPS6KA3	C	4	4
FAM47B	170062	broad.mit.edu	36	X	34871304	34871304	+	Silent	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:34871304C>A	uc004ddi.1	+	c.435C>A	c.(433-435)CTC>CTA	p.L145L		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	145										ovary(3)|breast(1)	4														0.183824	45.393293	58.164238	25	111	CC		KEEP	---	---	---	---	capture			Silent	SNP	34871304	34871304	5791	23	C	A	A	30	30	FAM47B	A	3	3
SYTL5	94122	broad.mit.edu	36	X	37850801	37850801	+	Missense_Mutation	SNP	C	A	A			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:37850801C>A	uc004ddx.1	+	c.1233C>A	c.(1231-1233)AAC>AAA	p.N411K	SYTL5_uc004ddu.1_Missense_Mutation_p.N389K|SYTL5_uc004ddv.1_Missense_Mutation_p.N389K|SYTL5_uc004ddw.1_Missense_Mutation_p.N389K	NM_138780	NP_620135	Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	389					intracellular protein transport	membrane	Rab GTPase binding|zinc ion binding				0														0.15528	142.620947	197.457926	75	408	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37850801	37850801	16007	23	C	A	A	17	17	SYTL5	A	3	3
PHF16	9767	broad.mit.edu	36	X	46803038	46803038	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46803038C>T	uc004dgx.1	+	c.2087C>T	c.(2086-2088)CCC>CTC	p.P696L	PHF16_uc004dgy.1_Missense_Mutation_p.P696L	NM_001077445	NP_055550	Q92613	JADE3_HUMAN	PHD finger protein 16	696					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.366667	19.395173	19.872	11	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46803038	46803038	12250	23	C	T	T	22	22	PHF16	T	2	2
ZNF157	7712	broad.mit.edu	36	X	47157574	47157574	+	Silent	SNP	C	T	T	rs61736396	unknown	TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47157574C>T	uc004dhr.1	+	c.1158C>T	c.(1156-1158)TAC>TAT	p.Y386Y		NM_003446	NP_003437	P51786	ZN157_HUMAN	zinc finger protein 157	386	C2H2-type 9.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.333333	11.0961	11.391258	4	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	47157574	47157574	18328	23	C	T	T	19	19	ZNF157	T	1	1
CCDC22	28952	broad.mit.edu	36	X	48980545	48980545	+	Silent	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48980545G>T	uc004dnd.1	+	c.99G>T	c.(97-99)CTG>CTT	p.L33L	CCDC22_uc004dnc.1_Non-coding_Transcript	NM_014008	NP_054727	O60826	CCD22_HUMAN	coiled-coil domain containing 22	33										central_nervous_system(1)	1														0.25	10.79625	11.702656	4	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	48980545	48980545	2919	23	G	T	T	47	47	CCDC22	T	3	3
HUWE1	10075	broad.mit.edu	36	X	53689044	53689044	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53689044G>A	uc004dso.1	-	c.448C>T	c.(448-450)CGT>TGT	p.R150C	HUWE1_uc004dsp.1_Missense_Mutation_p.R150C	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	150					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.277778	6.450043	7.263851	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53689044	53689044	7761	23	G	A	A	37	37	HUWE1	A	1	1
ZXDB	158586	broad.mit.edu	36	X	57636150	57636150	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:57636150T>A	uc004dvd.1	+	c.944T>A	c.(943-945)TTC>TAC	p.F315Y		NM_007157	NP_009088	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	315	Required for interaction with ZXDC (By similarity).|C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0														1	15.650211	15.634366	6	0	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57636150	57636150	18856	23	T	A	A	62	62	ZXDB	A	4	4
ZXDB	158586	broad.mit.edu	36	X	57636153	57636153	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:57636153C>G	uc004dvd.1	+	c.947C>G	c.(946-948)ACC>AGC	p.T316S		NM_007157	NP_009088	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	316	Required for interaction with ZXDC (By similarity).|C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0														1	41.102194	41.102162	15	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57636153	57636153	18856	23	C	G	G	18	18	ZXDB	G	3	3
ZMYM3	9203	broad.mit.edu	36	X	70383937	70383937	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70383937G>A	uc004dzh.1	-	c.2297C>T	c.(2296-2298)CCC>CTC	p.P766L	ZMYM3_uc004dzi.1_Missense_Mutation_p.P766L|ZMYM3_uc004dzj.1_Missense_Mutation_p.P766L	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	766					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)													0.4	7.1891	7.27873	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70383937	70383937	18292	23	G	A	A	43	43	ZMYM3	A	2	2
ACRC	93953	broad.mit.edu	36	X	70742262	70742262	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70742262A>C	uc004eae.1	+	c.1424A>C	c.(1423-1425)AAG>ACG	p.K475T		NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	475	Arg/Lys/Pro-rich.					nucleus				ovary(3)	3	Renal(35;0.156)													0.444444	7.086289	7.112056	4	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70742262	70742262	172	23	A	C	C	3	3	ACRC	C	4	4
SLC16A2	6567	broad.mit.edu	36	X	73661113	73661113	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1802-01	TCGA-06-1802-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:73661113T>G	uc004ebt.2	+	c.992T>G	c.(991-993)ATC>AGC	p.I331S	SLC16A2_uc010nlr.1_Missense_Mutation_p.I6S	NM_006517	NP_006508	P36021	MOT8_HUMAN	solute carrier family 16, member 2	257	Extracellular (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			breast(2)|ovary(1)	3					Pyruvic acid(DB00119)									0.888889	19.486571	20.143147	8	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73661113	73661113	14904	23	T	G	G	50	50	SLC16A2	G	4	4
KAL1	3730	broad.mit.edu	36	X	8482042	8482042	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:8482042G>T	uc004csf.1	-	c.1305C>A	c.(1303-1305)TTC>TTA	p.F435L		NM_000216	NP_000207	P23352	KALM_HUMAN	Kallmann syndrome 1 protein precursor	435	Fibronectin type-III 3.				axon guidance|cell adhesion|cellular component movement	cell surface|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|serine-type endopeptidase inhibitor activity			ovary(3)|pancreas(1)	4														0.4	6.686574	6.776807	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8482042	8482042	8278	23	G	T	T	33	33	KAL1	T	3	3
DIAPH2	1730	broad.mit.edu	36	X	95880316	95880316	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-1802-01	TCGA-06-1802-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:95880316C>T	uc004efu.2	+	c.241C>T	c.(241-243)CAA>TAA	p.Q81*	DIAPH2_uc004eft.2_Nonsense_Mutation_p.Q81*|DIAPH2_uc004efs.2_Nonsense_Mutation_p.Q81*	NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156	81					cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4														0.372881	37.281002	38.136558	22	37	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	95880316	95880316	4698	23	C	T	T	29	29	DIAPH2	T	5	2
SHROOM2	357	broad.mit.edu	36	X	9822980	9822982	+	Nonsense_Mutation	TNP	TGC	ATA	ATA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:9822980_9822982TGC>ATA	uc004csu.1	+	c.1032_1034TGC>ATA	c.(1030-1035)GCTGCG>GCATAG	p.A345*		NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	345	Poly-Ala.				apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	6		Hepatocellular(5;0.000888)												1	15.2555	15.239721	6	0	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	TNP	9822980	9822982	14789	23	TGC	ATA	ATA	55	55	SHROOM2	ATA	5	4
NLGN4Y	22829	broad.mit.edu	36	Y	15451163	15451163	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrY:15451163A>T	uc004ftg.1	+	c.971A>T	c.(970-972)AAG>ATG	p.K324M	NLGN4Y_uc004fte.1_Missense_Mutation_p.K156M|NLGN4Y_uc004ftf.1_Missense_Mutation_p.K17M|NLGN4Y_uc004fth.1_Missense_Mutation_p.K324M	NM_014893	NP_055708	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked	324	Extracellular (Potential).				brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of synaptic transmission|social behavior|territorial aggressive behavior|vocalization behavior	integral to membrane|plasma membrane|synapse	carboxylesterase activity|protein binding				0														0.222222	10.296911	11.569833	4	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15451163	15451163	10868	24	A	T	T	3	3	NLGN4Y	T	4	4
KDM5D	8284	broad.mit.edu	36	Y	20354014	20354015	+	Missense	DNP	AA	CT	CT			TCGA-06-1802-01	TCGA-06-1802-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrY:20354014A>C	uc004fug.1	-	c.936T>G	c.(934-936)ATT>ATG	p.I312M	KDM5D_uc010nwy.1_Missense_Mutation_p.I255M|KDM5D_uc004fuh.1_Missense_Mutation_p.I267M	NM_004653	NP_004644	Q9BY66	KDM5D_HUMAN	jumonji, AT rich interactive domain 1D	312					chromatin modification|oxidation-reduction process|spermatogenesis	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1					Vitamin C(DB00126)									0.857143	14.755492	15.604142	6	1	AA		KEEP	---	---	---	---	capture			Missense	DNP	20354014	20354015	8442	24	AA	CT	CT	5	5	KDM5D	CT	4	4
TBL1Y	90665	broad.mit.edu	36	Y	7015342	7015342	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1802-01	TCGA-06-1802-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrY:7015342G>T	uc004frb.1	+	c.1315G>T	c.(1315-1317)GTG>TTG	p.V439L	TBL1Y_uc004frc.1_Missense_Mutation_p.V439L|TBL1Y_uc004frd.1_Missense_Mutation_p.V439L	NM_033284	NP_599021	Q9BQ87	TBL1Y_HUMAN	transducin beta-like 1Y	439	WD 6.				transcription, DNA-dependent						0														0.131944	49.252934	87.192883	38	250	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7015342	7015342	16167	24	G	T	T	48	48	TBL1Y	T	3	3
SFXN3	81855	broad.mit.edu	36	10	102785339	102785343	+	Frame_Shift_Del	DEL	TGGTC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102785339_102785343delTGGTC	uc001ksp.1	+	c.269_273delTGGTC	c.(268-273)GTGGTCfs	p.V90fs	SFXN3_uc001ksq.1_Frame_Shift_Del_p.V90fs	NM_030971	NP_112233	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	90_91					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)										0.76			387	125				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	102785339	102785343	14687	10	TGGTC	-	-	59	59	SFXN3	-	5	5
SIRT1	23411	broad.mit.edu	36	10	69318724	69318729	+	In_Frame_Del	DEL	CAATAC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:69318724_69318729delCAATAC	uc001jnd.1	+	c.626_631delCAATAC	c.(625-633)ACAATACCT>ACT	p.IP210del	SIRT1_uc009xpp.1_In_Frame_Del_p.IP18del|SIRT1_uc001jne.1_5'Flank	NM_012238	NP_036370	Q96EB6	SIRT1_HUMAN	sirtuin 1 isoform a	210_211	Interaction with HIST1H1E.				apoptosis|cell aging|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|transcription repressor activity|zinc ion binding				0										395				0.45			76	94				---	---	---	---	capture_indel			In_Frame_Del	DEL	69318724	69318729	14832	10	CAATAC	-	-	17	17	SIRT1	-	5	5
FOXR1	283150	broad.mit.edu	36	11	118355420	118355430	+	Frame_Shift_Del	DEL	CCCCTCACAAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118355420_118355430delCCCCTCACAAA	uc001pui.1	+	c.443_453delCCCCTCACAAA	c.(442-453)TCCCCTCACAAAfs	p.S148fs	FOXR1_uc001puj.1_Intron|FOXR1_uc001puk.1_Intron	NM_181721	NP_859072	Q6PIV2	FOXR1_HUMAN	forkhead box R1	148_151					embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|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				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)										0.95			92	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	118355420	118355430	6277	11	CCCCTCACAAA	-	-	30	30	FOXR1	-	5	5
B3GAT1	27087	broad.mit.edu	36	11	133757866	133757874	+	In_Frame_Del	DEL	CGAAGGAGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:133757866_133757874delCGAAGGAGG	uc001qhq.1	-	c.858_866delCCTCCTTCG	c.(856-867)AGCCTCCTTCGA>AGA	p.SLL286del	B3GAT1_uc001qhr.1_In_Frame_Del_p.SLL286del	NM_018644	NP_473366	Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	286_288	Lumenal (Potential).				carbohydrate metabolic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)										0.63			66	38				---	---	---	---	capture_indel			In_Frame_Del	DEL	133757866	133757874	1274	11	CGAAGGAGG	-	-	31	31	B3GAT1	-	5	5
LSP1	4046	broad.mit.edu	36	11	1861343	1861343	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1861343_1861343delG	uc001luj.1	+	c.859_859delG	c.(859-861)GGGfs	p.G287fs	LSP1_uc001lui.1_Frame_Shift_Del_p.G159fs|LSP1_uc001luk.1_Frame_Shift_Del_p.G97fs|LSP1_uc001lul.1_Frame_Shift_Del_p.G97fs|LSP1_uc001lum.1_Frame_Shift_Del_p.G97fs	NM_001013255	NP_001013273	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 2	159					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)						91				0.79			11	3				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	1861343	1861343	9439	11	G	-	-	35	35	LSP1	-	5	5
LRP4	4038	broad.mit.edu	36	11	46864478	46864481	+	Frame_Shift_Del	DEL	CCCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46864478_46864481delCCCT	uc001ndn.2	-	c.2395_2398delAGGG	c.(2395-2400)AGGGCCfs	p.R799fs		NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	799_800	Extracellular (Potential).|LDL-receptor class B 6.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			ovary(1)	1				Lung(87;0.159)										0.55			12	10				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	46864478	46864481	9332	11	CCCT	-	-	26	26	LRP4	-	5	5
NRXN2	9379	broad.mit.edu	36	11	64154535	64154537	+	In_Frame_Del	DEL	TTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64154535_64154537delTTT	uc001oar.1	-	c.3670_3672delAAA	c.(3670-3672)AAAdel	p.K1224del	NRXN2_uc001oas.1_In_Frame_Del_p.K1184del|NRXN2_uc001oap.1_In_Frame_Del_p.K178del|NRXN2_uc001oaq.1_In_Frame_Del_p.K891del	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	178	Extracellular (Potential).|Laminin G-like.				cell adhesion	integral to membrane				ovary(2)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	6														0.63			57	33				---	---	---	---	capture_indel			In_Frame_Del	DEL	64154535	64154537	11071	11	TTT	-	-	52	52	NRXN2	-	5	5
CABP4	57010	broad.mit.edu	36	11	66980403	66980404	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66980403_66980404delGG	uc001olo.1	+	c.455_456delGG	c.(454-456)CGGfs	p.R152fs	CABP4_uc001oln.1_Frame_Shift_Del_p.R47fs	NM_145200	NP_660201	P57796	CABP4_HUMAN	calcium binding protein 4	152	1 (Potential).|EF-hand 1.				visual perception	cytoplasm|extracellular region|terminal button	calcium ion binding				0			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)											0.95			72	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	66980403	66980404	2649	11	GG	-	-	39	39	CABP4	-	5	5
TPCN2	219931	broad.mit.edu	36	11	68602946	68602946	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:68602946_68602946delG	uc001oos.2	+	c.1421_1421delG	c.(1420-1422)TGCfs	p.C474fs	TPCN2_uc001oot.2_Non-coding_Transcript|TPCN2_uc001oor.2_Frame_Shift_Del_p.C389fs	NM_139075	NP_620714	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	474	Helical; Name=S2 of repeat II; (Potential).					integral to membrane|lysosomal membrane	calcium channel activity|voltage-gated ion channel activity				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)											0.90			57	6				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	68602946	68602946	16940	11	G	-	-	46	46	TPCN2	-	5	5
C11orf54	28970	broad.mit.edu	36	11	93126767	93126768	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:93126767_93126768insC	uc001peh.1	+	c.246_247insC	c.(244-249)AAAATTfs	p.K82fs	C11orf54_uc001pee.1_Frame_Shift_Ins_p.K82fs|C11orf54_uc001pef.1_Frame_Shift_Ins_p.K82fs|C11orf54_uc009ywi.1_Frame_Shift_Ins_p.K82fs|C11orf54_uc001peg.1_Frame_Shift_Ins_p.K82fs|C11orf54_uc001pei.1_Frame_Shift_Ins_p.K63fs|C11orf54_uc001pej.1_Frame_Shift_Ins_p.K63fs|C11orf54_uc001pek.1_5'UTR	NM_014039	NP_054758	Q9H0W9	CK054_HUMAN	hypothetical protein LOC28970	82_83						nucleus	hydrolase activity, acting on ester bonds|protein binding|zinc ion binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.80			24	6				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	93126767	93126768	1688	11	-	C	C	1	1	C11orf54	C	5	5
DRAM1	55332	broad.mit.edu	36	12	100826171	100826172	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:100826171_100826172delAG	uc001tix.1	+	c.419_420delAG	c.(418-420)CAGfs	p.Q140fs		NM_018370	NP_060840	Q8N682	DRAM1_HUMAN	damage-regulated autophagy modulator	140					apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1														0.33			82	168				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	100826171	100826172	4937	12	AG	-	-	7	7	DRAM1	-	5	5
