Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
LOXL4	84171	broad.mit.edu	37	10	100015439	100015439	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:100015439G>A	uc001kpa.1	-	c.1486C>T	c.(1486-1488)CGC>TGC	p.R496C		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	496	SRCR 4.				oxidation-reduction process	extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)	4		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)										0.313725	41.579155	43.155465	16	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100015439	100015439	9275	10	G	A	A	A	494	38	LOXL4	1	1
C10orf2	56652	broad.mit.edu	37	10	102748989	102748989	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102748989G>T	uc001ksf.2	+	c.1022G>T	c.(1021-1023)CGT>CTT	p.R341L	MRPL43_uc001kry.1_5'Flank|MRPL43_uc010qpu.1_5'Flank|MRPL43_uc001krz.1_5'Flank|MRPL43_uc001ksa.1_5'Flank|MRPL43_uc001ksb.1_5'Flank|MRPL43_uc001ksd.1_5'Flank|MRPL43_uc001ksc.2_5'Flank|MRPL43_uc001kse.2_5'Flank|C10orf2_uc001ksg.2_Missense_Mutation_p.R341L|C10orf2_uc001ksi.2_Intron|C10orf2_uc010qpv.1_Intron|C10orf2_uc001ksh.2_Intron	NM_021830	NP_068602	Q96RR1	PEO1_HUMAN	twinkle isoform A	341					cell death|mitochondrial DNA replication|protein hexamerization|protein homooligomerization|transcription from mitochondrial promoter	mitochondrial nucleoid	5'-3' DNA helicase activity|ATP binding|protease binding|single-stranded DNA binding			ovary(1)	1		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)										0.717949	93.6076	95.269708	28	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102748989	102748989	1634	10	G	T	T	T	520	40	C10orf2	1	1
PDZD7	79955	broad.mit.edu	37	10	102781973	102781973	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102781973C>A	uc001ksn.2	-	c.712G>T	c.(712-714)GTG>TTG	p.V238L	PDZD7_uc001kso.1_Missense_Mutation_p.V238L	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	238	PDZ 2.				response to stimulus|visual perception	cilium|nucleus	protein binding			breast(1)|central_nervous_system(1)	2				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)										0.484848	53.29953	53.306089	16	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102781973	102781973	12125	10	C	A	A	A	221	17	PDZD7	2	2
MGEA5	10724	broad.mit.edu	37	10	103567562	103567562	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:103567562G>A	uc001ktv.2	-	c.577C>T	c.(577-579)CAT>TAT	p.H193Y	MGEA5_uc010qqe.1_Missense_Mutation_p.H193Y|MGEA5_uc009xws.2_Missense_Mutation_p.H193Y|MGEA5_uc001ktw.2_Missense_Mutation_p.H193Y|MGEA5_uc009xwt.2_Missense_Mutation_p.H51Y|MGEA5_uc010qqf.1_Non-coding_Transcript	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	193					glycoprotein catabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)	2		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)										0.651685	180.790398	182.577576	58	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103567562	103567562	9945	10	G	A	A	A	585	45	MGEA5	2	2
CPXM2	119587	broad.mit.edu	37	10	125521440	125521440	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:125521440G>T	uc001lhk.1	-	c.1725C>A	c.(1723-1725)TTC>TTA	p.F575L	CPXM2_uc001lhj.2_Non-coding_Transcript	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	575					cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)										0.785714	68.753146	70.858983	22	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125521440	125521440	3977	10	G	T	T	T	529	41	CPXM2	2	2
TRDMT1	1787	broad.mit.edu	37	10	17199442	17199442	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:17199442T>A	uc001iop.2	-	c.885A>T	c.(883-885)AAA>AAT	p.K295N	TRDMT1_uc001ioq.2_Missense_Mutation_p.K271N|TRDMT1_uc001ior.2_Missense_Mutation_p.K249N|TRDMT1_uc001ios.2_Missense_Mutation_p.K224N|TRDMT1_uc009xjt.2_Missense_Mutation_p.K214N|TRDMT1_uc010qcc.1_Missense_Mutation_p.K224N|TRDMT1_uc010qcd.1_Missense_Mutation_p.K172N	NM_004412	NP_004403	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1 isoform	295						nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|RNA binding|tRNA (cytosine-5-)-methyltransferase activity			ovary(1)	1														0.639344	127.539482	128.582006	39	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17199442	17199442	17011	10	T	A	A	A	725	56	TRDMT1	3	3
PTF1A	256297	broad.mit.edu	37	10	23481565	23481565	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:23481565C>G	uc001irp.2	+	c.106C>G	c.(106-108)CTG>GTG	p.L36V		NM_178161	NP_835455	Q7RTS3	PTF1A_HUMAN	pancreas specific transcription factor, 1a	36					endocrine pancreas development|exocrine pancreas development|regulation of transcription, DNA-dependent|tissue development|transcription, DNA-dependent	cytoplasm|transcription factor complex				pancreas(1)	1														0.722222	83.029179	84.61721	26	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23481565	23481565	13194	10	C	G	G	G	311	24	PTF1A	3	3