FICD	11153	broad.mit.edu	36	12	107436399	107436399	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107436399_107436399delG	uc001tmx.1	+	c.394_394delG	c.(394-396)GCCfs	p.A132fs		NM_007076	NP_009007	Q9BVA6	FICD_HUMAN	Huntingtin interacting protein E	132	TPR 1.				negative regulation of Rho GTPase activity	integral to membrane	binding|protein adenylyltransferase activity				0														0.66			37	19				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	107436399	107436399	6125	12	G	-	-	38	38	FICD	-	5	5
TAS2R10	50839	broad.mit.edu	36	12	10869920	10869940	+	In_Frame_Del	DEL	TGGAGAGAATATCTGTATAAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10869920_10869940delTGGAGAGAATATCTGTATAAA	uc001qyy.1	-	c.196_216delTTTATACAGATATTCTCTCCA	c.(196-216)TTTATACAGATATTCTCTCCAdel	p.FIQIFSP66del		NM_023921	NP_076410	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	66_72	Extracellular (Potential).				sensory perception of taste	integral to membrane	taste receptor activity				0														0.57			35	26				---	---	---	---	capture_indel			In_Frame_Del	DEL	10869920	10869940	16088	12	TGGAGAGAATATCTGTATAAA	-	-	63	63	TAS2R10	-	5	5
DTX1	1840	broad.mit.edu	36	12	112015780	112015793	+	Frame_Shift_Del	DEL	GCCCCCAAGCCCAT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:112015780_112015793delGCCCCCAAGCCCAT	uc001tuk.1	+	c.1057_1070delGCCCCCAAGCCCAT	c.(1057-1071)GCCCCCAAGCCCATCfs	p.A353fs		NM_004416	NP_004407	Q86Y01	DTX1_HUMAN	deltex homolog 1	353_357	Pro-rich.				negative regulation of neuron differentiation|Notch signaling pathway|regulation of Notch signaling pathway|transcription from RNA polymerase II promoter	cytoplasm|nucleus	Notch binding|SH3 domain binding|transcription coactivator activity|transcription regulator activity|ubiquitin protein ligase binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2										106				0.56			18	14				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	112015780	112015793	4978	12	GCCCCCAAGCCCAT	-	-	42	42	DTX1	-	5	5
RASAL1	8437	broad.mit.edu	36	12	112029282	112029305	+	Splice_Site_Del	DEL	CACCTTCATCCCCATCCACATCCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:112029282_112029305delCACCTTCATCCCCATCCACATCCA	uc001tun.1	-	c.e16_splice_site			RASAL1_uc001tul.2_Splice_Site_Del|RASAL1_uc001tum.1_Splice_Site_Del|RASAL1_uc001tuo.2_Splice_Site_Del	NM_004658	NP_004649			RAS protein activator like 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(1)	3														0.81			47	11				---	---	---	---	capture_indel			Splice_Site_Del	DEL	112029282	112029305	13524	12	CACCTTCATCCCCATCCACATCCA	-	-	29	29	RASAL1	-	5	5
MED13L	23389	broad.mit.edu	36	12	114931012	114931013	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:114931012_114931013insT	uc001tvw.1	-	c.1588_1589insA	c.(1588-1590)GCCfs	p.A530fs		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	530					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		RNA polymerase II transcription mediator activity			skin(3)|ovary(1)|lung(1)	5	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)						497				0.66			31	16				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	114931012	114931013	9820	12	-	T	T	42	42	MED13L	T	5	5
PSMD9	5715	broad.mit.edu	36	12	120825344	120825350	+	Frame_Shift_Del	DEL	AGAACTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120825344_120825350delAGAACTT	uc001ubl.1	+	c.503_509delAGAACTT	c.(502-510)CAGAACTTCfs	p.Q168fs	PSMD9_uc009zxj.1_Non-coding_Transcript|PSMD9_uc001ubm.1_Frame_Shift_Del_p.Q168fs	NM_002813	NP_002804	O00233	PSMD9_HUMAN	proteasome 26S non-ATPase subunit 9	168_170	PDZ.				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 insulin secretion|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of insulin secretion|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	nucleus|proteasome regulatory particle	bHLH transcription factor binding|transcription coactivator activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)										0.66			128	67				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	120825344	120825350	13158	12	AGAACTT	-	-	7	7	PSMD9	-	5	5
GLT1D1	144423	broad.mit.edu	36	12	128033540	128033540	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:128033540_128033540delC	uc001uhx.1	+	c.753_753delC	c.(751-753)GACfs	p.D251fs	GLT1D1_uc001uhy.1_Non-coding_Transcript	NM_144669	NP_653270	Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	331					biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)										0.41			15	22				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	128033540	128033540	6733	12	C	-	-	17	17	GLT1D1	-	5	5
PIWIL1	9271	broad.mit.edu	36	12	129417713	129417718	+	In_Frame_Del	DEL	CTTCCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:129417713_129417718delCTTCCT	uc001uik.1	+	c.2278_2283delCTTCCT	c.(2278-2283)CTTCCTdel	p.LP760del	PIWIL1_uc001uij.1_In_Frame_Del_p.LP760del	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	760_761	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)										0.42			32	44				---	---	---	---	capture_indel			In_Frame_Del	DEL	129417713	129417718	12381	12	CTTCCT	-	-	20	20	PIWIL1	-	5	5
VDR	7421	broad.mit.edu	36	12	46535817	46535818	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:46535817_46535818insG	uc001rql.1	-	c.767_768insC	c.(766-768)GATfs	p.D256fs	VDR_uc001rqm.1_Frame_Shift_Ins_p.D206fs|VDR_uc001rqn.1_Frame_Shift_Ins_p.D206fs	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor	206	Ligand-binding.				decidualization|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)					190				0.39			17	27				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	46535817	46535818	17716	12	-	G	G	12	12	VDR	G	5	5
KRT77	374454	broad.mit.edu	36	12	51383384	51383385	+	Frame_Shift_Ins	INS	-	CA	CA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:51383384_51383385insCA	uc001saw.1	-	c.101_102insTG	c.(100-102)GTGfs	p.V34fs	KRT77_uc009zmi.1_5'UTR	NM_175078	NP_778253	Q7Z794	K2C1B_HUMAN	keratin 77	34	Head.					keratin filament	structural molecule activity			ovary(1)	1														0.60			135	89				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	51383384	51383385	8805	12	-	CA	CA	21	21	KRT77	CA	5	5
ESPL1	9700	broad.mit.edu	36	12	51949748	51949750	+	In_Frame_Del	DEL	TGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:51949748_51949750delTGG	uc001sck.2	+	c.755_757delTGG	c.(754-759)TTGGAG>TAG	p.252_253LE>*	ESPL1_uc001scj.2_5'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	extra spindle poles like 1	252_253					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)	2						Colon(53;1069 1201 2587 5382)								0.67			26	13				---	---	---	---	capture_indel			In_Frame_Del	DEL	51949748	51949750	5446	12	TGG	-	-	63	63	ESPL1	-	5	5
NACA	4666	broad.mit.edu	36	12	55392852	55392852	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55392852_55392852delA	uc009zoy.1	-	c.6207_6207delT	c.(6205-6207)ATTfs	p.I2069fs	NACA_uc001slz.2_Frame_Shift_Del_p.I206fs|NACA_uc001sly.2_Frame_Shift_Del_p.I206fs|NACA_uc001smc.2_Frame_Shift_Del_p.I206fs|NACA_uc001sma.2_Frame_Shift_Del_p.I916fs|NACA_uc001smb.2_Frame_Shift_Del_p.I206fs	NM_001113203	NP_001106674	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	206	UBA.				interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1										449				0.43			87	113				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	55392852	55392852	10528	12	A	-	-	5	5	NACA	-	5	5
ARHGAP9	64333	broad.mit.edu	36	12	56152693	56152699	+	Frame_Shift_Del	DEL	CAGGTTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56152693_56152699delCAGGTTG	uc001sod.1	-	c.2334_2340delCAACCTG	c.(2332-2340)CACAACCTGfs	p.H778fs	ARHGAP9_uc001sny.1_Non-coding_Transcript|ARHGAP9_uc001snz.1_Frame_Shift_Del_p.H504fs|ARHGAP9_uc001soa.1_Frame_Shift_Del_p.H377fs|ARHGAP9_uc001sob.1_3'UTR|ARHGAP9_uc001soc.1_Frame_Shift_Del_p.H688fs	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	707_709	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)											0.74			64	22				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	56152693	56152699	903	12	CAGGTTG	-	-	21	21	ARHGAP9	-	5	5
DYRK2	8445	broad.mit.edu	36	12	66337988	66337989	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:66337988_66337989insG	uc001str.2	+	c.1034_1035insG	c.(1033-1035)ATTfs	p.I345fs	DYRK2_uc001sts.2_Frame_Shift_Ins_p.I272fs|DYRK2_uc009zqu.1_Frame_Shift_Ins_p.I272fs	NM_006482	NP_003574	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	345	Protein kinase.				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|protein phosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)						47				0.48			62	67				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	66337988	66337989	5042	12	-	G	G	52	52	DYRK2	G	5	5
KERA	11081	broad.mit.edu	36	12	89973769	89973772	+	Frame_Shift_Del	DEL	GCAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:89973769_89973772delGCAA	uc001tbl.1	-	c.418_421delTTGC	c.(418-423)TTGCCAfs	p.L140fs		NM_007035	NP_008966	O60938	KERA_HUMAN	keratocan	140_141	LRR 3.				response to stimulus|visual perception	proteinaceous extracellular matrix					0														0.40			35	53				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	89973769	89973772	8449	12	GCAA	-	-	42	42	KERA	-	5	5
PLXNC1	10154	broad.mit.edu	36	12	93142186	93142187	+	Frame_Shift_Del	DEL	AC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:93142186_93142187delAC	uc001tdc.1	+	c.1754_1755delAC	c.(1753-1755)GACfs	p.D585fs		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1	585	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3														0.53			88	77				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	93142186	93142187	12552	12	AC	-	-	10	10	PLXNC1	-	5	5
SOCS4	122809	broad.mit.edu	36	14	54580073	54580077	+	Frame_Shift_Del	DEL	TTTCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:54580073_54580077delTTTCT	uc001xbo.1	+	c.561_565delTTTCT	c.(559-567)TGTTTCTCAfs	p.C187fs	SOCS4_uc001xbp.1_Frame_Shift_Del_p.C187fs|SOCS4_uc010aon.1_Frame_Shift_Del_p.C187fs	NM_199421	NP_955453	Q8WXH5	SOCS4_HUMAN	suppressor of cytokine signaling 4	187_189					intracellular signal transduction|negative regulation of signal transduction|regulation of growth					ovary(1)|kidney(1)	2														0.31			38	83				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	54580073	54580077	15416	14	TTTCT	-	-	60	60	SOCS4	-	5	5
SYNE2	23224	broad.mit.edu	36	14	63674408	63674409	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63674408_63674409delGA	uc001xgl.1	+	c.14797_14798delGA	c.(14797-14799)GACfs	p.D4933fs	SYNE2_uc001xgm.1_Frame_Shift_Del_p.D4933fs|SYNE2_uc010apy.1_Frame_Shift_Del_p.D1318fs|SYNE2_uc001xgn.1_5'Flank	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4933	Potential.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.45			14	17				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	63674408	63674409	15967	14	GA	-	-	45	45	SYNE2	-	5	5
SYNE2	23224	broad.mit.edu	36	14	63682596	63682597	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63682596_63682597delAT	uc001xgl.1	+	c.15541_15542delAT	c.(15541-15543)ATCfs	p.I5181fs	SYNE2_uc001xgm.1_Frame_Shift_Del_p.I5181fs|SYNE2_uc010apy.1_Frame_Shift_Del_p.I1566fs|SYNE2_uc001xgn.1_Frame_Shift_Del_p.I143fs|SYNE2_uc001xgo.1_Non-coding_Transcript	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5181	Spectrin 3.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.49			52	55				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	63682596	63682597	15967	14	AT	-	-	12	12	SYNE2	-	5	5
SPTB	6710	broad.mit.edu	36	14	64320858	64320858	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64320858_64320858delG	uc001xhr.1	-	c.3862_3862delC	c.(3862-3864)CTCfs	p.L1288fs	SPTB_uc001xhs.1_Frame_Shift_Del_p.L1288fs|SPTB_uc001xht.1_Frame_Shift_Del_p.L1288fs|SPTB_uc001xhu.1_Frame_Shift_Del_p.L1288fs|SPTB_uc010aqi.1_5'Flank	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a	1288	Spectrin 10.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|lung(1)|central_nervous_system(1)	9		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)										0.39			42	65				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	64320858	64320858	15632	14	G	-	-	33	33	SPTB	-	5	5
C14orf148	122945	broad.mit.edu	36	14	76950220	76950220	+	Frame_Shift_Del	DEL	T	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:76950220_76950220delT	uc001xtr.2	-	c.159_159delA	c.(157-159)GCAfs	p.A53fs	C14orf148_uc001xts.2_Frame_Shift_Del_p.A53fs	NM_001113475	NP_001106946	Q6NXP6	CN148_HUMAN	hypothetical protein LOC122945 isoform 1	53					oxidation-reduction process|proline biosynthetic process		binding|pyrroline-5-carboxylate reductase activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)										0.50			44	44				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	76950220	76950220	1799	14	T	-	-	51	51	C14orf148	-	5	5
TRIP11	9321	broad.mit.edu	36	14	91505921	91505931	+	Frame_Shift_Del	DEL	ACAGCTGCCGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:91505921_91505931delACAGCTGCCGA	uc001xzy.2	-	c.5779_5789delTCGGCAGCTGT	c.(5779-5790)TCGGCAGCTGTAfs	p.S1927fs	TRIP11_uc010auf.1_Frame_Shift_Del_p.S1663fs	NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1927_1930					transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|kidney(2)|central_nervous_system(1)|breast(1)|skin(1)	11				COAD - Colon adenocarcinoma(157;0.223)		Ovarian(84;609 1888 9852 42686)				1481				0.41			17	24				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	91505921	91505931	17105	14	ACAGCTGCCGA	-	-	14	14	TRIP11	-	5	5
DDX24	57062	broad.mit.edu	36	14	93615284	93615284	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:93615284_93615284delA	uc001ycj.1	-	c.558_558delT	c.(556-558)GATfs	p.D186fs	IFI27L1_uc001ycl.1_5'Flank|IFI27L1_uc001yck.1_5'Flank	NM_020414	NP_065147	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	186					RNA metabolic process	cytoplasm|nucleolus|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|skin(1)	4		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)										0.67			42	21				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	93615284	93615284	4522	14	A	-	-	12	12	DDX24	-	5	5
ZSCAN29	146050	broad.mit.edu	36	15	41441219	41441220	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:41441219_41441220delAG	uc001zrk.1	-	c.1902_1903delCT	c.(1900-1905)AGCTTAfs	p.S634fs	ZSCAN29_uc001zrj.1_Frame_Shift_Del_p.S514fs|ZSCAN29_uc010bdf.1_3'UTR|ZSCAN29_uc001zrl.1_Non-coding_Transcript|ZSCAN29_uc010bdg.1_Frame_Shift_Del_p.S244fs	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690	634_635					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-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;8.97e-07)										0.46			62	73				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	41441219	41441220	18840	15	AG	-	-	3	3	ZSCAN29	-	5	5
DUOXA1	90527	broad.mit.edu	36	15	43197152	43197182	+	Frame_Shift_Del	DEL	CAACATAGCCCTGACTCCACATGCCCTCCTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43197152_43197182delCAACATAGCCCTGACTCCACATGCCCTCCTT	uc001zup.1	-	c.1275_1305delAAGGAGGGCATGTGGAGTCAGGGCTATGTTG	c.(1273-1305)GAAAGGAGGGCATGTGGAGTCAGGGCTATGTTGfs	p.E425fs	DUOXA2_uc001zuo.1_Intron|DUOXA2_uc010beb.1_Intron|DUOXA1_uc010bec.1_Frame_Shift_Del_p.E425fs	NM_144565	NP_653166	Q1HG43	DOXA1_HUMAN	Numb-interacting protein	Error:Variant_position_missing_in_Q1HG43_after_alignment					protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)										1.00			7	0				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	43197152	43197182	4987	15	CAACATAGCCCTGACTCCACATGCCCTCCTT	-	-	25	25	DUOXA1	-	5	5
PRTG	283659	broad.mit.edu	36	15	53758883	53758896	+	Frame_Shift_Del	DEL	GCCAGCTCGAGGCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:53758883_53758896delGCCAGCTCGAGGCC	uc002adg.1	-	c.1013_1026delGGCCTCGAGCTGGC	c.(1012-1026)AGGCCTCGAGCTGGCfs	p.R338fs		NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin	338_342	Ig-like 4.				multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)	2				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)										0.75			106	36				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	53758883	53758896	13089	15	GCCAGCTCGAGGCC	-	-	46	46	PRTG	-	5	5
C15orf27	123591	broad.mit.edu	36	15	74250444	74250445	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:74250444_74250445insC	uc002bbq.1	+	c.569_570insC	c.(568-570)GTGfs	p.V190fs	C15orf27_uc010bkp.1_Frame_Shift_Ins_p.V6fs|C15orf27_uc002bbr.1_Frame_Shift_Ins_p.V6fs	NM_152335	NP_689548	Q2M3C6	CO027_HUMAN	hypothetical protein LOC123591	190	Helical; (Potential).					integral to membrane					0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	74250444	74250445	1838	15	-	C	C	59	59	C15orf27	C	5	5
AKAP13	11214	broad.mit.edu	36	15	83926240	83926252	+	Frame_Shift_Del	DEL	AGTACTCCTGAGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:83926240_83926252delAGTACTCCTGAGG	uc002blu.1	+	c.3937_3949delAGTACTCCTGAGG	c.(3937-3951)AGTACTCCTGAGGAAfs	p.S1313fs	AKAP13_uc002blt.1_Frame_Shift_Del_p.S1313fs|AKAP13_uc002blv.1_Frame_Shift_Del_p.S1313fs|AKAP13_uc010bne.1_5'Flank	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	1313_1317					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)								0.56			40	32				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	83926240	83926252	452	15	AGTACTCCTGAGG	-	-	7	7	AKAP13	-	5	5
ABCC6	368	broad.mit.edu	36	16	16151593	16151594	+	Frame_Shift_Ins	INS	-	AGAA	AGAA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:16151593_16151594insAGAA	uc002den.2	-	c.4409_4410insTTCT	c.(4408-4410)CTGfs	p.L1470fs	ABCC6_uc002dem.1_Frame_Shift_Ins_p.L222fs|ABCC6_uc010bvo.1_Non-coding_Transcript	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	1470	Cytoplasmic (By similarity).|ABC transporter 2.				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)										0.50			7	7				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	16151593	16151594	58	16	-	AGAA	AGAA	21	21	ABCC6	AGAA	5	5
SBK1	388228	broad.mit.edu	36	16	28237994	28237995	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28237994_28237995insC	uc002dpd.1	+	c.404_405insC	c.(403-405)GACfs	p.D135fs		NM_001024401	NP_001019572	Q52WX2	SBK1_HUMAN	SH3-binding domain kinase 1	135	Protein kinase.					cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2										82				0.46			52	60				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	28237994	28237995	14341	16	-	C	C	10	10	SBK1	C	5	5
PRRT2	112476	broad.mit.edu	36	16	29732263	29732264	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:29732263_29732264delAG	uc002dud.2	+	c.387_388delAG	c.(385-390)GCAGCCfs	p.A129fs	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron|PRRT2_uc002due.2_Frame_Shift_Del_p.A129fs|PRRT2_uc002duf.1_Frame_Shift_Del_p.A129fs|C16orf53_uc002dug.2_5'Flank	NM_145239	NP_660282	Q7Z6L0	PRRT2_HUMAN	proline-rich transmembrane protein 2	129_130	Extracellular (Potential).				response to biotic stimulus	integral to membrane					0														0.38			5	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	29732263	29732264	13059	16	AG	-	-	7	7	PRRT2	-	5	5
ADCY9	115	broad.mit.edu	36	16	4104481	4104491	+	Frame_Shift_Del	DEL	CCTTCCCGTGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:4104481_4104491delCCTTCCCGTGC	uc002cvx.1	-	c.954_964delGCACGGGAAGG	c.(952-966)ATGCACGGGAAGGACfs	p.M318fs		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	318_322	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	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)	5														0.60			42	28				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	4104481	4104491	302	16	CCTTCCCGTGC	-	-	30	30	ADCY9	-	5	5
RPGRIP1L	23322	broad.mit.edu	36	16	52244178	52244183	+	In_Frame_Del	DEL	TCAAAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:52244178_52244183delTCAAAA	uc002ehp.1	-	c.1917_1922delTTTTGA	c.(1915-1923)GATTTTGAA>GAA	p.DF639del	RPGRIP1L_uc002ehn.1_In_Frame_Del_p.DF54del|RPGRIP1L_uc002eho.2_In_Frame_Del_p.DF639del|RPGRIP1L_uc010cbx.1_In_Frame_Del_p.DF639del	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	639_640	C2 1.				negative regulation of G-protein coupled receptor protein signaling pathway	centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)												0.35			28	51				---	---	---	---	capture_indel			In_Frame_Del	DEL	52244178	52244183	14029	16	TCAAAA	-	-	62	62	RPGRIP1L	-	5	5
IRX6	79190	broad.mit.edu	36	16	53917952	53917952	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:53917952_53917952delC	uc002ehy.1	+	c.249_249delC	c.(247-249)AGCfs	p.S83fs	IRX6_uc002ehx.2_Frame_Shift_Del_p.S83fs|IRX6_uc010ccb.1_Non-coding_Transcript	NM_024335	NP_077311	P78412	IRX6_HUMAN	iroquois homeobox protein 6	83					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			central_nervous_system(5)|ovary(1)	6														0.56			5	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	53917952	53917952	8152	16	C	-	-	28	28	IRX6	-	5	5
GPR56	9289	broad.mit.edu	36	16	56253329	56253330	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56253329_56253330insAG	uc002emb.1	+	c.1902_1903insAG	c.(1900-1905)ACCTTCfs	p.T634fs	GPR56_uc002ema.1_Frame_Shift_Ins_p.T459fs|GPR56_uc002emc.1_Frame_Shift_Ins_p.T628fs|GPR56_uc002eme.1_Frame_Shift_Ins_p.T628fs|GPR56_uc002emd.1_Frame_Shift_Ins_p.T628fs|GPR56_uc002emf.1_Frame_Shift_Ins_p.T628fs|GPR56_uc002emg.2_Frame_Shift_Ins_p.T628fs	NM_005682	NP_005673	Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56 isoform a	634_635	Extracellular (Potential).				brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity				0														0.43			132	176				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	56253329	56253330	6975	16	-	AG	AG	24	24	GPR56	AG	5	5
EXOC3L	283849	broad.mit.edu	36	16	65777744	65777745	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:65777744_65777745delCA	uc002erx.1	-	c.1392_1393delTG	c.(1390-1395)AGTGATfs	p.S464fs	KIAA0895L_uc002ert.1_5'Flank|KIAA0895L_uc002eru.1_5'Flank|EXOC3L_uc002erv.1_Non-coding_Transcript|EXOC3L_uc002erw.1_Frame_Shift_Del_p.S115fs|EXOC3L_uc002ery.1_Frame_Shift_Del_p.S366fs	NM_178516	NP_848611	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like	464_465					exocytosis|peptide hormone secretion	exocyst|stored secretory granule|transport vesicle					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0021)|Epithelial(162;0.0073)|all cancers(182;0.0616)								OREG0023874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.93			133	10				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	65777744	65777745	5497	16	CA	-	-	29	29	EXOC3L	-	5	5
KCTD19	146212	broad.mit.edu	36	16	65894686	65894699	+	Frame_Shift_Del	DEL	TTCTGTGTCTAACA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:65894686_65894699delTTCTGTGTCTAACA	uc002esu.2	-	c.494_507delTGTTAGACACAGAA	c.(493-507)CTGTTAGACACAGAAfs	p.L165fs	KCTD19_uc002est.2_5'UTR	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain	165_169						voltage-gated potassium channel complex	voltage-gated potassium channel activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)										0.83			116	23				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	65894686	65894699	8412	16	TTCTGTGTCTAACA	-	-	56	56	KCTD19	-	5	5
ZFHX3	463	broad.mit.edu	36	16	71387355	71387355	+	Frame_Shift_Del	DEL	T	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71387355_71387355delT	uc002fck.1	-	c.6727_6727delA	c.(6727-6729)AGGfs	p.R2243fs	ZFHX3_uc002fcl.1_Frame_Shift_Del_p.R1329fs	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	AT-binding transcription factor 1	2243	Homeobox 2.				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)												0.42			120	165				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	71387355	71387355	18222	16	T	-	-	54	54	ZFHX3	-	5	5
KARS	3735	broad.mit.edu	36	16	74220861	74220862	+	Frame_Shift_Del	DEL	GC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74220861_74220862delGC	uc002fer.1	-	c.1587_1588delGC	c.(1585-1590)GAGCTGfs	p.E529fs	KARS_uc002feq.1_Frame_Shift_Del_p.E501fs|KARS_uc002fes.1_Frame_Shift_Del_p.E345fs	NM_005548	NP_005539	Q15046	SYK_HUMAN	lysyl-tRNA synthetase isoform 2	501_502					interspecies interaction between organisms|lysyl-tRNA aminoacylation|tRNA processing	cytosol|extracellular region|mitochondrial matrix|nucleus|plasma membrane|soluble fraction	ATP binding|lysine-tRNA ligase activity|metal ion binding|tRNA binding			ovary(2)	2					L-Lysine(DB00123)									0.64			25	14				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	74220861	74220862	8284	16	GC	-	-	34	34	KARS	-	5	5
FOXC2	2303	broad.mit.edu	36	16	85158999	85159000	+	Frame_Shift_Ins	INS	-	CACCA	CACCA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85158999_85159000insCACCA	uc002fjq.1	+	c.557_558insCACCA	c.(556-558)CCGfs	p.P186fs		NM_005251	NP_005242	Q99958	FOXC2_HUMAN	forkhead box C2	186					anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|embryonic viscerocranium morphogenesis|insulin receptor signaling pathway|lymphangiogenesis|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neural crest cell fate commitment|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of cell adhesion mediated by integrin|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of vascular wound healing|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|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				0														1.00			9	0				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	85158999	85159000	6237	16	-	CACCA	CACCA	23	23	FOXC2	CACCA	5	5
TOP3A	7156	broad.mit.edu	36	17	18150985	18150986	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18150985_18150986insT	uc002gsx.1	-	c.334_335insA	c.(334-336)GTCfs	p.V112fs	TOP3A_uc002gsw.1_5'UTR|TOP3A_uc010cqa.1_Non-coding_Transcript	NM_004618	NP_004609	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	112	Toprim.				DNA topological change|DNA unwinding involved in replication|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(2)	2														0.62			26	16				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	18150985	18150986	16909	17	-	T	T	10	10	TOP3A	T	5	5
MAP2K3	5606	broad.mit.edu	36	17	21146044	21146064	+	Splice_Site_Del	DEL	ACAGGGAGACGTGTGGATCTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:21146044_21146064delACAGGGAGACGTGTGGATCTG	uc002gys.1	+	c.e6_splice_site			MAP2K3_uc002gyt.1_Splice_Site_Del|MAP2K3_uc002gyu.1_Splice_Site_Del	NM_145109	NP_002747			mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)						346				0.93			40	3				---	---	---	---	capture_indel			Splice_Site_Del	DEL	21146044	21146064	9621	17	ACAGGGAGACGTGTGGATCTG	-	-	6	6	MAP2K3	-	5	5
NEK8	284086	broad.mit.edu	36	17	24089070	24089075	+	In_Frame_Del	DEL	AGAGGT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:24089070_24089075delAGAGGT	uc002hcp.1	+	c.996_1001delAGAGGT	c.(994-1002)ACAGAGGTG>ACG	p.EV333del		NM_178170	NP_835464	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	333_334	RCC1 1.				protein phosphorylation	cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|pancreas(1)|stomach(1)|liver(1)|skin(1)	5	Lung NSC(42;0.0158)					NSCLC(6;19 293 14866 25253 49845)				183				0.96			154	6				---	---	---	---	capture_indel			In_Frame_Del	DEL	24089070	24089075	10729	17	AGAGGT	-	-	7	7	NEK8	-	5	5
UNC45B	146862	broad.mit.edu	36	17	30521052	30521053	+	Frame_Shift_Del	DEL	AC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:30521052_30521053delAC	uc002hja.1	+	c.1536_1537delAC	c.(1534-1539)AAACAGfs	p.K512fs	UNC45B_uc002hjb.1_Frame_Shift_Del_p.K512fs|UNC45B_uc002hjc.1_Frame_Shift_Del_p.K512fs|UNC45B_uc010cto.1_Intron	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	512_513					cell differentiation|muscle organ development		binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)												0.78			111	31				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	30521052	30521053	17547	17	AC	-	-	2	2	UNC45B	-	5	5
RASL10B	91608	broad.mit.edu	36	17	31092269	31092270	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31092269_31092270insA	uc002hju.1	+	c.444_445insA	c.(442-447)CGCAAGfs	p.R148fs		NM_033315	NP_201572	Q96S79	RSLAB_HUMAN	RAS-like, family 10, member B	148_149	Small GTPase-like.				small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			breast(2)|lung(1)	3				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.89			89	11				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	31092269	31092270	13541	17	-	A	A	25	25	RASL10B	A	5	5
P2RX5	5026	broad.mit.edu	36	17	3541833	3541834	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:3541833_3541834insG	uc002fwh.1	-	c.141_142insC	c.(139-144)TGGGTGfs	p.W47fs	P2RX5_uc002fwd.1_Non-coding_Transcript|P2RX5_uc002fwi.1_Frame_Shift_Ins_p.W47fs|P2RX5_uc002fwj.1_Frame_Shift_Ins_p.W47fs|P2RX5_uc002fwk.1_Frame_Shift_Ins_p.W47fs|P2RX5_uc002fwl.1_Frame_Shift_Ins_p.W47fs|P2RX5_uc002fwm.1_Frame_Shift_Ins_p.W47fs	NM_002561	NP_002552	Q93086	P2RX5_HUMAN	purinergic receptor P2X5 isoform A	47_48	Helical; Name=1; (Potential).				nervous system development|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0														0.85			124	22				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	3541833	3541834	11756	17	-	G	G	18	18	P2RX5	G	5	5
KAT2A	2648	broad.mit.edu	36	17	37525573	37525573	+	Splice_Site_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37525573_37525573delC	uc002hyx.2	-	c.e4_splice_site			HSPB9_uc002hyy.1_5'Flank	NM_021078	NP_066564			GCN5 general control of amino-acid synthesis						chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity				0														0.68			215	100				---	---	---	---	capture_indel			Splice_Site_Del	DEL	37525573	37525573	8285	17	C	-	-	18	18	KAT2A	-	5	5
IFI35	3430	broad.mit.edu	36	17	38418880	38418889	+	Frame_Shift_Del	DEL	CCAGCCCTTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38418880_38418889delCCAGCCCTTG	uc010cyv.1	+	c.339_348delCCAGCCCTTG	c.(337-348)GTCCAGCCCTTGfs	p.V113fs		NM_005533	NP_005524	P80217	IN35_HUMAN	interferon-induced protein 35	113_116					response to virus|type I interferon-mediated signaling pathway	nucleus	protein binding			ovary(1)	1		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)										0.89			34	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	38418880	38418889	7817	17	CCAGCCCTTG	-	-	30	30	IFI35	-	5	5
ASB16	92591	broad.mit.edu	36	17	39603860	39603865	+	In_Frame_Del	DEL	AGCTGT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39603860_39603865delAGCTGT	uc002ifl.1	+	c.177_182delAGCTGT	c.(175-183)CCAGCTGTC>CCC	p.AV60del	ASB16_uc002ifm.1_Non-coding_Transcript	NM_080863	NP_543139	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box-containing protein	60_61	ANK 1.				intracellular signal transduction		protein binding			kidney(2)	2		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)										0.91			124	12				---	---	---	---	capture_indel			In_Frame_Del	DEL	39603860	39603865	1038	17	AGCTGT	-	-	7	7	ASB16	-	5	5
ITGA2B	3674	broad.mit.edu	36	17	39822291	39822295	+	Frame_Shift_Del	DEL	GCAGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39822291_39822295delGCAGC	uc002igt.1	-	c.73_77delGCTGC	c.(73-78)GCTGCCfs	p.A25fs		NM_000419	NP_000410	P08514	ITA2B_HUMAN	integrin alpha 2b preproprotein	25_26					axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Tirofiban(DB00775)									0.71			20	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	39822291	39822295	8180	17	GCAGC	-	-	42	42	ITGA2B	-	5	5
WNT9B	7484	broad.mit.edu	36	17	42308992	42308996	+	Frame_Shift_Del	DEL	CCTTC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42308992_42308996delCCTTC	uc002ikw.1	+	c.983_987delCCTTC	c.(982-987)GCCTTCfs	p.A328fs	WNT9B_uc002ikx.1_Intron	NM_003396	NP_003387	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family,	328_329					anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|collecting duct development|cornea development in camera-type eye|endoderm development|establishment of planar polarity involved in nephron morphogenesis|kidney rudiment formation|male genitalia development|mesonephric duct formation|metanephric tubule development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|palate development|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|uterus morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway|Wnt receptor signaling pathway, planar cell polarity pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding				0			BRCA - Breast invasive adenocarcinoma(9;0.0257)											0.42			22	30				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	42308992	42308996	17973	17	CCTTC	-	-	26	26	WNT9B	-	5	5
EME1	146956	broad.mit.edu	36	17	45811185	45811193	+	In_Frame_Del	DEL	ACTGACATC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:45811185_45811193delACTGACATC	uc010dbp.1	+	c.1042_1050delACTGACATC	c.(1042-1050)ACTGACATCdel	p.TDI348del	EME1_uc002iqs.1_In_Frame_Del_p.TDI348del|EME1_uc010dbq.1_5'Flank	NM_152463	NP_689676	Q96AY2	EME1_HUMAN	essential meiotic endonuclease 1 homolog 1	348_350					DNA recombination|DNA repair	nucleolus	DNA binding|endonuclease activity|metal ion binding|protein binding				0	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)											0.35			423	770				---	---	---	---	capture_indel			In_Frame_Del	DEL	45811185	45811193	5280	17	ACTGACATC	-	-	2	2	EME1	-	5	5