KIAA1217	56243	broad.mit.edu	37	10	24762579	24762579	+	Silent	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:24762579A>G	uc001iru.3	+	c.1269A>G	c.(1267-1269)GCA>GCG	p.A423A	KIAA1217_uc001irs.2_Silent_p.A343A|KIAA1217_uc001irt.3_Silent_p.A423A|KIAA1217_uc010qcy.1_Silent_p.A423A|KIAA1217_uc010qcz.1_Silent_p.A423A|KIAA1217_uc001irv.1_Silent_p.A273A|KIAA1217_uc010qda.1_Non-coding_Transcript|KIAA1217_uc001irw.2_Silent_p.A141A|KIAA1217_uc001irz.2_Silent_p.A141A|KIAA1217_uc001irx.2_Silent_p.A141A|KIAA1217_uc001iry.2_Silent_p.A141A	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	423					embryonic skeletal system development	cytoplasm				ovary(5)	5														0.7	65.401957	66.499046	21	9	KEEP	---	---	---	---	capture		Silent	SNP	24762579	24762579	8524	10	A	G	G	G	93	8	KIAA1217	4	4
PCDH15	65217	broad.mit.edu	37	10	56287633	56287633	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:56287633G>A	uc010qhy.1	-	c.111C>T	c.(109-111)TGC>TGT	p.C37C	PCDH15_uc010qhq.1_Silent_p.C37C|PCDH15_uc010qhr.1_Silent_p.C32C|PCDH15_uc010qhs.1_Silent_p.C37C|PCDH15_uc010qht.1_Silent_p.C32C|PCDH15_uc010qhu.1_Silent_p.C32C|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.C32C|PCDH15_uc010qhw.1_Silent_p.C32C|PCDH15_uc010qhx.1_Silent_p.C32C|PCDH15_uc010qhz.1_Silent_p.C32C|PCDH15_uc010qia.1_Intron|PCDH15_uc001jju.1_Silent_p.C32C|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Silent_p.C32C	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	32	Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.567568	64.676272	64.822914	21	16	KEEP	---	---	---	---	capture		Silent	SNP	56287633	56287633	11931	10	G	A	A	A	594	46	PCDH15	2	2
IPMK	253430	broad.mit.edu	37	10	59997554	59997555	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:59997554_59997555CC>AA	uc001jkb.2	-	c.211_212GG>TT	c.(211-213)GGC>TTC	p.G71F		NM_152230	NP_689416	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase	71						nucleus	ATP binding|inositol trisphosphate 6-kinase activity			ovary(1)	1														0.571429	67.304627	67.460175	20	15	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	59997554	59997555	8093	10	CC	AA	AA	AA	338	26	IPMK	2	2
FAM13C	220965	broad.mit.edu	37	10	61112135	61112135	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:61112135G>A	uc010qif.1	-	c.285C>T	c.(283-285)ACC>ACT	p.T95T	FAM13C_uc001jkn.2_Silent_p.T73T|FAM13C_uc001jko.2_Silent_p.T73T|FAM13C_uc010qid.1_5'UTR|FAM13C_uc010qie.1_5'UTR|FAM13C_uc001jkp.2_5'UTR	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1	73										ovary(1)	1														0.807692	71.941793	74.221103	21	5	KEEP	---	---	---	---	capture		Silent	SNP	61112135	61112135	5651	10	G	A	A	A	496	39	FAM13C	1	1
JMJD1C	221037	broad.mit.edu	37	10	64974642	64974642	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:64974642T>A	uc001jmn.2	-	c.1285A>T	c.(1285-1287)AAT>TAT	p.N429Y	JMJD1C_uc001jml.2_Missense_Mutation_p.N210Y|JMJD1C_uc001jmm.2_Missense_Mutation_p.N141Y|JMJD1C_uc010qiq.1_Missense_Mutation_p.N247Y|JMJD1C_uc009xpi.2_Missense_Mutation_p.N247Y|JMJD1C_uc009xpj.1_Non-coding_Transcript|JMJD1C_uc001jmp.1_Missense_Mutation_p.N141Y	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	429					blood coagulation|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)	5	Prostate(12;0.0119)|all_hematologic(501;0.191)													0.424242	79.939173	80.279001	28	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64974642	64974642	8254	10	T	A	A	A	832	64	JMJD1C	3	3
SLC29A3	55315	broad.mit.edu	37	10	73111446	73111446	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73111446T>C	uc001jrr.3	+	c.511T>C	c.(511-513)TGC>CGC	p.C171R	SLC29A3_uc001jrs.3_Missense_Mutation_p.C171R|SLC29A3_uc010qjq.1_Missense_Mutation_p.C25R|SLC29A3_uc001jrt.3_Intron|SLC29A3_uc001jru.3_Intron	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside	171	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0						Esophageal Squamous(200;1319 2142 18949 31248 39672)								0.815789	88.480834	92.026581	31	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73111446	73111446	15033	10	T	C	C	C	715	55	SLC29A3	4	4
CDH23	64072	broad.mit.edu	37	10	73567303	73567303	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73567303A>T	uc001jrx.3	+	c.8339A>T	c.(8338-8340)CAG>CTG	p.Q2780L	CDH23_uc001jsg.3_Missense_Mutation_p.Q540L|CDH23_uc001jsh.3_Missense_Mutation_p.Q540L|CDH23_uc001jsi.3_Missense_Mutation_p.Q540L	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	2780	Cadherin 26.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.148148	7.082109	10.290794	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73567303	73567303	3237	10	A	T	T	T	91	7	CDH23	3	3
USP54	159195	broad.mit.edu	37	10	75276381	75276381	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75276381C>A	uc001juo.2	-	c.3803G>T	c.(3802-3804)AGG>ATG	p.R1268M	USP54_uc010qkk.1_Missense_Mutation_p.R450M|USP54_uc001juk.2_Missense_Mutation_p.R356M|USP54_uc001jul.2_Missense_Mutation_p.R356M|USP54_uc001jum.2_Non-coding_Transcript|USP54_uc001jun.2_Non-coding_Transcript	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1268					ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(1)|kidney(1)	2	Prostate(51;0.0112)					Colon(195;880 2046 8854 25025 38456)								0.609756	80.189505	80.625927	25	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75276381	75276381	17649	10	C	A	A	A	312	24	USP54	2	2
WAPAL	23063	broad.mit.edu	37	10	88277334	88277334	+	Missense_Mutation	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:88277334T>G	uc001kdn.2	-	c.622A>C	c.(622-624)ACT>CCT	p.T208P	WAPAL_uc001kdo.2_Missense_Mutation_p.T165P|WAPAL_uc009xsw.2_Missense_Mutation_p.T165P|WAPAL_uc010qmh.1_Missense_Mutation_p.T165P|WAPAL_uc010qmi.1_Missense_Mutation_p.T202P|WAPAL_uc010qmj.1_Missense_Mutation_p.T165P	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog	165	Mediates interaction with the cohesin complex.				cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1														0.27451	39.528073	41.864356	14	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88277334	88277334	17820	10	T	G	G	G	780	60	WAPAL	4	4
C10orf12	26148	broad.mit.edu	37	10	98744545	98744545	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98744545G>C	uc001kmv.2	+	c.3398G>C	c.(3397-3399)AGC>ACC	p.S1133T		NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	1133											0		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)										0.6	27.959697	28.087914	9	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98744545	98744545	1624	10	G	C	C	C	442	34	C10orf12	3	3
CRTAC1	55118	broad.mit.edu	37	10	99625320	99625320	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:99625320G>A	uc001kou.1	-	c.1971C>T	c.(1969-1971)TGC>TGT	p.C657C	GOLGA7B_uc001kos.2_Intron|CRTAC1_uc001kot.1_3'UTR	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	657						proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)										0.291667	17.418216	18.349767	7	17	KEEP	---	---	---	---	capture		Silent	SNP	99625320	99625320	4035	10	G	A	A	A	490	38	CRTAC1	1	1
NNMT	4837	broad.mit.edu	37	11	114167428	114167428	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:114167428C>T	uc001por.1	+	c.150C>T	c.(148-150)TGC>TGT	p.C50C	NNMT_uc001pos.1_Silent_p.C50C	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	50					xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)									0.162791	13.896764	18.544698	7	36	KEEP	---	---	---	---	capture		Silent	SNP	114167428	114167428	10912	11	C	T	T	T	337	26	NNMT	2	2
SOX6	55553	broad.mit.edu	37	11	16340103	16340103	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:16340103T>A	uc001mme.2	-	c.373A>T	c.(373-375)ATG>TTG	p.M125L	SOX6_uc001mmd.2_Missense_Mutation_p.M115L|SOX6_uc001mmf.2_Missense_Mutation_p.M112L|SOX6_uc001mmg.2_Missense_Mutation_p.M112L|SOX6_uc001mmh.1_Non-coding_Transcript|SOX6_uc009ygs.2_Non-coding_Transcript|SOX6_uc001mmi.3_Missense_Mutation_p.M112L|SOX6_uc001mmj.2_Missense_Mutation_p.M112L	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	112					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.595506	171.485044	172.194085	53	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16340103	16340103	15455	11	T	A	A	A	676	52	SOX6	3	3
USH1C	10083	broad.mit.edu	37	11	17522677	17522677	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17522677G>T	uc001mne.2	-	c.2301C>A	c.(2299-2301)GCC>GCA	p.A767A	USH1C_uc001mnf.2_Silent_p.A467A|USH1C_uc009yhb.2_Silent_p.A448A|USH1C_uc001mng.2_Non-coding_Transcript|USH1C_uc001mnd.2_Silent_p.A431A	NM_153676	NP_710142	Q9Y6N9	USH1C_HUMAN	harmonin isoform b3	467	PDZ 3.				equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1														0.5	21.624173	21.624173	7	7	KEEP	---	---	---	---	capture		Silent	SNP	17522677	17522677	17596	11	G	T	T	T	548	43	USH1C	2	2
ANO5	203859	broad.mit.edu	37	11	22281220	22281220	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22281220G>A	uc001mqi.2	+	c.1563G>A	c.(1561-1563)TTG>TTA	p.L521L	ANO5_uc001mqj.2_Silent_p.L520L	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	521	Helical; (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.692308	89.23914	90.526061	27	12	KEEP	---	---	---	---	capture		Silent	SNP	22281220	22281220	708	11	G	A	A	A	581	45	ANO5	2	2
CSTF3	1479	broad.mit.edu	37	11	33112133	33112133	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:33112133T>C	uc001muh.2	-	c.1586A>G	c.(1585-1587)AAG>AGG	p.K529R	TCP11L1_uc001muf.1_Intron	NM_001326	NP_001317	Q12996	CSTF3_HUMAN	cleavage stimulation factor subunit 3 isoform 1	529					mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0														0.196429	28.392533	33.200913	11	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33112133	33112133	4127	11	T	C	C	C	728	56	CSTF3	4	4
C11orf41	25758	broad.mit.edu	37	11	33689482	33689482	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:33689482A>T	uc001mup.3	+	c.5350A>T	c.(5350-5352)AGG>TGG	p.R1784W		NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	1778						integral to membrane				ovary(2)	2														0.25	10.146957	11.301887	5	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33689482	33689482	1679	11	A	T	T	T	88	7	C11orf41	3	3
RAG1	5896	broad.mit.edu	37	11	36596365	36596365	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36596365A>C	uc001mwu.3	+	c.1511A>C	c.(1510-1512)CAT>CCT	p.H504P	RAG1_uc001mwt.2_Non-coding_Transcript	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	504					histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4	all_lung(20;0.226)	all_hematologic(20;0.107)				Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)				117				0.418182	152.348117	152.986206	46	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36596365	36596365	13463	11	A	C	C	C	104	8	RAG1	4	4