SPAG9	9043	broad.mit.edu	36	17	46427535	46427536	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46427535_46427536insT	uc002itc.1	-	c.2107_2108insA	c.(2107-2109)GGTfs	p.G703fs	SPAG9_uc002ita.1_Frame_Shift_Ins_p.G38fs|SPAG9_uc002itb.1_Frame_Shift_Ins_p.G689fs|SPAG9_uc002itd.1_Frame_Shift_Ins_p.G693fs|SPAG9_uc002ite.2_Frame_Shift_Ins_p.G533fs|SPAG9_uc002itf.2_Frame_Shift_Ins_p.G524fs	NM_003971	NP_003962	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 3	703					positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(1)	1			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)											0.42			46	63				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	46427535	46427536	15488	17	-	T	T	18	18	SPAG9	T	5	5
SPAG9	9043	broad.mit.edu	36	17	46512023	46512024	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46512023_46512024insT	uc002itc.1	-	c.344_345insA	c.(343-345)AAGfs	p.K115fs	SPAG9_uc002itb.1_Frame_Shift_Ins_p.K115fs|SPAG9_uc002itd.1_Frame_Shift_Ins_p.K115fs|SPAG9_uc002itf.2_5'UTR	NM_003971	NP_003962	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 3	115	Potential.				positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(1)	1			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	46512023	46512024	15488	17	-	T	T	24	24	SPAG9	T	5	5
CAMTA2	23125	broad.mit.edu	36	17	4824254	4824265	+	In_Frame_Del	DEL	CAGTGCCTACAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4824254_4824265delCAGTGCCTACAA	uc002gah.1	-	c.1076_1087delTTGTAGGCACTG	c.(1075-1089)GTTGTAGGCACTGAG>GAG	p.VVGT359del	CAMTA2_uc010cku.1_In_Frame_Del_p.VVGT382del|CAMTA2_uc002gag.1_In_Frame_Del_p.VVGT358del|CAMTA2_uc002gai.1_In_Frame_Del_p.VVGT361del|CAMTA2_uc010ckv.1_In_Frame_Del_p.VVGT6del	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	359_362					cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding|transcription regulator activity			ovary(1)	1												OREG0024111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.49			40	41				---	---	---	---	capture_indel			In_Frame_Del	DEL	4824254	4824265	2731	17	CAGTGCCTACAA	-	-	29	29	CAMTA2	-	5	5
USP6	9098	broad.mit.edu	36	17	5012133	5012134	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:5012133_5012134insT	uc002gau.1	+	c.3219_3220insT	c.(3217-3222)CCACCCfs	p.P1073fs	USP6_uc002gav.1_Frame_Shift_Ins_p.P1073fs|USP6_uc010ckz.1_Frame_Shift_Ins_p.P756fs	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6	1073_1074					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)	1										464				0.36			21	37				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	5012133	5012134	17650	17	-	T	T	6	6	USP6	T	5	5
ZNF594	84622	broad.mit.edu	36	17	5027394	5027398	+	Frame_Shift_Del	DEL	GGGTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:5027394_5027398delGGGTT	uc010cla.1	-	c.878_882delAACCC	c.(877-882)AAACCCfs	p.K293fs	ZNF594_uc002gbe.2_Frame_Shift_Del_p.K293fs	NM_032530	NP_115919	Q96JF6	ZN594_HUMAN	zinc finger protein 594	293_294					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.46			62	72				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	5027394	5027398	18619	17	GGGTT	-	-	43	43	ZNF594	-	5	5
RNFT1	51136	broad.mit.edu	36	17	55395429	55395445	+	Splice_Site_Del	DEL	TAAAAAATCAAATAAAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:55395429_55395445delTAAAAAATCAAATAAAA	uc002iya.1	-	c.e2_splice_site			RNFT1_uc002iyb.1_Splice_Site_Del|RNFT1_uc002iyc.1_Splice_Site_Del|RNFT1_uc002iyd.2_Splice_Site_Del	NM_016125	NP_057209			PTD016 protein							integral to membrane	zinc ion binding				0	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)											0.51			48	46				---	---	---	---	capture_indel			Splice_Site_Del	DEL	55395429	55395445	13980	17	TAAAAAATCAAATAAAA	-	-	53	53	RNFT1	-	5	5
ACOX1	51	broad.mit.edu	36	17	71456117	71456118	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:71456117_71456118insG	uc002jqe.1	-	c.1744_1745insC	c.(1744-1746)GAGfs	p.E582fs	ACOX1_uc002jqf.1_Frame_Shift_Ins_p.E582fs	NM_004035	NP_004026	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1, palmitoyl isoform a	582					fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1														0.88			68	9				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	71456117	71456118	159	17	-	G	G	54	54	ACOX1	G	5	5
SHBG	6462	broad.mit.edu	36	17	7476893	7476895	+	In_Frame_Del	DEL	GAG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7476893_7476895delGAG	uc002gie.1	+	c.951_953delGAG	c.(949-954)TTGAGC>TTC	p.317_318LS>F	SHBG_uc010cmo.1_In_Frame_Del_p.205_206LS>F|SHBG_uc010cmp.1_Intron|SHBG_uc010cmq.1_Intron|SHBG_uc010cmr.1_Intron|SHBG_uc010cms.1_Intron|SHBG_uc010cmt.1_In_Frame_Del_p.259_260LS>F|SHBG_uc010cmu.1_Intron|SHBG_uc010cmv.1_Intron|SHBG_uc010cmw.1_Intron|SHBG_uc010cmx.1_Intron|SHBG_uc010cmy.1_In_Frame_Del_p.259_260LS>F|SHBG_uc002gid.2_Intron|SHBG_uc010cmz.1_Intron|SHBG_uc010cna.1_Intron|SHBG_uc010cnb.1_Intron|SHBG_uc010cnc.1_Intron|SHBG_uc010cnd.1_Intron	NM_001040	NP_001031	P04278	SHBG_HUMAN	sex hormone-binding globulin	317_318	Laminin G-like 2.				hormone transport	extracellular region	androgen binding|protein homodimerization activity	p.0?(1)			0		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Dromostanolone(DB00858)|Estradiol(DB00783)|Estrone(DB00655)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Mitotane(DB00648)|Norethindrone(DB00717)|Testosterone(DB00624)							OREG0024140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.73			119	44				---	---	---	---	capture_indel			In_Frame_Del	DEL	7476893	7476895	14761	17	GAG	-	-	45	45	SHBG	-	5	5
RNF213	57674	broad.mit.edu	36	17	75946811	75946811	+	Frame_Shift_Del	DEL	T	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:75946811_75946811delT	uc002jyh.1	+	c.5210_5210delT	c.(5209-5211)CTTfs	p.L1737fs	RNF213_uc010dhw.1_Frame_Shift_Del_p.L119fs	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)											0.98			1037	19				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	75946811	75946811	13955	17	T	-	-	56	56	RNF213	-	5	5
RNF213	57674	broad.mit.edu	36	17	75958254	75958254	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:75958254_75958254delG	uc002jyh.1	+	c.6636_6636delG	c.(6634-6636)TTGfs	p.L2212fs	RNF213_uc010dhw.1_Frame_Shift_Del_p.L594fs	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)											0.72			83	33				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	75958254	75958254	13955	17	G	-	-	45	45	RNF213	-	5	5
PCYT2	5833	broad.mit.edu	36	17	77456890	77456906	+	Splice_Site_Del	DEL	ACTTCTGACACGTACTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77456890_77456906delACTTCTGACACGTACTG	uc002kch.1	-	c.e11_splice_site			PCYT2_uc002kce.1_Splice_Site_Del|PCYT2_uc002kcf.1_Splice_Site_Del|PCYT2_uc002kcg.1_Splice_Site_Del|PCYT2_uc002kci.1_Splice_Site_Del|PCYT2_uc010dii.1_Splice_Site_Del	NM_002861	NP_002852			phosphate cytidylyltransferase 2, ethanolamine						phospholipid biosynthetic process		ethanolamine-phosphate cytidylyltransferase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)											0.88			116	16				---	---	---	---	capture_indel			Splice_Site_Del	DEL	77456890	77456906	12033	17	ACTTCTGACACGTACTG	-	-	6	6	PCYT2	-	5	5
HEXDC	284004	broad.mit.edu	36	17	77975616	77975616	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77975616_77975616delA	uc002kev.2	+	c.142_142delA	c.(142-144)ATGfs	p.M48fs	HEXDC_uc010diq.1_Frame_Shift_Del_p.M48fs|HEXDC_uc002kew.1_Frame_Shift_Del_p.M48fs	NM_173620	NP_775891	Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20,	48					carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)											0.77			72	21				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	77975616	77975616	7358	17	A	-	-	8	8	HEXDC	-	5	5
HEXDC	284004	broad.mit.edu	36	17	77992235	77992240	+	In_Frame_Del	DEL	TGTTAG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77992235_77992240delTGTTAG	uc002kev.2	+	c.1056_1061delTGTTAG	c.(1054-1062)CCTGTTAGG>CCG	p.VR353del	HEXDC_uc010diq.1_Splice_Site_Del|HEXDC_uc002kew.1_In_Frame_Del_p.VR353del	NM_173620	NP_775891	Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20,	353_354					carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)											0.94			47	3				---	---	---	---	capture_indel			In_Frame_Del	DEL	77992235	77992240	7358	17	TGTTAG	-	-	55	55	HEXDC	-	5	5
HAUS1	115106	broad.mit.edu	36	18	41939231	41939257	+	In_Frame_Del	DEL	AGATTTTACATCACCTTTCAGAACGCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:41939231_41939257delAGATTTTACATCACCTTTCAGAACGCA	uc002lbu.1	+	c.104_130delAGATTTTACATCACCTTTCAGAACGCA	c.(103-132)GAGATTTTACATCACCTTTCAGAACGCAAC>GAC	p.35_44EILHHLSERN>D	HAUS1_uc002lbv.1_5'UTR|ATP5A1_uc002lbt.1_5'Flank	NM_138443	NP_612452	Q96CS2	HAUS1_HUMAN	coiled-coil domain containing 5 (spindle	35_44					cell division|centrosome organization|mitosis|spindle assembly	HAUS complex|microtubule|microtubule organizing center|spindle pole				ovary(1)	1						NSCLC(79;183 1423 5813 15597 38427)								0.58			42	31				---	---	---	---	capture_indel			In_Frame_Del	DEL	41939231	41939257	7247	18	AGATTTTACATCACCTTTCAGAACGCA	-	-	11	11	HAUS1	-	5	5
EMR2	30817	broad.mit.edu	36	19	14738084	14738095	+	In_Frame_Del	DEL	CGGAATCGGTTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:14738084_14738095delCGGAATCGGTTG	uc002mzp.1	-	c.586_597delCAACCGATTCCG	c.(586-597)CAACCGATTCCGdel	p.QPIP196del	EMR2_uc010dzs.1_5'Flank|EMR2_uc002mzo.1_In_Frame_Del_p.QPIP196del|EMR2_uc002mzq.1_Intron|EMR2_uc002mzr.1_Intron|EMR2_uc002mzs.1_Intron|EMR2_uc002mzt.1_Intron|EMR2_uc002mzu.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	196_199	EGF-like 4; calcium-binding (Potential).|Extracellular (Potential).				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)	1														0.31			10	22				---	---	---	---	capture_indel			In_Frame_Del	DEL	14738084	14738095	5298	19	CGGAATCGGTTG	-	-	23	23	EMR2	-	5	5
BRD4	23476	broad.mit.edu	36	19	15225979	15225991	+	Frame_Shift_Del	DEL	GCTGTCAGAGGAG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15225979_15225991delGCTGTCAGAGGAG	uc002nar.1	-	c.2130_2142delCTCCTCTGACAGC	c.(2128-2142)AGCTCCTCTGACAGCfs	p.S710fs	BRD4_uc002nas.1_Frame_Shift_Del_p.S710fs|BRD4_uc002nat.2_Frame_Shift_Del_p.S710fs	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	710_714	Poly-Ser.|Ser-rich.				interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of gene-specific transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)							269				0.95			256	14				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	15225979	15225991	1535	19	GCTGTCAGAGGAG	-	-	38	38	BRD4	-	5	5
MBD3	53615	broad.mit.edu	36	19	1533619	1533620	+	Splice_Site_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1533619_1533620insC	uc002ltl.1	-	c.e4_splice_site			MBD3_uc002ltj.2_Splice_Site_Ins|MBD3_uc002ltk.2_Splice_Site_Ins	NM_003926	NP_003917			methyl-CpG binding domain protein 3						transcription, DNA-dependent	NuRD complex	DNA binding|protein binding			ovary(1)|pancreas(1)	2		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.179)|STAD - Stomach adenocarcinoma(1328;0.18)										0.35			23	43				---	---	---	---	capture_indel			Splice_Site_Ins	INS	1533619	1533620	9728	19	-	C	C	6	6	MBD3	C	5	5
SLC5A5	6528	broad.mit.edu	36	19	17844257	17844262	+	In_Frame_Del	DEL	CGCTGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17844257_17844262delCGCTGA	uc002nhr.2	+	c.129_134delCGCTGA	c.(127-135)AGCGCTGAG>AGG	p.43_45SAE>R		NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide	43_45	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process	integral to membrane|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			ovary(1)|central_nervous_system(1)	2						Melanoma(65;1008 1708 7910 46650)								0.62			31	19				---	---	---	---	capture_indel			In_Frame_Del	DEL	17844257	17844262	15165	19	CGCTGA	-	-	27	27	SLC5A5	-	5	5
ZNF599	148103	broad.mit.edu	36	19	39942551	39942561	+	Frame_Shift_Del	DEL	ATCCTCATATG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:39942551_39942561delATCCTCATATG	uc010edn.1	-	c.985_995delCATATGAGGAT	c.(985-996)CATATGAGGATTfs	p.H329fs	ZNF599_uc010edm.1_Frame_Shift_Del_p.H292fs	NM_001007248	NP_001007249	Q96NL3	ZN599_HUMAN	zinc finger protein 599	329_332	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)											0.41			78	112				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	39942551	39942561	18624	19	ATCCTCATATG	-	-	4	4	ZNF599	-	5	5
HKR1	284459	broad.mit.edu	36	19	42545205	42545207	+	In_Frame_Del	DEL	GGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42545205_42545207delGGA	uc002ogb.1	+	c.668_670delGGA	c.(667-672)CGGAGG>CGG	p.223_224RR>R	HKR1_uc002ofx.1_5'UTR|HKR1_uc002ofy.1_5'UTR|HKR1_uc002oga.2_In_Frame_Del_p.205_206RR>R|HKR1_uc002ogc.1_In_Frame_Del_p.204_205RR>R|HKR1_uc002ogd.1_In_Frame_Del_p.162_163RR>R	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	223_224					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.75			101	33				---	---	---	---	capture_indel			In_Frame_Del	DEL	42545205	42545207	7485	19	GGA	-	-	39	39	HKR1	-	5	5
ZFP30	22835	broad.mit.edu	36	19	42817982	42817996	+	In_Frame_Del	DEL	CAAAATGAATACTCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42817982_42817996delCAAAATGAATACTCT	uc002ogv.1	-	c.1286_1300delAGAGTATTCATTTTG	c.(1285-1302)CAGAGTATTCATTTTGGT>CGT	p.429_434QSIHFG>R	ZFP30_uc002ogw.1_In_Frame_Del_p.429_434QSIHFG>R|ZFP30_uc002ogx.1_In_Frame_Del_p.429_434QSIHFG>R	NM_014898	NP_055713	Q9Y2G7	ZFP30_HUMAN	zinc finger protein 30 homolog	429_434					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.38			69	114				---	---	---	---	capture_indel			In_Frame_Del	DEL	42817982	42817996	18232	19	CAAAATGAATACTCT	-	-	21	21	ZFP30	-	5	5
SAMD4B	55095	broad.mit.edu	36	19	44552150	44552150	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44552150_44552150delG	uc002olb.1	+	c.212_212delG	c.(211-213)TGGfs	p.W71fs	SAMD4B_uc002ola.2_Frame_Shift_Del_p.W71fs	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	71							protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)											0.54			55	47				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	44552150	44552150	14302	19	G	-	-	47	47	SAMD4B	-	5	5
MAP3K10	4294	broad.mit.edu	36	19	45396244	45396252	+	In_Frame_Del	DEL	TGGATGGCG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45396244_45396252delTGGATGGCG	uc002ona.1	+	c.805_813delTGGATGGCG	c.(805-813)TGGATGGCGdel	p.WMA269del	MAP3K10_uc002onb.1_5'UTR	NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase	269_271	Protein kinase.				activation of JUN kinase activity|induction of apoptosis|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|protein homodimerization activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6										92				0.56			32	25				---	---	---	---	capture_indel			In_Frame_Del	DEL	45396244	45396252	9627	19	TGGATGGCG	-	-	55	55	MAP3K10	-	5	5
NPAS1	4861	broad.mit.edu	36	19	52234597	52234602	+	In_Frame_Del	DEL	ACTCCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52234597_52234602delACTCCA	uc002pfw.1	+	c.897_902delACTCCA	c.(895-903)CCACTCCAT>CCT	p.LH300del	NPAS1_uc002pfx.1_In_Frame_Del_p.LH125del|NPAS1_uc002pfy.1_In_Frame_Del_p.LH300del	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	300_301	PAS 2.				central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)										0.81			22	5				---	---	---	---	capture_indel			In_Frame_Del	DEL	52234597	52234602	10966	19	ACTCCA	-	-	6	6	NPAS1	-	5	5
ZC3H4	23211	broad.mit.edu	36	19	52285255	52285260	+	In_Frame_Del	DEL	GTGGCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52285255_52285260delGTGGCA	uc002pga.2	-	c.519_524delTGCCAC	c.(517-525)CATGCCACG>CAG	p.173_175HAT>Q	ZC3H4_uc002pgb.1_5'UTR	NM_015168	NP_055983	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	173_175							nucleic acid binding|zinc ion binding			ovary(2)	2		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)										0.81			157	37				---	---	---	---	capture_indel			In_Frame_Del	DEL	52285255	52285260	18158	19	GTGGCA	-	-	40	40	ZC3H4	-	5	5
CPT1C	126129	broad.mit.edu	36	19	54892518	54892518	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54892518_54892518delG	uc002ppj.1	+	c.265_265delG	c.(265-267)GAGfs	p.E89fs	CPT1C_uc002ppl.2_Frame_Shift_Del_p.E89fs|CPT1C_uc002ppi.1_Frame_Shift_Del_p.E6fs|CPT1C_uc010eng.1_Frame_Shift_Del_p.E89fs|CPT1C_uc010enh.1_Frame_Shift_Del_p.E89fs|CPT1C_uc002ppk.1_Frame_Shift_Del_p.E89fs	NM_152359	NP_689572	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C isoform 2	89	Mitochondrial intermembrane (Potential).				fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)										0.35			20	37				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	54892518	54892518	3972	19	G	-	-	33	33	CPT1C	-	5	5