RAG1	5896	broad.mit.edu	37	11	36597145	36597145	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36597145G>T	uc001mwu.3	+	c.2291G>T	c.(2290-2292)CGT>CTT	p.R764L	RAG1_uc001mwt.2_Non-coding_Transcript	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	764					histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4	all_lung(20;0.226)	all_hematologic(20;0.107)				Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)				117				0.5	111.81126	111.81126	33	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36597145	36597145	13463	11	G	T	T	T	520	40	RAG1	1	1
LRRC4C	57689	broad.mit.edu	37	11	40136099	40136100	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40136099_40136100CC>AA	uc001mxa.1	-	c.1743_1744GG>TT	c.(1741-1746)ATGGAA>ATTTAA	p.581_582ME>I*	LRRC4C_uc001mxc.1_Nonsense_Mutation_p.577_578ME>I*|LRRC4C_uc001mxd.1_Nonsense_Mutation_p.577_578ME>I*|LRRC4C_uc001mxb.1_Nonsense_Mutation_p.577_578ME>I*	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	581_582					regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5		all_lung(304;0.0575)|Lung NSC(402;0.138)												0.158879	31.373273	43.184973	17	90	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	40136099	40136100	9383	11	CC	AA	AA	AA	390	30	LRRC4C	5	2
LRRC4C	57689	broad.mit.edu	37	11	40136282	40136282	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40136282C>T	uc001mxa.1	-	c.1561G>A	c.(1561-1563)GAG>AAG	p.E521K	LRRC4C_uc001mxc.1_Missense_Mutation_p.E517K|LRRC4C_uc001mxd.1_Missense_Mutation_p.E517K|LRRC4C_uc001mxb.1_Missense_Mutation_p.E517K	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	521					regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5		all_lung(304;0.0575)|Lung NSC(402;0.138)												0.186047	16.877266	20.847272	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40136282	40136282	9383	11	C	T	T	T	377	29	LRRC4C	2	2
KIAA0652	9776	broad.mit.edu	37	11	46677781	46677781	+	Splice_Site_SNP	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46677781A>G	uc001nda.2	+	c.459_splice	c.e7-2	p.R153_splice	KIAA0652_uc009yld.2_Splice_Site_SNP_p.R153_splice|KIAA0652_uc001ndb.2_Splice_Site_SNP_p.R153_splice|KIAA0652_uc001ncz.2_Splice_Site_SNP_p.R153_splice|KIAA0652_uc001ndc.2_Splice_Site_SNP_p.R153_splice|KIAA0652_uc010rgv.1_Splice_Site_SNP_p.R74_splice	NM_014741	NP_001136145			autophagy-related protein 13 isoform 2						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)										0.40625	72.429506	72.922925	26	38	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	46677781	46677781	8495	11	A	G	G	G	91	7	KIAA0652	5	4
OR4A5	81318	broad.mit.edu	37	11	51411896	51411896	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:51411896C>A	uc001nhi.1	-	c.500G>T	c.(499-501)GGT>GTT	p.G167V		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	167	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		all_lung(304;0.236)												0.541667	42.276091	42.312258	13	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51411896	51411896	11449	11	C	A	A	A	234	18	OR4A5	2	2
OR4C15	81309	broad.mit.edu	37	11	55322792	55322792	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55322792C>A	uc010rig.1	+	c.1010C>A	c.(1009-1011)CCT>CAT	p.P337H		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	283	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.268456	103.530776	110.743835	40	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55322792	55322792	11454	11	C	A	A	A	312	24	OR4C15	2	2
OR9G4	283189	broad.mit.edu	37	11	56510794	56510794	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56510794A>G	uc010rjo.1	-	c.494T>C	c.(493-495)ATA>ACA	p.I165T		NM_001005284	NP_001005284	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G,	165	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.571429	94.109991	94.329598	28	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56510794	56510794	11662	11	A	G	G	G	208	16	OR9G4	4	4
OR56B1	387748	broad.mit.edu	37	11	5757979	5757979	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5757979T>C	uc001mbt.1	+	c.233T>C	c.(232-234)GTA>GCA	p.V78A	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|OR56B1_uc001mbs.1_Missense_Mutation_p.V78A|OR56B1_uc009yev.1_Missense_Mutation_p.V78A	NM_001005180	NP_001005180	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B,	78	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)										0.606061	68.602893	68.9275	20	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5757979	5757979	11547	11	T	C	C	C	741	57	OR56B1	4	4
OR1S2	219958	broad.mit.edu	37	11	57970940	57970940	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57970940G>A	uc010rkb.1	-	c.714C>T	c.(712-714)GTC>GTT	p.V238V		NM_001004459	NP_001004459	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S,	238	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)												0.298246	48.077161	50.137108	17	40	KEEP	---	---	---	---	capture		Silent	SNP	57970940	57970940	11379	11	G	A	A	A	522	41	OR1S2	2	2