PTOV1	53635	broad.mit.edu	36	19	55049539	55049549	+	Frame_Shift_Del	DEL	GGGGTCTGGCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55049539_55049549delGGGGTCTGGCC	uc002pqf.1	+	c.236_246delGGGGTCTGGCC	c.(235-246)GGGGGTCTGGCCfs	p.G79fs	PTOV1_uc002ppz.2_Non-coding_Transcript|PTOV1_uc002pqb.2_Frame_Shift_Del_p.G47fs|PTOV1_uc002pqa.1_Non-coding_Transcript|PTOV1_uc002pqc.1_Non-coding_Transcript|PTOV1_uc002pqd.2_Non-coding_Transcript|PTOV1_uc002pqe.1_Non-coding_Transcript	NM_017432	NP_059128	Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	79_82					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|plasma membrane					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)										0.89			71	9				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	55049539	55049549	13224	19	GGGGTCTGGCC	-	-	43	43	PTOV1	-	5	5
CNOT3	4849	broad.mit.edu	36	19	59339233	59339233	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:59339233_59339233delG	uc002qdj.1	+	c.194_194delG	c.(193-195)TGGfs	p.W65fs	CNOT3_uc002qdi.2_De_novo_Start_OutOfFrame|CNOT3_uc002qdk.1_Frame_Shift_Del_p.W65fs|CNOT3_uc010ere.1_Non-coding_Transcript	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	65					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding|transcription regulator activity			ovary(2)	2	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)													0.85			33	6				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	59339233	59339233	3758	19	G	-	-	47	47	CNOT3	-	5	5
ZNF470	388566	broad.mit.edu	36	19	61781449	61781461	+	Frame_Shift_Del	DEL	TGTCATACTGGTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:61781449_61781461delTGTCATACTGGTG	uc002qnl.2	+	c.1840_1852delTGTCATACTGGTG	c.(1840-1854)TGTCATACTGGTGAGfs	p.C614fs	ZNF470_uc010etn.1_Intron	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	614_618					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)										0.72			108	42				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	61781449	61781461	18523	19	TGTCATACTGGTG	-	-	51	51	ZNF470	-	5	5
ZNF329	79673	broad.mit.edu	36	19	63331149	63331156	+	Frame_Shift_Del	DEL	GGCTGGGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:63331149_63331156delGGCTGGGA	uc002qrn.1	-	c.1527_1534delTCCCAGCC	c.(1525-1536)GGTCCCAGCCGGfs	p.G509fs	ZNF329_uc010euk.1_Non-coding_Transcript|ZNF329_uc002qro.1_Non-coding_Transcript|ZNF329_uc002qrp.1_Non-coding_Transcript|ZNF329_uc010eul.1_Frame_Shift_Del_p.G509fs	NM_024620	NP_078896	Q86UD4	ZN329_HUMAN	zinc finger protein 329	509_512	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)										0.82			50	11				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	63331149	63331156	18439	19	GGCTGGGA	-	-	39	39	ZNF329	-	5	5
INSR	3643	broad.mit.edu	36	19	7083281	7083283	+	In_Frame_Del	DEL	GCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7083281_7083283delGCC	uc002mgd.1	-	c.2728_2730delGGC	c.(2728-2730)GGCdel	p.G910del	INSR_uc002mge.1_In_Frame_Del_p.G898del	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	910	Fibronectin type-III 3.|Extracellular (Potential).				activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of gene-specific transcription|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding	p.G910V(1)		ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)				p.G910G(HEC59-Tumor)	649				0.44			8	10				---	---	---	---	capture_indel			In_Frame_Del	DEL	7083281	7083283	8074	19	GCC	-	-	34	34	INSR	-	5	5
ZNF560	147741	broad.mit.edu	36	19	9438595	9438596	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9438595_9438596insAG	uc002mlp.1	-	c.2027_2028insCT	c.(2026-2028)AAAfs	p.K676fs	ZNF560_uc010dwr.1_Frame_Shift_Ins_p.K570fs	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	676	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|large_intestine(1)|liver(1)|pancreas(1)	4														0.47			147	167				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	9438595	9438596	18586	19	-	AG	AG	64	64	ZNF560	AG	5	5
HIAT1	64645	broad.mit.edu	36	1	100306709	100306710	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:100306709_100306710insT	uc001dst.1	+	c.798_799insT	c.(796-801)AGCTTTfs	p.S266fs		NM_033055	NP_149044	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	266_267	Cytoplasmic (Potential).				response to antibiotic	integral to membrane	tetracycline:hydrogen antiporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)										0.36			126	224				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	100306709	100306710	7382	1	-	T	T	28	28	HIAT1	T	5	5
OLFM3	118427	broad.mit.edu	36	1	102042450	102042465	+	Frame_Shift_Del	DEL	TCCAGGCATAGAGAGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:102042450_102042465delTCCAGGCATAGAGAGC	uc001duf.2	-	c.1354_1369delGCTCTCTATGCCTGGA	c.(1354-1371)GCTCTCTATGCCTGGAACfs	p.A452fs	OLFM3_uc001dug.2_Frame_Shift_Del_p.A432fs|OLFM3_uc001duh.2_Non-coding_Transcript|OLFM3_uc001dui.2_Non-coding_Transcript|OLFM3_uc001duj.2_Frame_Shift_Del_p.A357fs|OLFM3_uc001due.2_Non-coding_Transcript	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	452_457	Olfactomedin-like.					extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)										0.74			114	41				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	102042450	102042465	11259	1	TCCAGGCATAGAGAGC	-	-	62	62	OLFM3	-	5	5
KIF1B	23095	broad.mit.edu	36	1	10320121	10320127	+	Frame_Shift_Del	DEL	CAGTGTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10320121_10320127delCAGTGTT	uc001aqz.2	+	c.3365_3371delCAGTGTT	c.(3364-3372)ACAGTGTTGfs	p.T1122fs	KIF1B_uc001aqw.2_Frame_Shift_Del_p.T1076fs|KIF1B_uc001aqx.2_Frame_Shift_Del_p.T1122fs|KIF1B_uc001aqy.2_Frame_Shift_Del_p.T1096fs|KIF1B_uc001ara.2_Frame_Shift_Del_p.T1082fs|KIF1B_uc001arb.2_Frame_Shift_Del_p.T1108fs	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	1122_1124					anterograde axon cargo transport|apoptosis|nerve-nerve synaptic transmission|neuromuscular synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)	2	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)										0.46			79	92				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	10320121	10320127	8595	1	CAGTGTT	-	-	17	17	KIF1B	-	5	5
CELSR2	1952	broad.mit.edu	36	1	109597277	109597291	+	In_Frame_Del	DEL	ACAACCCACCAGTGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109597277_109597291delACAACCCACCAGTGC	uc001dxa.2	+	c.3053_3067delACAACCCACCAGTGC	c.(3052-3069)GACAACCCACCAGTGCTG>GTG	p.1018_1023DNPPVL>V		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	1018_1023	Extracellular (Potential).|Cadherin 8.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of gene-specific transcription|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)	3		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		NSCLC(158;1285 2011 34800 34852 42084)								0.92			49	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	109597277	109597291	3355	1	ACAACCCACCAGTGC	-	-	10	10	CELSR2	-	5	5
PTCHD2	57540	broad.mit.edu	36	1	11502072	11502082	+	Frame_Shift_Del	DEL	GGAGGCAGCCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11502072_11502082delGGAGGCAGCCC	uc001ash.2	+	c.1963_1973delGGAGGCAGCCC	c.(1963-1974)GGAGGCAGCCCTfs	p.G655fs	PTCHD2_uc001asi.1_Frame_Shift_Del_p.G655fs	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	655_658	Cytoplasmic (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)										1.00			12	0				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	11502072	11502082	13187	1	GGAGGCAGCCC	-	-	47	47	PTCHD2	-	5	5
SPAG17	200162	broad.mit.edu	36	1	118437431	118437432	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118437431_118437432insC	uc001ehk.1	-	c.1043_1044insG	c.(1042-1044)ATTfs	p.I348fs		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	348						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)										0.42			5	7				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	118437431	118437432	15482	1	-	C	C	5	5	SPAG17	C	5	5
HMGCS2	3158	broad.mit.edu	36	1	120101476	120101482	+	Frame_Shift_Del	DEL	AAGTCAT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120101476_120101482delAAGTCAT	uc001eid.1	-	c.953_959delATGACTT	c.(952-960)AATGACTTCfs	p.N318fs	HMGCS2_uc001eie.1_Frame_Shift_Del_p.N226fs	NM_005518	NP_005509	P54868	HMCS2_HUMAN	hydroxymethylglutaryl-CoA synthase 2	318_320					acetoacetic acid biosynthetic process|cholesterol biosynthetic process|isoprenoid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA synthase activity			ovary(2)	2	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)										0.49			37	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	120101476	120101482	7524	1	AAGTCAT	-	-	9	9	HMGCS2	-	5	5
BCL9	607	broad.mit.edu	36	1	145558667	145558674	+	Frame_Shift_Del	DEL	AAAAGGAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145558667_145558674delAAAAGGAA	uc001epq.1	+	c.2082_2089delAAAAGGAA	c.(2080-2091)CCAAAAGGAATTfs	p.P694fs	NBPF11_uc009wjd.1_Intron|NBPF11_uc009wje.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	694_697	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			large_intestine(2)|ovary(2)	4	all_hematologic(923;0.115)								p.G696A(CAL851-Tumor)	202				0.32			18	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	145558667	145558674	1402	1	AAAAGGAA	-	-	5	5	BCL9	-	5	5
ENSA	2029	broad.mit.edu	36	1	148864852	148864858	+	Frame_Shift_Del	DEL	CTTATTC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:148864852_148864858delCTTATTC	uc009wly.1	-	c.303_309delGAATAAG	c.(301-309)AAGAATAAGfs	p.K101fs	ENSA_uc001evb.1_Frame_Shift_Del_p.K90fs|ENSA_uc001evc.1_Frame_Shift_Del_p.K74fs|ENSA_uc001evd.1_Frame_Shift_Del_p.K94fs|ENSA_uc001eve.1_Frame_Shift_Del_p.K78fs|ENSA_uc001evf.1_Frame_Shift_Del_p.K74fs|ENSA_uc001evg.1_Frame_Shift_Del_p.K94fs|ENSA_uc001evh.1_Frame_Shift_Del_p.K78fs|ENSA_uc009wlz.1_Frame_Shift_Del_p.K101fs	NM_207043	NP_997051	O43768	ENSA_HUMAN	endosulfine alpha isoform 2	78_80					cell division|G2/M transition of mitotic cell cycle|mitosis|response to nutrient|transport	cytoplasm	ion channel inhibitor activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity|receptor binding			central_nervous_system(1)	1	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			Esophageal Squamous(188;763 2078 3002 3411 26027)								0.57			48	36				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	148864852	148864858	5329	1	CTTATTC	-	-	28	28	ENSA	-	5	5
RORC	6097	broad.mit.edu	36	1	150054199	150054206	+	Frame_Shift_Del	DEL	CCCGCTCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:150054199_150054206delCCCGCTCA	uc001ezh.1	-	c.618_625delTGAGCGGG	c.(616-627)CCTGAGCGGGGCfs	p.P206fs	RORC_uc001ezg.1_Frame_Shift_Del_p.P185fs	NM_005060	NP_005051	P51449	RORG_HUMAN	RAR-related orphan receptor C isoform a	206_209	Hinge (Potential).				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)											0.34			89	171				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	150054199	150054206	14009	1	CCCGCTCA	-	-	22	22	RORC	-	5	5
LAMC1	3915	broad.mit.edu	36	1	181361923	181361925	+	In_Frame_Del	DEL	CCG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181361923_181361925delCCG	uc001gpy.2	+	c.2847_2849delCCG	c.(2845-2850)ATCCGC>ATC	p.R950del		NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor	950	Laminin EGF-like 10.				axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.90			325	38				---	---	---	---	capture_indel			In_Frame_Del	DEL	181361923	181361925	8937	1	CCG	-	-	30	30	LAMC1	-	5	5
PRKCZ	5590	broad.mit.edu	36	1	1976792	1976792	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1976792_1976792delG	uc001aiq.1	+	c.124_124delG	c.(124-126)GAGfs	p.E42fs		NM_002744	NP_001028754	Q05513	KPCZ_HUMAN	protein kinase C, zeta isoform 1	42	OPR.				anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|insulin receptor substrate binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)						2432				0.87			72	11				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	1976792	1976792	12960	1	G	-	-	45	45	PRKCZ	-	5	5
FAM177B	400823	broad.mit.edu	36	1	220986513	220986523	+	Frame_Shift_Del	DEL	GGAGATTGACG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220986513_220986523delGGAGATTGACG	uc001hnt.1	+	c.3_13delGGAGATTGACG	c.(1-15)ATGGAGATTGACGGTfs	p.M1fs	FAM177B_uc009xeb.1_Non-coding_Transcript	NM_207468	NP_997351	A6PVY3	F177B_HUMAN	hypothetical protein LOC400823	1_5										ovary(1)	1														0.89			99	12				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	220986513	220986523	5708	1	GGAGATTGACG	-	-	47	47	FAM177B	-	5	5
SEPN1	57190	broad.mit.edu	36	1	26004254	26004273	+	Frame_Shift_Del	DEL	GTTGCCCCCTGACCCTAGCG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26004254_26004273delGTTGCCCCCTGACCCTAGCG	uc001bko.1	+	c.438_457delGTTGCCCCCTGACCCTAGCG	c.(436-459)GAGTTGCCCCCTGACCCTAGCGAGfs	p.E146fs	SEPN1_uc001bkp.1_Frame_Shift_Del_p.E112fs	NM_020451	NP_065184	Q9NZV5	SELN_HUMAN	selenoprotein N, 1 isoform 1 precursor	146_153						endoplasmic reticulum membrane|extracellular region	protein binding			ovary(2)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)										0.49			45	46				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	26004254	26004273	14542	1	GTTGCCCCCTGACCCTAGCG	-	-	36	36	SEPN1	-	5	5
KDM4A	9682	broad.mit.edu	36	1	43930541	43930541	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43930541_43930541delG	uc001cjx.1	+	c.2347_2347delG	c.(2347-2349)GGGfs	p.G783fs		NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	783					interspecies interaction between organisms|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|transcription repressor activity|zinc ion binding				0														0.88			1309	172				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	43930541	43930541	8434	1	G	-	-	35	35	KDM4A	-	5	5
ST6GALNAC5	81849	broad.mit.edu	36	1	77282644	77282644	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:77282644_77282644delC	uc001dhi.1	+	c.429_429delC	c.(427-429)GTCfs	p.V143fs	ST6GALNAC5_uc009wbw.1_Non-coding_Transcript	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E	143	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)	1														0.86			36	6				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	77282644	77282644	15745	1	C	-	-	29	29	ST6GALNAC5	-	5	5
ZNF337	26152	broad.mit.edu	36	20	25604935	25604938	+	Frame_Shift_Del	DEL	GTAT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:25604935_25604938delGTAT	uc002wva.1	-	c.986_989delATAC	c.(985-990)TATACTfs	p.Y329fs	ZNF337_uc002wvb.1_Frame_Shift_Del_p.Y329fs|ZNF337_uc002wvc.1_Frame_Shift_Del_p.Y329fs	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	329_330	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.62			236	145				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	25604935	25604938	18445	20	GTAT	-	-	36	36	ZNF337	-	5	5
TTLL9	164395	broad.mit.edu	36	20	29949991	29949995	+	Frame_Shift_Del	DEL	CGTCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:29949991_29949995delCGTCC	uc010gdx.1	+	c.168_172delCGTCC	c.(166-174)GACGTCCTTfs	p.D56fs	TTLL9_uc002wwy.1_Non-coding_Transcript|TTLL9_uc002wwz.1_Non-coding_Transcript|TTLL9_uc002wxa.1_Non-coding_Transcript|TTLL9_uc002wxb.1_Non-coding_Transcript|TTLL9_uc002wxc.1_Frame_Shift_Del_p.R66fs	NM_001008409	NP_001008409	Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	56_58	TTL.				protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)											0.66			123	63				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	29949991	29949995	17289	20	CGTCC	-	-	19	19	TTLL9	-	5	5
ITPA	3704	broad.mit.edu	36	20	3150526	3150528	+	In_Frame_Del	DEL	TGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:3150526_3150528delTGG	uc002wid.1	+	c.451_453delTGG	c.(451-453)TGGdel	p.W151del	ITPA_uc002wie.1_In_Frame_Del_p.W134del|ITPA_uc002wif.1_Non-coding_Transcript	NM_033453	NP_258412	Q9BY32	ITPA_HUMAN	inosine triphosphatase isoform a	151					nucleotide metabolic process	cytoplasm	metal ion binding|nucleoside-triphosphate diphosphatase activity			ovary(1)	1														0.89			193	24				---	---	---	---	capture_indel			In_Frame_Del	DEL	3150526	3150528	8219	20	TGG	-	-	55	55	ITPA	-	5	5