OR10V1	390201	broad.mit.edu	37	11	59481123	59481123	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59481123G>T	uc001nof.1	-	c.196C>A	c.(196-198)CTG>ATG	p.L66M		NM_001005324	NP_001005324	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V,	66	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.4	11.732434	11.808708	4	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59481123	59481123	11326	11	G	T	T	T	425	33	OR10V1	2	2
NLRP14	338323	broad.mit.edu	37	11	7059854	7059854	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7059854T>C	uc001mfb.1	+	c.37T>C	c.(37-39)TTT>CTT	p.F13L		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	13	DAPIN.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|lung(1)|pancreas(1)	7				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)										0.236111	46.27073	50.833444	17	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7059854	7059854	10879	11	T	C	C	C	832	64	NLRP14	4	4
STAB2	55576	broad.mit.edu	37	12	103984725	103984725	+	Silent	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:103984725A>C	uc001tjw.2	+	c.132A>C	c.(130-132)CGA>CGC	p.R44R		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	44	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(1)	10														0.163043	31.813395	41.703036	15	77	KEEP	---	---	---	---	capture		Silent	SNP	103984725	103984725	15756	12	A	C	C	C	145	12	STAB2	4	4
KLRC1	3821	broad.mit.edu	37	12	10600141	10600141	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10600141A>C	uc001qyl.2	-	c.580T>G	c.(580-582)TTC>GTC	p.F194V	KLRC1_uc009zhm.1_Missense_Mutation_p.F194V|KLRC1_uc001qym.2_Missense_Mutation_p.F176V|KLRC1_uc001qyn.2_Missense_Mutation_p.F194V|KLRC1_uc001qyo.2_Missense_Mutation_p.F176V	NM_002259	NP_002250	P26715	NKG2A_HUMAN	killer cell lectin-like receptor subfamily C,	194	C-type lectin.|Extracellular (Potential).				cell surface receptor linked signaling pathway|regulation of immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0														0.23913	26.496919	29.360373	11	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10600141	10600141	8729	12	A	C	C	C	13	1	KLRC1	4	4
RFX4	5992	broad.mit.edu	37	12	107080751	107080751	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107080751C>A	uc001tlt.2	+	c.494C>A	c.(493-495)ACG>AAG	p.T165K	RFX4_uc001tlr.2_Missense_Mutation_p.T156K|RFX4_uc010swv.1_Non-coding_Transcript|RFX4_uc001tls.2_Missense_Mutation_p.T165K|RFX4_uc001tlv.2_Missense_Mutation_p.T62K	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	156					transcription, DNA-dependent	nucleus	DNA binding				0														0.162791	29.437897	38.698256	14	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107080751	107080751	13737	12	C	A	A	A	247	19	RFX4	1	1
SSH1	54434	broad.mit.edu	37	12	109182837	109182837	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:109182837G>A	uc001tnm.2	-	c.2077C>T	c.(2077-2079)CAC>TAC	p.H693Y	SSH1_uc001tnl.2_Missense_Mutation_p.H381Y	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1	693					actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4														0.195122	19.57687	23.129693	8	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109182837	109182837	15700	12	G	A	A	A	611	47	SSH1	2	2
TAS2R14	50840	broad.mit.edu	37	12	11091748	11091748	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:11091748C>G	uc010shi.1	-	c.59G>C	c.(58-60)GGA>GCA	p.G20A	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_023922	NP_076411	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	20	Helical; Name=1; (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste	integral to membrane	bitter taste receptor activity				0														0.6	99.633299	100.02667	27	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11091748	11091748	16090	12	C	G	G	G	390	30	TAS2R14	3	3
CCDC60	160777	broad.mit.edu	37	12	119961558	119961558	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:119961558C>T	uc001txe.2	+	c.1164C>T	c.(1162-1164)GCC>GCT	p.A388A		NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	388										ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)										0.694444	77.918038	79.113034	25	11	KEEP	---	---	---	---	capture		Silent	SNP	119961558	119961558	2954	12	C	T	T	T	262	21	CCDC60	2	2
WDR66	144406	broad.mit.edu	37	12	122396983	122396983	+	Nonsense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:122396983C>T	uc009zxk.2	+	c.2116C>T	c.(2116-2118)CAG>TAG	p.Q706*		NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	706	WD 8.						calcium ion binding			ovary(1)	1	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		Esophageal Squamous(85;849 1794 49757 52143)								0.118182	17.399416	33.15287	13	97	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	122396983	122396983	17890	12	C	T	T	T	273	21	WDR66	5	2
RILPL1	353116	broad.mit.edu	37	12	123983237	123983237	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:123983237C>A	uc001ufe.2	-	c.655G>T	c.(655-657)GGG>TGG	p.G219W	RILPL1_uc001ufd.2_Missense_Mutation_p.G68W|RILPL1_uc010tas.1_Missense_Mutation_p.G219W	NM_178314	NP_847884	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	219	Potential.				neuroprotection	cytosol					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)										0.621359	199.901494	201.229221	64	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123983237	123983237	13836	12	C	A	A	A	286	22	RILPL1	2	2