SPAG4	6676	broad.mit.edu	36	20	33672073	33672077	+	Frame_Shift_Del	DEL	TGTTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33672073_33672077delTGTTG	uc002xdb.1	+	c.1131_1135delTGTTG	c.(1129-1137)GATGTTGAGfs	p.D377fs		NM_003116	NP_003107	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	377_379	SUN.				spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity				0	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)											0.97			39	1				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	33672073	33672077	15483	20	TGTTG	-	-	51	51	SPAG4	-	5	5
TGIF2	60436	broad.mit.edu	36	20	34640746	34640748	+	In_Frame_Del	DEL	TGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34640746_34640748delTGA	uc002xfn.1	+	c.155_157delTGA	c.(154-159)CTGAGC>CGC	p.52_53LS>R	C20orf24_uc002xfo.1_In_Frame_Del_p.52_53LS>R	NM_021809	NP_068581	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	52_53	Homeobox; TALE-type.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)												0.34			12	23				---	---	---	---	capture_indel			In_Frame_Del	DEL	34640746	34640748	16354	20	TGA	-	-	55	55	TGIF2	-	5	5
TGM2	7052	broad.mit.edu	36	20	36217819	36217836	+	In_Frame_Del	DEL	CCACGGTGGCTGTCCAGT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:36217819_36217836delCCACGGTGGCTGTCCAGT	uc002xhr.1	-	c.260_277delACTGGACAGCCACCGTGG	c.(259-279)GACTGGACAGCCACCGTGGTG>GTG	p.DWTATV87del	TGM2_uc002xhs.1_In_Frame_Del_p.DWTATV63del|TGM2_uc002xht.1_In_Frame_Del_p.DWTATV87del|TGM2_uc002xhu.2_In_Frame_Del_p.DWTATV87del	NM_004613	NP_004604	P21980	TGM2_HUMAN	transglutaminase 2 isoform a	87_92					apoptotic cell clearance|peptide cross-linking|positive regulation of cell adhesion		acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(1)|lung(1)|ovary(1)	3		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)									0.64			25	14				---	---	---	---	capture_indel			In_Frame_Del	DEL	36217819	36217836	16358	20	CCACGGTGGCTGTCCAGT	-	-	18	18	TGM2	-	5	5
RALGAPB	57148	broad.mit.edu	36	20	36559570	36559571	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:36559570_36559571delCA	uc002xiw.1	+	c.550_551delCA	c.(550-552)CAAfs	p.Q184fs	RALGAPB_uc002xix.1_Frame_Shift_Del_p.Q184fs|RALGAPB_uc002xiy.1_Frame_Shift_Del_p.Q184fs|RALGAPB_uc002xiz.1_5'UTR	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	hypothetical protein LOC57148	184					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)	1														0.82			115	25				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	36559570	36559571	13475	20	CA	-	-	29	29	RALGAPB	-	5	5
PABPC1L	80336	broad.mit.edu	36	20	42981008	42981018	+	Frame_Shift_Del	DEL	GGGCGCGGGCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42981008_42981018delGGGCGCGGGCC	uc010ggv.1	+	c.551_561delGGGCGCGGGCC	c.(550-561)GGGGCGCGGGCCfs	p.G184fs		NM_001124756	NP_001118228	Q4VXU2	PAP1L_HUMAN	poly(A)-binding protein, cytoplasmic 1-like	184_187							nucleotide binding|RNA binding			ovary(1)	1														0.67			126	61				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	42981008	42981018	11777	20	GGGCGCGGGCC	-	-	43	43	PABPC1L	-	5	5
ZSWIM3	140831	broad.mit.edu	36	20	43939713	43939714	+	Frame_Shift_Ins	INS	-	GA	GA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43939713_43939714insGA	uc002xqd.1	+	c.1109_1110insGA	c.(1108-1110)TGGfs	p.W370fs		NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	370							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)												0.32			97	208				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	43939713	43939714	18846	20	-	GA	GA	47	47	ZSWIM3	GA	5	5
ANGPT4	51378	broad.mit.edu	36	20	802960	802973	+	Frame_Shift_Del	DEL	AGTGGTCGTTGTCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:802960_802973delAGTGGTCGTTGTCT	uc002wei.1	-	c.1305_1318delAGACAACGACCACT	c.(1303-1320)TCAGACAACGACCACTGTfs	p.S435fs		NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4	435_440	Fibrinogen C-terminal.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						Pancreas(181;481 2077 3259 31286 49856)								0.56			35	27				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	802960	802973	615	20	AGTGGTCGTTGTCT	-	-	7	7	ANGPT4	-	5	5
DSCAM	1826	broad.mit.edu	36	21	40647541	40647541	+	Splice_Site_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:40647541_40647541delC	uc002yyq.1	-	c.e5_splice_site			DSCAM_uc002yyr.1_Splice_Site_Del	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.92			12	1				---	---	---	---	capture_indel			Splice_Site_Del	DEL	40647541	40647541	4952	21	C	-	-	32	32	DSCAM	-	5	5
RRP1B	23076	broad.mit.edu	36	21	43931930	43931931	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43931930_43931931delCA	uc002zdk.1	+	c.1247_1248delCA	c.(1246-1248)CCAfs	p.P416fs	RRP1B_uc002zdl.1_5'UTR	NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B	416					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding				0				STAD - Stomach adenocarcinoma(101;0.178)										0.92			60	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	43931930	43931931	14168	21	CA	-	-	21	21	RRP1B	-	5	5
CCDC116	164592	broad.mit.edu	36	22	20321202	20321204	+	In_Frame_Del	DEL	AGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:20321202_20321204delAGC	uc002zve.1	+	c.1685_1687delAGC	c.(1684-1689)AAGCTC>ATC	p.562_563KL>I		NM_152612	NP_689825	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	35_36										ovary(1)	1	Colorectal(54;0.105)													0.47			118	132				---	---	---	---	capture_indel			In_Frame_Del	DEL	20321202	20321204	2873	22	AGC	-	-	3	3	CCDC116	-	5	5
NEFH	4744	broad.mit.edu	36	22	28214977	28214977	+	Frame_Shift_Del	DEL	T	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:28214977_28214977delT	uc003afo.1	+	c.1348_1348delT	c.(1348-1350)TCTfs	p.S450fs	NEFH_uc003afp.2_5'Flank	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	450	Tail.				cell death|nervous system development	neurofilament					0														0.35			30	55				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	28214977	28214977	10713	22	T	-	-	58	58	NEFH	-	5	5
MYH9	4627	broad.mit.edu	36	22	35040191	35040192	+	Frame_Shift_Ins	INS	-	AC	AC			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:35040191_35040192insAC	uc003apg.1	-	c.1498_1499insGT	c.(1498-1500)AACfs	p.N500fs	MYH9_uc003aph.1_Frame_Shift_Ins_p.N364fs	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	500	Myosin head-like.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	10										1624				0.79			38	10				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	35040191	35040192	10437	22	-	AC	AC	60	60	MYH9	AC	5	5
EFCAB6	64800	broad.mit.edu	36	22	42267364	42267365	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42267364_42267365insT	uc003bdy.1	-	c.3854_3855insA	c.(3853-3855)GGGfs	p.G1285fs	EFCAB6_uc003bdz.1_Frame_Shift_Ins_p.G1133fs|EFCAB6_uc010gzi.1_Frame_Shift_Ins_p.G1133fs	NM_022785	NP_942153	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	1285					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|pancreas(1)	4		Ovarian(80;0.0247)|all_neural(38;0.025)												0.81			135	32				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	42267364	42267365	5126	22	-	T	T	18	18	EFCAB6	T	5	5
ACR	49	broad.mit.edu	36	22	49525067	49525086	+	Frame_Shift_Del	DEL	CAAGAGAGATATGTGGAGAA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:49525067_49525086delCAAGAGAGATATGTGGAGAA	uc003bnh.2	+	c.361_380delCAAGAGAGATATGTGGAGAA	c.(361-381)CAAGAGAGATATGTGGAGAAAfs	p.Q121fs	ACR_uc010hbh.1_Frame_Shift_Del_p.Q121fs	NM_001097	NP_001088	P10323	ACRO_HUMAN	acrosin precursor	121_127	Peptidase S1.				acrosome matrix dispersal|activation of adenylate cyclase activity	acrosomal matrix|protein complex	amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding				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;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)										0.70			337	147				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	49525067	49525086	170	22	CAAGAGAGATATGTGGAGAA	-	-	25	25	ACR	-	5	5
ALS2CR12	130540	broad.mit.edu	36	2	201924332	201924336	+	Frame_Shift_Del	DEL	GGGTC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:201924332_201924336delGGGTC	uc010ftg.1	-	c.37_41delGACCC	c.(37-42)GACCCCfs	p.D13fs	ALS2CR12_uc002uya.2_Frame_Shift_Del_p.D13fs|ALS2CR12_uc010fth.1_Non-coding_Transcript	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	13_14					regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3														0.47			35	40				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	201924332	201924336	556	2	GGGTC	-	-	43	43	ALS2CR12	-	5	5
SLC19A3	80704	broad.mit.edu	36	2	228271750	228271750	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228271750_228271750delA	uc002vpi.1	-	c.925_925delT	c.(925-927)TCCfs	p.S309fs	SLC19A3_uc002vpj.2_Non-coding_Transcript	NM_025243	NP_079519	Q9BZV2	S19A3_HUMAN	solute carrier family 19, member 3	309	Extracellular (Potential).				thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|reduced folate carrier activity|thiamine uptake transmembrane transporter activity			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)									0.80			28	7				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	228271750	228271750	14926	2	A	-	-	12	12	SLC19A3	-	5	5
PRKD3	23683	broad.mit.edu	36	2	37397007	37397013	+	Frame_Shift_Del	DEL	GCCTCTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:37397007_37397013delGCCTCTG	uc002rqd.1	-	c.159_165delCAGAGGC	c.(157-165)TCCAGAGGCfs	p.S53fs	PRKD3_uc002rqf.1_Frame_Shift_Del_p.S53fs	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	53_55					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|protein phosphorylation	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				Melanoma(80;621 1355 8613 11814 51767)			p.G55C(HEC6-Tumor)	569				0.71			137	57				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	37397007	37397013	12963	2	GCCTCTG	-	-	34	34	PRKD3	-	5	5
MSH6	2956	broad.mit.edu	36	2	47880567	47880574	+	Frame_Shift_Del	DEL	AAGTGATG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:47880567_47880574delAAGTGATG	uc002rwd.2	+	c.1941_1948delAAGTGATG	c.(1939-1950)CTAAGTGATGGCfs	p.L647fs	MSH6_uc002rwc.2_Frame_Shift_Del_p.L647fs|MSH6_uc010fbj.1_Frame_Shift_Del_p.L345fs	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	647_650					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|endometrium(28)|central_nervous_system(27)|stomach(21)|haematopoietic_and_lymphoid_tissue(9)|skin(6)|urinary_tract(5)|lung(5)|ovary(3)|breast(2)|thyroid(1)	160		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)							517				0.60			101	67				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	47880567	47880574	10267	2	AAGTGATG	-	-	13	13	MSH6	-	5	5
STON1-GTF2A1L	286749	broad.mit.edu	36	2	48663207	48663208	+	Splice_Site_Ins	INS	-	A	A			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48663207_48663208insA	uc002rwp.1	+	c.e2_splice_site			STON1_uc002rwo.2_Splice_Site_Ins|STON1_uc010fbm.1_Splice_Site_Ins|STON1_uc002rwr.1_Splice_Site_Ins|STON1_uc002rwq.1_Splice_Site_Ins	NM_172311	NP_758515			STON1-GTF2A1L protein						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex	RNA polymerase II transcription factor activity			ovary(3)|pancreas(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)											0.84			138	27				---	---	---	---	capture_indel			Splice_Site_Ins	INS	48663207	48663208	15837	2	-	A	A	36	36	STON1-GTF2A1L	A	5	5
TTC31	64427	broad.mit.edu	36	2	74573037	74573046	+	Frame_Shift_Del	DEL	CCCGGGGCCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74573037_74573046delCCCGGGGCCT	uc002slt.1	+	c.1118_1127delCCCGGGGCCT	c.(1117-1128)CCCCGGGGCCTCfs	p.P373fs	TTC31_uc002sls.1_3'UTR|TTC31_uc002slu.1_Frame_Shift_Del_p.P227fs	NM_022492	NP_071937	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	373_376	TPR 3.						binding				0														0.32			11	23				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	74573037	74573046	17255	2	CCCGGGGCCT	-	-	22	22	TTC31	-	5	5
LRRTM1	347730	broad.mit.edu	36	2	80383804	80383805	+	Frame_Shift_Del	DEL	GC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:80383804_80383805delGC	uc002sok.1	-	c.651_652delGC	c.(649-654)GAGCACfs	p.E217fs	CTNNA2_uc002sog.1_Intron|CTNNA2_uc002soh.1_Intron|CTNNA2_uc002soi.1_Intron|LRRTM1_uc002soj.2_Non-coding_Transcript|LRRTM1_uc010ffy.1_Frame_Shift_Del_p.E217fs	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	217_218	LRR 6.|Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)	3														0.59			22	15				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	80383804	80383805	9415	2	GC	-	-	46	46	LRRTM1	-	5	5
DPPA4	55211	broad.mit.edu	36	3	110530540	110530542	+	In_Frame_Del	DEL	GGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:110530540_110530542delGGC	uc003dxq.2	-	c.763_765delGCC	c.(763-765)GCCdel	p.A255del		NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	255						nucleus	protein binding				0														0.51			71	68				---	---	---	---	capture_indel			In_Frame_Del	DEL	110530540	110530542	4920	3	GGC	-	-	35	35	DPPA4	-	5	5
MFSD1	64747	broad.mit.edu	36	3	160020144	160020144	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:160020144_160020144delG	uc003fcl.1	+	c.665_665delG	c.(664-666)TGTfs	p.C222fs	MFSD1_uc003fcm.1_Non-coding_Transcript|MFSD1_uc003fcn.1_Frame_Shift_Del_p.C125fs	NM_022736	NP_073573	Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing	222	Helical; (Potential).				transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			Pancreas(62;1186 1654 36636 37908)								0.32			6	13				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	160020144	160020144	9917	3	G	-	-	48	48	MFSD1	-	5	5
RFTN1	23180	broad.mit.edu	36	3	16425912	16425916	+	Frame_Shift_Del	DEL	TCTGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:16425912_16425916delTCTGG	uc003cay.1	-	c.411_415delCCAGA	c.(409-417)GACCAGAAAfs	p.D137fs	RFTN1_uc010hes.1_Frame_Shift_Del_p.D101fs	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein	137_139						plasma membrane				ovary(3)|central_nervous_system(1)	4														0.49			33	35				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	16425912	16425916	13730	3	TCTGG	-	-	62	62	RFTN1	-	5	5
MECOM	2122	broad.mit.edu	36	3	170293489	170293490	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:170293489_170293490insA	uc003ffl.2	-	c.3003_3004insT	c.(3001-3006)TTCATTfs	p.F1001fs	MECOM_uc010hwk.1_Frame_Shift_Ins_p.F864fs|MECOM_uc010hwl.1_Frame_Shift_Ins_p.F914fs|MECOM_uc003ffi.2_Frame_Shift_Ins_p.F850fs|MECOM_uc003ffj.2_Frame_Shift_Ins_p.F915fs|MECOM_uc003ffn.2_Frame_Shift_Ins_p.F840fs|MECOM_uc010hwm.1_Frame_Shift_Ins_p.F850fs|MECOM_uc003ffk.2_Frame_Shift_Ins_p.F831fs	NM_005241	NP_005232	Q13465	MDS1_HUMAN	ecotropic viral integration site 1 isoform b	Error:Variant_position_missing_in_Q13465_after_alignment							sequence-specific DNA binding transcription factor activity			lung(3)|skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	8										646				0.32			16	34				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	170293489	170293490	9811	3	-	A	A	51	51	MECOM	A	5	5
AP2M1	1173	broad.mit.edu	36	3	185380734	185380735	+	Splice_Site_Ins	INS	-	T	T			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185380734_185380735insT	uc010hxu.1	+	c.e3_splice_site			AP2M1_uc010hxt.1_Splice_Site_Ins|AP2M1_uc003fmw.1_Splice_Site_Ins|AP2M1_uc003fmx.1_Splice_Site_Ins|AP2M1_uc003fmy.1_Splice_Site_Ins	NM_004068	NP_004059			adaptor-related protein complex 2, mu 1 subunit						axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)											0.75			70	23				---	---	---	---	capture_indel			Splice_Site_Ins	INS	185380734	185380735	752	3	-	T	T	44	44	AP2M1	T	5	5
EIF4G1	1981	broad.mit.edu	36	3	185523324	185523328	+	Frame_Shift_Del	DEL	TAGAG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185523324_185523328delTAGAG	uc010hxx.1	+	c.1838_1842delTAGAG	c.(1837-1842)CTAGAGfs	p.L613fs	EIF4G1_uc003fno.1_Frame_Shift_Del_p.L547fs|EIF4G1_uc010hxw.1_Frame_Shift_Del_p.L442fs|EIF4G1_uc003fnp.1_Frame_Shift_Del_p.L606fs|EIF4G1_uc003fnt.1_Frame_Shift_Del_p.L317fs|EIF4G1_uc003fnq.1_Frame_Shift_Del_p.L519fs|EIF4G1_uc003fnr.1_Frame_Shift_Del_p.L442fs|EIF4G1_uc003fns.1_Frame_Shift_Del_p.L566fs|EIF4G1_uc010hxy.1_Frame_Shift_Del_p.L613fs|EIF4G1_uc003fnu.2_Frame_Shift_Del_p.L606fs|EIF4G1_uc003fnv.2_Frame_Shift_Del_p.L606fs|EIF4G1_uc003fnw.1_Frame_Shift_Del_p.L613fs|EIF4G1_uc003fnx.2_Frame_Shift_Del_p.L410fs|EIF4G1_uc003fny.2_Frame_Shift_Del_p.L410fs|SNORD66_uc003fnz.1_5'Flank	NM_004953	NP_004944	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	606_607	EIF4E-binding.|MIF4G.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|large_intestine(1)|central_nervous_system(1)	6	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)							439				0.42			35	48				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	185523324	185523328	5227	3	TAGAG	-	-	53	53	EIF4G1	-	5	5