AACS	65985	broad.mit.edu	37	12	125621357	125621357	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:125621357G>T	uc001uhc.2	+	c.1828G>T	c.(1828-1830)GGC>TGC	p.G610C	AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Non-coding_Transcript|AACS_uc009zyi.2_Missense_Mutation_p.G208C	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	610					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)										0.113924	10.525079	22.13176	9	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125621357	125621357	10	12	G	T	T	T	559	43	AACS	2	2
PIK3C2G	5288	broad.mit.edu	37	12	18435367	18435367	+	Nonsense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:18435367C>T	uc010sib.1	+	c.352C>T	c.(352-354)CAA>TAA	p.Q118*	PIK3C2G_uc001rdt.2_Nonsense_Mutation_p.Q118*|PIK3C2G_uc010sia.1_Non-coding_Transcript|PIK3C2G_uc010sic.1_5'UTR	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma	118					cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			central_nervous_system(6)|lung(4)|ovary(2)|breast(1)	13		Hepatocellular(102;0.194)								655				0.151515	16.103342	23.784498	10	56	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	18435367	18435367	12335	12	C	T	T	T	377	29	PIK3C2G	5	2
SOX5	6660	broad.mit.edu	37	12	23716278	23716278	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:23716278C>A	uc001rfw.2	-	c.1402G>T	c.(1402-1404)GAG>TAG	p.E468*	SOX5_uc001rfx.2_Nonsense_Mutation_p.E455*|SOX5_uc001rfy.2_Intron|SOX5_uc001rfv.2_Nonsense_Mutation_p.E82*|SOX5_uc010siv.1_Nonsense_Mutation_p.E455*|SOX5_uc010siw.1_Non-coding_Transcript|SOX5_uc001rfz.1_Nonsense_Mutation_p.E420*	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	468	Potential.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6														0.117021	9.787429	23.327789	11	83	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	23716278	23716278	15454	12	C	A	A	A	390	30	SOX5	5	2
C12orf11	55726	broad.mit.edu	37	12	27081679	27081679	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:27081679C>G	uc001rhk.3	-	c.460G>C	c.(460-462)GTT>CTT	p.V154L	C12orf11_uc010sjk.1_Missense_Mutation_p.V53L	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	154					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)													0.176471	34.474652	42.858331	15	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27081679	27081679	1719	12	C	G	G	G	221	17	C12orf11	3	3
GXYLT1	283464	broad.mit.edu	37	12	42499835	42499835	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:42499835C>G	uc001rms.3	-	c.649G>C	c.(649-651)GAC>CAC	p.D217H	GXYLT1_uc001rmt.3_Missense_Mutation_p.D186H	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3	217	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0														0.153846	16.179175	22.126226	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42499835	42499835	7183	12	C	G	G	G	403	31	GXYLT1	3	3
OR6C6	283365	broad.mit.edu	37	12	55688394	55688394	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55688394G>T	uc010sph.1	-	c.623C>A	c.(622-624)ACA>AAA	p.T208K		NM_001005493	NP_001005493	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C,	208	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)	1														0.666667	121.918155	123.252664	36	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55688394	55688394	11604	12	G	T	T	T	624	48	OR6C6	2	2
SHMT2	6472	broad.mit.edu	37	12	57627019	57627019	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57627019G>T	uc001snf.1	+	c.914G>T	c.(913-915)CGG>CTG	p.R305L	SHMT2_uc001sng.1_Missense_Mutation_p.R201L|SHMT2_uc001snh.1_Missense_Mutation_p.R144L|SHMT2_uc009zpk.1_Missense_Mutation_p.R295L|SHMT2_uc001sni.1_Missense_Mutation_p.R284L|SHMT2_uc010srg.1_Missense_Mutation_p.R314L|SHMT2_uc001snj.1_Missense_Mutation_p.R209L|SHMT2_uc010srh.1_Missense_Mutation_p.R284L|SHMT2_uc001snk.1_Missense_Mutation_p.R209L|SHMT2_uc010sri.1_Missense_Mutation_p.R284L|SHMT2_uc001snl.2_Missense_Mutation_p.R209L|SHMT2_uc010srj.1_5'UTR	NM_005412	NP_005403	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2	305						microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	Esophageal Squamous(150;1369 2416 49071 49364)								0.170732	15.410148	19.605087	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57627019	57627019	14781	12	G	T	T	T	507	39	SHMT2	1	1
FAM19A2	338811	broad.mit.edu	37	12	62148764	62148764	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:62148764G>A	uc001sqw.2	-	c.148C>T	c.(148-150)CAC>TAC	p.H50Y	FAM19A2_uc001sqv.2_Non-coding_Transcript|FAM19A2_uc001sqx.2_Missense_Mutation_p.H50Y|FAM19A2_uc001sqy.2_Non-coding_Transcript	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine	50						cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)										0.485714	52.370501	52.380133	17	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62148764	62148764	5746	12	G	A	A	A	611	47	FAM19A2	2	2
CAND1	55832	broad.mit.edu	37	12	67698483	67698483	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:67698483A>T	uc001stn.2	+	c.1392A>T	c.(1390-1392)GTA>GTT	p.V464V	CAND1_uc001sto.2_Intron	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	464	HEAT 10.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)	1			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)										0.170213	15.990585	20.81262	8	39	KEEP	---	---	---	---	capture		Silent	SNP	67698483	67698483	2732	12	A	T	T	T	197	16	CAND1	3	3
TPH2	121278	broad.mit.edu	37	12	72338118	72338118	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:72338118G>T	uc009zrw.1	+	c.300G>T	c.(298-300)CGG>CGT	p.R100R	TPH2_uc001swy.2_Silent_p.R10R	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	100	ACT.				aromatic amino acid family metabolic process|hormone biosynthetic process|oxidation-reduction process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)	3					L-Tryptophan(DB00150)									0.507692	98.848309	98.851218	33	32	KEEP	---	---	---	---	capture		Silent	SNP	72338118	72338118	16946	12	G	T	T	T	535	42	TPH2	2	2
PZP	5858	broad.mit.edu	37	12	9305864	9305864	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:9305864C>A	uc001qvl.2	-	c.3850G>T	c.(3850-3852)GTC>TTC	p.V1284F	PZP_uc009zgl.2_Missense_Mutation_p.V1070F	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|large_intestine(1)	4						Melanoma(125;1402 1695 4685 34487 38571)								0.157895	22.15166	30.632767	12	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9305864	9305864	13327	12	C	A	A	A	234	18	PZP	2	2
C12orf63	374467	broad.mit.edu	37	12	97158003	97158003	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:97158003G>T	uc001tet.1	+	c.3390G>T	c.(3388-3390)TGG>TGT	p.W1130C		NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467	1130										ovary(1)	1														0.619048	40.177962	40.438504	13	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97158003	97158003	1750	12	G	T	T	T	533	41	C12orf63	2	2
ANKS1B	56899	broad.mit.edu	37	12	99793432	99793432	+	Missense_Mutation	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:99793432T>G	uc001tge.1	-	c.1733A>C	c.(1732-1734)AAG>ACG	p.K578T	ANKS1B_uc001tgf.1_Missense_Mutation_p.K158T|ANKS1B_uc009ztt.1_Missense_Mutation_p.K544T	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	578						Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)										0.107692	6.073927	16.000131	7	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99793432	99793432	697	12	T	G	G	G	728	56	ANKS1B	4	4
COL4A2	1284	broad.mit.edu	37	13	111134904	111134904	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:111134904C>A	uc001vqx.2	+	c.2800C>A	c.(2800-2802)CCT>ACT	p.P934T		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	934	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)											0.590278	252.161587	253.189861	85	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111134904	111134904	3828	13	C	A	A	A	338	26	COL4A2	2	2
SACS	26278	broad.mit.edu	37	13	23914212	23914212	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:23914212T>A	uc001uon.2	-	c.3803A>T	c.(3802-3804)GAT>GTT	p.D1268V	SACS_uc001uoo.2_Missense_Mutation_p.D1121V|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	1268					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)|skin(1)	11		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)						738				0.521739	36.699788	36.709189	12	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23914212	23914212	14284	13	T	A	A	A	650	50	SACS	3	3
SLC46A3	283537	broad.mit.edu	37	13	29287437	29287437	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:29287437A>G	uc001usj.2	-	c.440T>C	c.(439-441)TTT>TCT	p.F147S	SLC46A3_uc001usg.2_Missense_Mutation_p.F72S|SLC46A3_uc001usi.2_Missense_Mutation_p.F147S|SLC46A3_uc001ush.2_Missense_Mutation_p.F147S|SLC46A3_uc001usk.2_Missense_Mutation_p.F72S	NM_001135919	NP_001129391	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3 isoform b	147	Helical; (Potential).				transmembrane transport	integral to membrane				central_nervous_system(1)	1		Lung SC(185;0.0367)		all cancers(112;0.159)										0.194444	19.606259	22.739275	7	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29287437	29287437	15143	13	A	G	G	G	13	1	SLC46A3	4	4
CSNK1A1L	122011	broad.mit.edu	37	13	37678436	37678436	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:37678436G>T	uc001uwm.1	-	c.958C>A	c.(958-960)CAA>AAA	p.Q320K		NM_145203	NP_660204	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	320					protein phosphorylation|Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)	1		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)						53				0.568627	92.987956	93.19971	29	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37678436	37678436	4092	13	G	T	T	T	611	47	CSNK1A1L	2	2
RB1	5925	broad.mit.edu	37	13	48954377	48954377	+	Nonsense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:48954377A>T	uc001vcb.2	+	c.1498A>T	c.(1498-1500)AGA>TGA	p.R500*		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	500	Domain A.|Pocket; binds T and E1A.		R -> G (in RB).	RS -> SN (in Ref. 7; AAN64133).	androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding			lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6		568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.636364	22.327115	22.506993	7	4	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	48954377	48954377	13559	13	A	T	T	T	88	7	RB1	5	3