ETV5	2119	broad.mit.edu	36	3	187257613	187257628	+	Frame_Shift_Del	DEL	TGGGCATTGGCTGGGT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:187257613_187257628delTGGGCATTGGCTGGGT	uc003fpy.1	-	c.1265_1280delACCCAGCCAATGCCCA	c.(1264-1281)GACCCAGCCAATGCCCACfs	p.D422fs	ETV5_uc003fpz.1_Frame_Shift_Del_p.D380fs	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	380_385	ETS.				cellular response to oxidative stress|regulation of transcription, DNA-dependent	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)							170				0.89			220	27				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	187257613	187257628	5475	3	TGGGCATTGGCTGGGT	-	-	59	59	ETV5	-	5	5
SLC4A7	9497	broad.mit.edu	36	3	27468934	27468937	+	Frame_Shift_Del	DEL	CTTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:27468934_27468937delCTTG	uc003cdv.1	-	c.90_93delCAAG	c.(88-93)ACCAAGfs	p.T30fs	SLC4A7_uc003cdw.1_Frame_Shift_Del_p.T30fs|SLC4A7_uc003cdu.2_Frame_Shift_Del_p.T35fs|SLC4A7_uc010hfm.1_Frame_Shift_Del_p.T35fs	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	30_31	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)	4														0.71			37	15				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	27468934	27468937	15155	3	CTTG	-	-	20	20	SLC4A7	-	5	5
TTC21A	199223	broad.mit.edu	36	3	39128993	39128994	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39128993_39128994delAG	uc003cje.2	+	c.476_477delAG	c.(475-477)AAGfs	p.K159fs	TTC21A_uc003cja.2_Frame_Shift_Del_p.K159fs|TTC21A_uc010hho.1_Intron|TTC21A_uc003cjb.2_Intron|TTC21A_uc003cjc.2_Frame_Shift_Del_p.K159fs|TTC21A_uc003cjd.2_Non-coding_Transcript	NM_001105513	NP_001098983	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 1	159	TPR 3.						binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)										0.57			40	30				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	39128993	39128994	17241	3	AG	-	-	3	3	TTC21A	-	5	5
CSRNP1	64651	broad.mit.edu	36	3	39159737	39159738	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39159737_39159738insA	uc003cjg.1	-	c.1582_1583insT	c.(1582-1584)AGCfs	p.S528fs	CSRNP1_uc003cjh.1_Frame_Shift_Ins_p.S528fs	NM_033027	NP_149016	Q96S65	CSRN1_HUMAN	AXIN1 up-regulated 1	528					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(4)|skin(1)	5														0.73			95	35				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	39159737	39159738	4104	3	-	A	A	28	28	CSRNP1	A	5	5
CSPG5	10675	broad.mit.edu	36	3	47589285	47589293	+	In_Frame_Del	DEL	ACGGCCACG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47589285_47589293delACGGCCACG	uc003crp.2	-	c.1269_1277delCGTGGCCGT	c.(1267-1278)TGCGTGGCCGTG>TGG	p.423_426CVAV>W	CSPG5_uc003crn.1_In_Frame_Del_p.285_288CVAV>W|CSPG5_uc003cro.2_In_Frame_Del_p.423_426CVAV>W	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	423_426	Helical; (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)										0.64			197	110				---	---	---	---	capture_indel			In_Frame_Del	DEL	47589285	47589293	4102	3	ACGGCCACG	-	-	6	6	CSPG5	-	5	5
MAP4	4134	broad.mit.edu	36	3	47933532	47933533	+	Frame_Shift_Ins	INS	-	TCCTTGA	TCCTTGA			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47933532_47933533insTCCTTGA	uc003csb.1	-	c.788_789insTCAAGGA	c.(787-789)GACfs	p.D263fs	MAP4_uc003csc.2_Frame_Shift_Ins_p.D263fs|MAP4_uc003csf.2_Frame_Shift_Ins_p.D280fs	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1	263	17 X 14 AA tandem repeats.|2.				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)										0.47			517	583				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	47933532	47933533	9641	3	-	TCCTTGA	TCCTTGA	48	48	MAP4	TCCTTGA	5	5
UQCRC1	7384	broad.mit.edu	36	3	48617188	48617192	+	Frame_Shift_Del	DEL	CAGGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48617188_48617192delCAGGG	uc003cuc.1	-	c.323_327delCCCTG	c.(322-327)GCCCTGfs	p.A108fs	UQCRC1_uc003cua.1_5'UTR|UQCRC1_uc003cub.1_Frame_Shift_Del_p.A108fs|UQCRC1_uc003cud.1_Frame_Shift_Del_p.A108fs	NM_003365	NP_003356	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I	108_109					aerobic respiration|proteolysis		metalloendopeptidase activity|ubiquinol-cytochrome-c reductase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	Atovaquone(DB01117)	NSCLC(81;1112 1427 27031 32409 45529)								0.65			15	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	48617188	48617192	17580	3	CAGGG	-	-	21	21	UQCRC1	-	5	5
MST1R	4486	broad.mit.edu	36	3	49899993	49899998	+	In_Frame_Del	DEL	TTGGTA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49899993_49899998delTTGGTA	uc003cxy.2	-	c.3949_3954delTACCAA	c.(3949-3954)TACCAAdel	p.YQ1317del		NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	1317_1318	Cytoplasmic (Potential).|Protein kinase.				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|protein phosphorylation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)						205				0.80			70	17				---	---	---	---	capture_indel			In_Frame_Del	DEL	49899993	49899998	10284	3	TTGGTA	-	-	56	56	MST1R	-	5	5
CNGA1	1259	broad.mit.edu	36	4	47633707	47633707	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47633707_47633707delC	uc003gxu.1	-	c.1768_1768delG	c.(1768-1770)GAAfs	p.E590fs	CNGA1_uc003gxs.1_Frame_Shift_Del_p.E521fs|CNGA1_uc003gxt.2_Frame_Shift_Del_p.E521fs	NM_000087	NP_000078	P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1 isoform	521	cGMP (Potential).|Cytoplasmic (Potential).				response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2														0.38			39	64				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	47633707	47633707	3734	4	C	-	-	30	30	CNGA1	-	5	5
FAT2	2196	broad.mit.edu	36	5	150925645	150925654	+	Frame_Shift_Del	DEL	CAGAGAGTCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150925645_150925654delCAGAGAGTCC	uc003lue.2	-	c.3032_3041delGGACTCTCTG	c.(3031-3042)AGGACTCTCTGCfs	p.R1011fs	FAT2_uc010jhx.1_Frame_Shift_Del_p.R1011fs	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1011_1014	Extracellular (Potential).|Cadherin 8.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.69			18	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	150925645	150925654	5926	5	CAGAGAGTCC	-	-	25	25	FAT2	-	5	5
ACTBL2	345651	broad.mit.edu	36	5	56813239	56813246	+	Frame_Shift_Del	DEL	GGACAGGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:56813239_56813246delGGACAGGC	uc003jrm.1	-	c.1046_1053delGCCTGTCC	c.(1045-1053)AGCCTGTCCfs	p.S349fs		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	349_351						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)										0.78			171	49				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	56813239	56813246	195	5	GGACAGGC	-	-	47	47	ACTBL2	-	5	5
NLN	57486	broad.mit.edu	36	5	65119965	65119975	+	Frame_Shift_Del	DEL	TGACAGATGCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:65119965_65119975delTGACAGATGCT	uc003juf.1	+	c.1223_1233delTGACAGATGCT	c.(1222-1233)ATGACAGATGCTfs	p.M408fs	NLN_uc003jug.1_Frame_Shift_Del_p.M237fs|NLN_uc010iww.1_Frame_Shift_Del_p.M103fs|NLN_uc003jue.2_Frame_Shift_Del_p.M408fs	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin	408_411					proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)										0.74			339	120				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	65119965	65119975	10870	5	TGACAGATGCT	-	-	51	51	NLN	-	5	5
RAET1G	353091	broad.mit.edu	36	6	150281035	150281036	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:150281035_150281036delGG	uc010kii.1	-	c.809_810delCC	c.(808-810)ACCfs	p.T270fs	RAET1G_uc003qnm.2_Non-coding_Transcript	NM_001001788	NP_001001788	Q6H3X3	RET1G_HUMAN	retinoic acid early transcript 1G	270	Cytoplasmic (Potential).				antigen processing and presentation|immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)										0.36			43	78				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	150281035	150281036	13460	6	GG	-	-	35	35	RAET1G	-	5	5
LY6G6F	259215	broad.mit.edu	36	6	31783301	31783305	+	Frame_Shift_Del	DEL	TGTCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31783301_31783305delTGTCA	uc003nwb.1	+	c.140_144delTGTCA	c.(139-144)CTGTCAfs	p.L47fs	LY6G6F_uc003nwa.1_Frame_Shift_Del_p.L47fs	NM_001003693	NP_001003693	Q5SQ64	LY66F_HUMAN	G6f protein	47_48	Extracellular (Potential).|Ig-like V-type.					integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2														0.56			31	24				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	31783301	31783305	9473	6	TGTCA	-	-	55	55	LY6G6F	-	5	5
SKIV2L	6499	broad.mit.edu	36	6	32042594	32042595	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32042594_32042595insC	uc003nyn.1	+	c.2332_2333insC	c.(2332-2334)GACfs	p.D778fs		NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	778						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4														0.81			50	12				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	32042594	32042595	14854	6	-	C	C	33	33	SKIV2L	C	5	5
BACH2	60468	broad.mit.edu	36	6	90717243	90717257	+	In_Frame_Del	DEL	AGGAGAAGATCACGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:90717243_90717257delAGGAGAAGATCACGC	uc003pnv.1	-	c.1289_1303delGCGTGATCTTCTCCT	c.(1288-1305)AGCGTGATCTTCTCCTCC>ACC	p.430_435SVIFSS>T	BACH2_uc003pnw.1_In_Frame_Del_p.430_435SVIFSS>T|BACH2_uc010kch.1_In_Frame_Del_p.430_435SVIFSS>T	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	430_435					regulation of transcription, DNA-dependent	nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|lung(1)|pancreas(1)	5		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)										0.71			54	22				---	---	---	---	capture_indel			In_Frame_Del	DEL	90717243	90717257	1305	6	AGGAGAAGATCACGC	-	-	11	11	BACH2	-	5	5
EPHA7	2045	broad.mit.edu	36	6	94123448	94123457	+	Frame_Shift_Del	DEL	TTGGTTGATG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:94123448_94123457delTTGGTTGATG	uc003poe.1	-	c.1023_1032delCATCAACCAA	c.(1021-1032)AACATCAACCAAfs	p.N341fs	EPHA7_uc003pof.1_Frame_Shift_Del_p.N341fs	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7	341_344	Extracellular (Potential).|Fibronectin type-III 1.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(7)|lung(6)|central_nervous_system(3)|large_intestine(2)|skin(2)|pancreas(1)	21		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)						635				0.53			49	44				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	94123448	94123457	5365	6	TTGGTTGATG	-	-	64	64	EPHA7	-	5	5
FUT9	10690	broad.mit.edu	36	6	96758154	96758154	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:96758154_96758154delG	uc003pop.2	+	c.402_402delG	c.(400-402)ATGfs	p.M134fs	FUT9_uc010kcj.1_Frame_Shift_Del_p.M134fs	NM_006581	NP_006572	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3)	134	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)	1		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		Melanoma(98;1369 1476 6592 22940 26587)								0.62			40	25				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	96758154	96758154	6362	6	G	-	-	45	45	FUT9	-	5	5
MLL5	55904	broad.mit.edu	36	7	104491137	104491139	+	In_Frame_Del	DEL	TTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:104491137_104491139delTTG	uc003vcm.1	+	c.290_292delTTG	c.(289-294)TTTGAT>TAT	p.97_98FD>Y	MLL5_uc010lja.1_5'UTR|MLL5_uc010ljb.1_In_Frame_Del_p.97_98FD>Y|MLL5_uc003vcl.2_In_Frame_Del_p.97_98FD>Y|MLL5_uc010ljc.1_In_Frame_Del_p.97_98FD>Y	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	97_98					cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3														0.31			36	80				---	---	---	---	capture_indel			In_Frame_Del	DEL	104491137	104491139	10014	7	TTG	-	-	64	64	MLL5	-	5	5
WEE2	494551	broad.mit.edu	36	7	141075898	141075903	+	In_Frame_Del	DEL	AACGCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141075898_141075903delAACGCC	uc003vwn.2	+	c.1634_1639delAACGCC	c.(1633-1641)AAACGCCTG>ATG	p.545_547KRL>M	FLJ40852_uc010lnm.1_Intron|FLJ40852_uc010lnn.1_Intron|FLJ40852_uc003vwm.2_Intron|FLJ40852_uc010lno.1_Intron	NM_001105558	NP_001099028	P0C1S8	WEE2_HUMAN	WEE1 homolog 2	545_547					egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|protein phosphorylation|regulation of meiosis I	centrosome|nucleus	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2	Melanoma(164;0.0171)									241				0.63			43	25				---	---	---	---	capture_indel			In_Frame_Del	DEL	141075898	141075903	17919	7	AACGCC	-	-	1	1	WEE2	-	5	5
MACC1	346389	broad.mit.edu	36	7	20164526	20164535	+	Frame_Shift_Del	DEL	AACTTTTTCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20164526_20164535delAACTTTTTCT	uc003sus.2	-	c.1974_1983delAGAAAAAGTT	c.(1972-1983)TCAGAAAAAGTTfs	p.S658fs	MACC1_uc010kug.1_Frame_Shift_Del_p.S658fs	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5	658_661					positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)	2														0.45			20	24				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	20164526	20164535	9520	7	AACTTTTTCT	-	-	1	1	MACC1	-	5	5
ITGB8	3696	broad.mit.edu	36	7	20407973	20407974	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20407973_20407974insC	uc003suu.1	+	c.1386_1387insC	c.(1384-1389)CATATAfs	p.H462fs		NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	462_463	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(2)	2									p.H462H(RKO-Tumor)	842				0.47			28	31				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	20407973	20407974	8205	7	-	C	C	49	49	ITGB8	C	5	5
DFNA5	1687	broad.mit.edu	36	7	24708968	24708970	+	In_Frame_Del	DEL	TCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:24708968_24708970delTCT	uc010kus.1	-	c.1191_1193delAGA	c.(1189-1194)CCAGAT>CCT	p.D398del	DFNA5_uc003swz.2_In_Frame_Del_p.D234del|DFNA5_uc003sxa.1_In_Frame_Del_p.D398del|DFNA5_uc010kut.1_In_Frame_Del_p.D234del	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	398					sensory perception of sound					ovary(1)	1						GBM(78;184 1250 20134 20900 23600)				312				0.44			70	90				---	---	---	---	capture_indel			In_Frame_Del	DEL	24708968	24708970	4633	7	TCT	-	-	50	50	DFNA5	-	5	5
SPDYE1	285955	broad.mit.edu	36	7	44013681	44013690	+	Frame_Shift_Del	DEL	GCTTGGGTTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44013681_44013690delGCTTGGGTTT	uc003tjf.1	+	c.922_931delGCTTGGGTTT	c.(922-933)GCTTGGGTTTCCfs	p.A308fs	POLR2J4_uc003tjc.1_Intron|POLR2J4_uc003tjd.1_Intron|POLR2J4_uc010kxw.1_Intron|POLR2J4_uc003tje.2_Intron	NM_175064	NP_778234	Q8NFV5	SPDE1_HUMAN	Williams Beuren syndrome chromosome region 19	308_311										ovary(1)	1														0.66			58	30				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	44013681	44013690	15539	7	GCTTGGGTTT	-	-	42	42	SPDYE1	-	5	5
ADCY1	107	broad.mit.edu	36	7	45691190	45691191	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:45691190_45691191insA	uc003tne.2	+	c.2071_2072insA	c.(2071-2073)GTGfs	p.V691fs		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	brain adenylate cyclase 1	691	Helical; (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 membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|central_nervous_system(1)	4					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)									0.57			82	61				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	45691190	45691191	293	7	-	A	A	48	48	ADCY1	A	5	5
COBL	23242	broad.mit.edu	36	7	51063820	51063827	+	Frame_Shift_Del	DEL	GGTGGGCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:51063820_51063827delGGTGGGCA	uc003tpr.2	-	c.2460_2467delTGCCCACC	c.(2458-2469)TCTGCCCACCATfs	p.S820fs	COBL_uc003tpp.2_Frame_Shift_Del_p.S606fs|COBL_uc003tpq.2_Frame_Shift_Del_p.S761fs|COBL_uc003tps.1_Frame_Shift_Del_p.S793fs|COBL_uc003tpo.2_Frame_Shift_Del_p.S362fs	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	820_823										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.79			70	19				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	51063820	51063827	3791	7	GGTGGGCA	-	-	47	47	COBL	-	5	5
GUSB	2990	broad.mit.edu	36	7	65066870	65066886	+	Splice_Site_Del	DEL	AGAGGTGGATCCTAGGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:65066870_65066886delAGAGGTGGATCCTAGGA	uc003tun.1	-	c.e11_splice_site				NM_000181	NP_000172			glucuronidase, beta						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0														0.59			41	28				---	---	---	---	capture_indel			Splice_Site_Del	DEL	65066870	65066886	7182	7	AGAGGTGGATCCTAGGA	-	-	7	7	GUSB	-	5	5
ELN	2006	broad.mit.edu	36	7	73113368	73113369	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73113368_73113369insG	uc003tzw.1	+	c.1767_1768insG	c.(1765-1770)GTACCTfs	p.V589fs	ELN_uc003tzn.1_Frame_Shift_Ins_p.V583fs|ELN_uc003tzz.1_Frame_Shift_Ins_p.V502fs|ELN_uc003tzo.1_Frame_Shift_Ins_p.V535fs|ELN_uc003tzp.1_Frame_Shift_Ins_p.V494fs|ELN_uc003tzq.1_Frame_Shift_Ins_p.V447fs|ELN_uc003tzr.1_Non-coding_Transcript|ELN_uc003tzs.1_Frame_Shift_Ins_p.V564fs|ELN_uc003tzt.1_Frame_Shift_Ins_p.V588fs|ELN_uc003tzu.1_Frame_Shift_Ins_p.V569fs|ELN_uc003tzv.1_Frame_Shift_Ins_p.V554fs|ELN_uc010lbk.1_Non-coding_Transcript|ELN_uc003tzx.1_Frame_Shift_Ins_p.V573fs|ELN_uc003tzy.1_Frame_Shift_Ins_p.V559fs	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	645_646	Ala-rich.				blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)					434				0.37			7	12				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	73113368	73113369	5263	7	-	G	G	14	14	ELN	G	5	5
HIP1	3092	broad.mit.edu	36	7	75026999	75027005	+	Frame_Shift_Del	DEL	CCTTCTC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:75026999_75027005delCCTTCTC	uc003uds.1	-	c.1342_1348delGAGAAGG	c.(1342-1350)GAGAAGGCTfs	p.E448fs		NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	448_450	Potential.|pDED.				activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			pancreas(2)|ovary(1)|central_nervous_system(1)	4										1179				0.39			117	180				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	75026999	75027005	7399	7	CCTTCTC	-	-	26	26	HIP1	-	5	5
COL14A1	7373	broad.mit.edu	36	8	121332033	121332035	+	Splice_Site_Del	DEL	TTA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:121332033_121332035delTTA	uc003yox.1	+	c.e22_splice_site			COL14A1_uc003yoy.2_Splice_Site_Del	NM_021110	NP_066933			collagen, type XIV, alpha 1						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)							1131				0.55			367	305				---	---	---	---	capture_indel			Splice_Site_Del	DEL	121332033	121332035	3809	8	TTA	-	-	64	64	COL14A1	-	5	5
SLC45A4	57210	broad.mit.edu	36	8	142307487	142307490	+	Frame_Shift_Del	DEL	TCAG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:142307487_142307490delTCAG	uc003ywd.1	-	c.58_61delCTGA	c.(58-63)CTGAGGfs	p.L20fs	SLC45A4_uc003ywc.1_Frame_Shift_Del_p.L20fs|SLC45A4_uc010meq.1_Intron	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	Error:Variant_position_missing_in_Q5BKX6_after_alignment					transmembrane transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)											0.38			36	59				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	142307487	142307490	15140	8	TCAG	-	-	54	54	SLC45A4	-	5	5
RPL8	6132	broad.mit.edu	36	8	145987641	145987643	+	In_Frame_Del	DEL	AGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145987641_145987643delAGG	uc003zeb.1	-	c.322_324delCCT	c.(322-324)CCTdel	p.P108del	RPL8_uc003zdz.1_Non-coding_Transcript|RPL8_uc003zea.1_In_Frame_Del_p.P72del|RPL8_uc003zec.1_In_Frame_Del_p.P108del|RPL8_uc010mgc.1_3'UTR	NM_033301	NP_150644	P62917	RL8_HUMAN	ribosomal protein L8	108					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	rRNA binding|structural constituent of ribosome				0	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.191)										0.75			27	9				---	---	---	---	capture_indel			In_Frame_Del	DEL	145987641	145987643	14081	8	AGG	-	-	7	7	RPL8	-	5	5
SORBS3	10174	broad.mit.edu	36	8	22484623	22484624	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:22484623_22484624insC	uc003xbv.1	+	c.1687_1688insC	c.(1687-1689)TCCfs	p.S563fs	SORBS3_uc003xbw.2_Frame_Shift_Ins_p.S221fs	NM_005775	NP_005766	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3 isoform 1	563					muscle contraction|positive regulation of stress fiber assembly	cytoskeleton|cytosol|nucleus	protein binding|structural constituent of cytoskeleton|vinculin binding				0		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	22484623	22484624	15429	8	-	C	C	54	54	SORBS3	C	5	5
EXTL3	2137	broad.mit.edu	36	8	28629920	28629927	+	Frame_Shift_Del	DEL	ACAAGGAG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:28629920_28629927delACAAGGAG	uc003xgz.1	+	c.425_432delACAAGGAG	c.(424-432)TACAAGGAGfs	p.Y142fs		NM_001440	NP_001431	O43909	EXTL3_HUMAN	Reg receptor	142_144	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding				0		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)										0.82			101	22				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	28629920	28629927	5521	8	ACAAGGAG	-	-	14	14	EXTL3	-	5	5
PALM2-AKAP2	445815	broad.mit.edu	36	9	111939941	111939944	+	Frame_Shift_Del	DEL	GGCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:111939941_111939944delGGCC	uc004bei.2	+	c.2992_2995delGGCC	c.(2992-2997)GGCCGAfs	p.G998fs	PALM2-AKAP2_uc004bek.2_Frame_Shift_Del_p.G766fs|PALM2-AKAP2_uc004bej.2_Frame_Shift_Del_p.G766fs|PALM2-AKAP2_uc004bel.1_Frame_Shift_Del_p.G576fs|AKAP2_uc004bem.1_Frame_Shift_Del_p.G624fs|PALM2-AKAP2_uc010mtw.1_Frame_Shift_Del_p.G584fs|PALM2-AKAP2_uc004ben.1_Frame_Shift_Del_p.G535fs	NM_001004065	NP_001004065	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 1	535_536							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.72			18	7				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	111939941	111939944	11826	9	GGCC	-	-	43	43	PALM2-AKAP2	-	5	5
C9orf117	286207	broad.mit.edu	36	9	129511584	129511607	+	In_Frame_Del	DEL	AGCTGGCCAATAACAAGAAGGAGA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:129511584_129511607delAGCTGGCCAATAACAAGAAGGAGA	uc004brn.1	+	c.224_247delAGCTGGCCAATAACAAGAAGGAGA	c.(223-249)CAGCTGGCCAATAACAAGAAGGAGATT>CTT	p.75_83QLANNKKEI>L	PTRH1_uc004brm.2_Intron|C9orf117_uc010mxl.1_Non-coding_Transcript	NM_001012502	NP_001012520	Q5JU67	CI117_HUMAN	hypothetical protein LOC286207	75_83	Potential.										0														0.98			710	12				---	---	---	---	capture_indel			In_Frame_Del	DEL	129511584	129511607	2564	9	AGCTGGCCAATAACAAGAAGGAGA	-	-	7	7	C9orf117	-	5	5
SPTAN1	6709	broad.mit.edu	36	9	130428670	130428670	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130428670_130428670delC	uc004bvm.2	+	c.6459_6459delC	c.(6457-6459)AACfs	p.N2153fs	SPTAN1_uc004bvl.2_Frame_Shift_Del_p.N2148fs|SPTAN1_uc004bvn.2_Frame_Shift_Del_p.N2128fs|SPTAN1_uc010mye.1_5'UTR|SPTAN1_uc010myf.1_5'UTR	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	2148	Spectrin 22.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						NSCLC(120;833 1744 2558 35612 37579)				1105				0.80			20	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	130428670	130428670	15631	9	C	-	-	18	18	SPTAN1	-	5	5
WDR34	89891	broad.mit.edu	36	9	130435940	130435962	+	Frame_Shift_Del	DEL	GCCCTGGGCATCGCCCGCAGCCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130435940_130435962delGCCCTGGGCATCGCCCGCAGCCA	uc004bvq.1	-	c.1493_1515delTGGCTGCGGGCGATGCCCAGGGC	c.(1492-1515)TTGGCTGCGGGCGATGCCCAGGGCfs	p.L498fs	WDR34_uc004bvr.1_Frame_Shift_Del_p.L470fs|WDR34_uc004bvs.1_Frame_Shift_Del_p.L489fs	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34	498_505	WD 5.					cytoplasm				central_nervous_system(2)|skin(1)	3														0.61			11	7				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	130435940	130435962	17861	9	GCCCTGGGCATCGCCCGCAGCCA	-	-	46	46	WDR34	-	5	5
C9orf98	158067	broad.mit.edu	36	9	134590985	134590986	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134590985_134590986delTG	uc004cbu.1	-	c.1350_1351delCA	c.(1348-1353)GCCATCfs	p.A450fs	C9orf98_uc010mzx.1_Frame_Shift_Del_p.A278fs|C9orf98_uc004cbv.1_Frame_Shift_Del_p.A246fs	NM_152572	NP_689785	Q96MA6	KAD8_HUMAN	putative adenylate kinase-like protein C9orf98	450_451	Adenylate kinase.					cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)										0.83			39	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	134590985	134590986	2625	9	TG	-	-	51	51	C9orf98	-	5	5
WDR85	92715	broad.mit.edu	36	9	139569807	139569822	+	Frame_Shift_Del	DEL	GACCACGAGGGGGCCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139569807_139569822delGACCACGAGGGGGCCC	uc004cnk.1	-	c.1049_1064delGGGCCCCCTCGTGGTC	c.(1048-1065)CGGGCCCCCTCGTGGTCCfs	p.R350fs	WDR85_uc004cnl.1_Frame_Shift_Del_p.R174fs|WDR85_uc004cnm.1_Frame_Shift_Del_p.R111fs|WDR85_uc004cnn.1_Frame_Shift_Del_p.R79fs|WDR85_uc004cnj.1_Frame_Shift_Del_p.R79fs|WDR85_uc004cni.2_Non-coding_Transcript	NM_138778	NP_620133	Q9BTV6	WDR85_HUMAN	WD repeat domain 85	350_355					peptidyl-diphthamide biosynthetic process from peptidyl-histidine						0	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.00029)|Epithelial(140;0.000509)										0.81			30	7				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	139569807	139569822	17906	9	GACCACGAGGGGGCCC	-	-	41	41	WDR85	-	5	5
TESK1	7016	broad.mit.edu	36	9	35599237	35599242	+	In_Frame_Del	DEL	TGGGCC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35599237_35599242delTGGGCC	uc003zxa.1	+	c.1379_1384delTGGGCC	c.(1378-1386)GTGGGCCCC>GCC	p.460_462VGP>A	TESK1_uc003zwz.1_Non-coding_Transcript|TESK1_uc010mks.1_In_Frame_Del_p.300_302VGP>A	NM_006285	NP_006276	Q15569	TESK1_HUMAN	testis-specific protein kinase 1	460_462					cell junction assembly|protein phosphorylation|spermatogenesis	cytosol	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)						p.G461G(NCIH2405-Tumor)	56				0.59			41	28				---	---	---	---	capture_indel			In_Frame_Del	DEL	35599237	35599242	16294	9	TGGGCC	-	-	59	59	TESK1	-	5	5
ZCCHC7	84186	broad.mit.edu	36	9	37116940	37116941	+	Splice_Site_Ins	INS	-	GT	GT			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:37116940_37116941insGT	uc003zzq.1	+	c.e2_splice_site			ZCCHC7_uc003zzr.1_Splice_Site_Ins|ZCCHC7_uc010mlt.1_Splice_Site_Ins|ZCCHC7_uc003zzs.1_Splice_Site_Ins	NM_032226	NP_115602			zinc finger, CCHC domain containing 7								nucleic acid binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.0137)										0.44			22	28				---	---	---	---	capture_indel			Splice_Site_Ins	INS	37116940	37116941	18181	9	-	GT	GT	44	44	ZCCHC7	GT	5	5
SHB	6461	broad.mit.edu	36	9	37910000	37910003	+	Splice_Site_Del	DEL	TCCT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:37910000_37910003delTCCT	uc004aax.1	-	c.e6_splice_site				NM_003028	NP_003019			Src homology 2 domain containing adaptor protein						angiogenesis|apoptosis|cell differentiation|signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity			central_nervous_system(2)	2		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)										0.93			104	8				---	---	---	---	capture_indel			Splice_Site_Del	DEL	37910000	37910003	14760	9	TCCT	-	-	54	54	SHB	-	5	5
UBQLN1	29979	broad.mit.edu	36	9	85484552	85484557	+	In_Frame_Del	DEL	TGGATT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:85484552_85484557delTGGATT	uc004amv.1	-	c.664_669delAATCCA	c.(664-669)AATCCAdel	p.NP222del	UBQLN1_uc004amw.1_In_Frame_Del_p.NP222del	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1	222_223					apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						Melanoma(186;1284 2073 12755 14558 18426)								0.36			21	38				---	---	---	---	capture_indel			In_Frame_Del	DEL	85484552	85484557	17454	9	TGGATT	-	-	55	55	UBQLN1	-	5	5
HSD17B3	3293	broad.mit.edu	36	9	98104142	98104146	+	Frame_Shift_Del	DEL	CGCCA	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:98104142_98104146delCGCCA	uc004awa.1	-	c.62_66delTGGCG	c.(61-66)CTGGCGfs	p.L21fs	HSD17B3_uc010msc.1_Frame_Shift_Del_p.L21fs	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3	21_22					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)									0.73			82	31				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	98104142	98104146	7680	9	CGCCA	-	-	31	31	HSD17B3	-	5	5
MCART6	401612	broad.mit.edu	36	X	103236328	103236337	+	Frame_Shift_Del	DEL	AACGTCTTGG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:103236328_103236337delAACGTCTTGG	uc004elu.1	-	c.260_269delCCAAGACGTT	c.(259-270)TCCAAGACGTTGfs	p.S87fs	MCART6_uc010npb.1_Frame_Shift_Del_p.S87fs	NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	87_90	Helical; Name=2; (Potential).|Solcar 1.				transport	integral to membrane|mitochondrial inner membrane					0														0.99			133	2				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	103236328	103236337	9760	23	AACGTCTTGG	-	-	5	5	MCART6	-	5	5
ATP1B4	23439	broad.mit.edu	36	X	119388721	119388729	+	Splice_Site_Del	DEL	CTCCTGGTG	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:119388721_119388729delCTCCTGGTG	uc004esr.1	+	c.e3_splice_site			ATP1B4_uc004esq.1_Splice_Site_Del	NM_012069	NP_036201			ATPase, (Na+)/K+ transporting, beta 4						ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2														0.70			43	18				---	---	---	---	capture_indel			Splice_Site_Del	DEL	119388721	119388729	1154	23	CTCCTGGTG	-	-	24	24	ATP1B4	-	5	5
SLITRK2	84631	broad.mit.edu	36	X	144712234	144712247	+	Frame_Shift_Del	DEL	GCGTCCTTGAACAT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:144712234_144712247delGCGTCCTTGAACAT	uc004fcc.1	+	c.599_612delGCGTCCTTGAACAT	c.(598-612)GGCGTCCTTGAACATfs	p.G200fs	SLITRK2_uc010nso.1_Frame_Shift_Del_p.G200fs|SLITRK2_uc004fcd.1_Frame_Shift_Del_p.G200fs|SLITRK2_uc004fce.1_Frame_Shift_Del_p.G200fs|SLITRK2_uc004fcg.1_Frame_Shift_Del_p.G200fs|SLITRK2_uc010nsp.1_Frame_Shift_Del_p.G200fs	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	200_204	Extracellular (Potential).					integral to membrane				ovary(4)|pancreas(1)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.72			72	28				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	144712234	144712247	15241	23	GCGTCCTTGAACAT	-	-	42	42	SLITRK2	-	5	5
ATP6AP1	537	broad.mit.edu	36	X	153310624	153310636	+	Frame_Shift_Del	DEL	CCACATCACCAGC	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153310624_153310636delCCACATCACCAGC	uc004flf.1	+	c.198_210delCCACATCACCAGC	c.(196-210)GGCCACATCACCAGCfs	p.G66fs	ATP6AP1_uc004flg.1_Non-coding_Transcript|ATP6AP1_uc004flh.1_Frame_Shift_Del_p.G26fs	NM_001183	NP_001174	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory	66_70					ATP hydrolysis coupled proton transport	integral to membrane|proton-transporting V-type ATPase, V1 domain|vacuolar membrane	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(3)|breast(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.64			28	16				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	153310624	153310636	1184	23	CCACATCACCAGC	-	-	26	26	ATP6AP1	-	5	5
MAGEB2	4113	broad.mit.edu	36	X	30147558	30147559	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:30147558_30147559insC	uc004dbz.1	+	c.940_941insC	c.(940-942)GAAfs	p.E314fs	MAGEB2_uc010ngf.1_Frame_Shift_Ins_p.E314fs	NM_002364	NP_002355	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	314							protein binding			ovary(1)	1														0.38			5	8				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	30147558	30147559	9557	23	-	C	C	45	45	MAGEB2	C	5	5
MID1IP1	58526	broad.mit.edu	36	X	38549344	38549345	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:38549344_38549345insC	uc004dei.2	+	c.201_202insC	c.(199-204)ACGCCCfs	p.T67fs	MID1IP1_uc010ngz.1_Frame_Shift_Ins_p.T67fs|MID1IP1_uc004dej.2_Frame_Shift_Ins_p.T67fs|MID1IP1_uc010nha.1_Frame_Shift_Ins_p.T67fs	NM_001098790	NP_067065	Q9NPA3	M1IP1_HUMAN	MID1 interacting G12-like protein	67_68					lipid biosynthetic process|negative regulation of microtubule depolymerization|positive regulation of fatty acid biosynthetic process|positive regulation of ligase activity|protein polymerization	cytosol|microtubule|nucleus					0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	38549344	38549345	9967	23	-	C	C	38	38	MID1IP1	C	5	5
PHF16	9767	broad.mit.edu	36	X	46802575	46802585	+	Frame_Shift_Del	DEL	AAGTTAAAAAT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:46802575_46802585delAAGTTAAAAAT	uc004dgx.1	+	c.1624_1634delAAGTTAAAAAT	c.(1624-1635)AAGTTAAAAATGfs	p.K542fs	PHF16_uc004dgy.1_Frame_Shift_Del_p.K542fs	NM_001077445	NP_055550	Q92613	JADE3_HUMAN	PHD finger protein 16	542_545					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.48			109	116				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	46802575	46802585	12250	23	AAGTTAAAAAT	-	-	9	9	PHF16	-	5	5
KLF8	11279	broad.mit.edu	36	X	56327543	56327546	+	Frame_Shift_Del	DEL	ATTT	-	-			TCGA-06-1802-01	TCGA-06-1802-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:56327543_56327546delATTT	uc004dur.1	+	c.971_974delATTT	c.(970-975)CATTTCfs	p.H324fs	KLF8_uc010nkh.1_Non-coding_Transcript	NM_007250	NP_009181	O95600	KLF8_HUMAN	Kruppel-like factor 8	324_325	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.66			21	11				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	56327543	56327546	8664	23	ATTT	-	-	8	8	KLF8	-	5	5