C14orf73	91828	broad.mit.edu	37	14	103566613	103566613	+	Silent	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:103566613T>A	uc001ymk.2	+	c.57T>A	c.(55-57)GCT>GCA	p.A19A		NM_001077594	NP_001071062	Q17RC7	EX3L4_HUMAN	hypothetical protein LOC91828	19											0		Melanoma(154;0.155)	Epithelial(46;0.221)											0.428571	9.924085	9.955207	3	4	KEEP	---	---	---	---	capture		Silent	SNP	103566613	103566613	1829	14	T	A	A	A	704	55	C14orf73	3	3
EIF5	1983	broad.mit.edu	37	14	103805183	103805183	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:103805183G>A	uc001ymq.2	+	c.697G>A	c.(697-699)GAA>AAA	p.E233K	EIF5_uc001ymr.2_Missense_Mutation_p.E233K|EIF5_uc001yms.2_Missense_Mutation_p.E233K|EIF5_uc001ymt.2_Missense_Mutation_p.E233K|EIF5_uc001ymu.2_Missense_Mutation_p.E233K	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	233	W2.				regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			breast(1)|pancreas(1)	2		Melanoma(154;0.155)	Epithelial(46;0.182)											0.12069	6.939728	15.08047	7	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103805183	103805183	5231	14	G	A	A	A	533	41	EIF5	2	2
AHNAK2	113146	broad.mit.edu	37	14	105418113	105418113	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105418113G>T	uc010axc.1	-	c.3675C>A	c.(3673-3675)GGC>GGA	p.G1225G	AHNAK2_uc001ypx.2_Silent_p.G1125G	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1225						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.211111	37.482101	44.4318	19	71	KEEP	---	---	---	---	capture		Silent	SNP	105418113	105418113	418	14	G	T	T	T	535	42	AHNAK2	2	2
MTA1	9112	broad.mit.edu	37	14	105916508	105916508	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105916508G>A	uc001yqx.2	+	c.355G>A	c.(355-357)GCC>ACC	p.A119T	MTA1_uc001yqy.2_Non-coding_Transcript|MTA1_uc001yqz.1_Missense_Mutation_p.A33T|MTA1_uc001yra.1_Missense_Mutation_p.A33T	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein	119	BAH.				regulation of transcription, DNA-dependent|signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)										0.25	67.946126	75.221883	32	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105916508	105916508	10301	14	G	A	A	A	494	38	MTA1	1	1
POTEG	404785	broad.mit.edu	37	14	19553542	19553542	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:19553542C>A	uc001vuz.1	+	c.126C>A	c.(124-126)AAC>AAA	p.N42K	POTEG_uc001vva.1_Non-coding_Transcript|POTEG_uc010ahc.1_Non-coding_Transcript	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	42										ovary(1)	1														0.084906	12.777146	86.881927	36	388	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19553542	19553542	12696	14	C	A	A	A	246	19	POTEG	1	1
OR4K13	390433	broad.mit.edu	37	14	20502513	20502513	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20502513G>T	uc010tkz.1	-	c.405C>A	c.(403-405)ATC>ATA	p.I135I		NM_001004714	NP_001004714	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K,	135	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)										0.075758	-5.507571	31.009262	15	183	KEEP	---	---	---	---	capture		Silent	SNP	20502513	20502513	11478	14	G	T	T	T	577	45	OR4K13	2	2
MIPOL1	145282	broad.mit.edu	37	14	37838830	37838830	+	Splice_Site_SNP	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:37838830G>C	uc001wuc.2	+	c.936_splice	c.e11+1	p.K312_splice	MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Splice_Site_SNP_p.K281_splice|MIPOL1_uc001wud.2_Splice_Site_SNP_p.K312_splice|MIPOL1_uc010ams.2_Splice_Site_SNP_p.K312_splice|MIPOL1_uc001wue.2_Splice_Site_SNP_p.K281_splice|MIPOL1_uc010amt.2_Splice_Site_SNP_p.K131_splice	NM_138731	NP_620059			mirror-image polydactyly 1											ovary(1)	1	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)										0.222222	17.042492	18.953808	6	21	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	37838830	37838830	9983	14	G	C	C	C	572	44	MIPOL1	5	3
FANCM	57697	broad.mit.edu	37	14	45633758	45633758	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:45633758G>C	uc001wwd.3	+	c.1778G>C	c.(1777-1779)CGA>CCA	p.R593P	FANCM_uc001wwc.2_Missense_Mutation_p.R593P|FANCM_uc010anf.2_Missense_Mutation_p.R567P|FANCM_uc001wwe.3_Intron	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	593	Helicase C-terminal.				DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(2)|breast(1)	3										793				0.52381	35.408656	35.418216	11	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45633758	45633758	5907	14	G	C	C	C	481	37	FANCM	3	3
C14orf149	112849	broad.mit.edu	37	14	59946027	59946027	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:59946027T>C	uc001xee.1	-	c.551A>G	c.(550-552)GAC>GGC	p.D184G	C14orf149_uc010trx.1_3'UTR	NM_144581	NP_653182	Q96EM0	PRCM_HUMAN	proline racemase-like	184							proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)									0.365385	58.715315	59.542279	19	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59946027	59946027	1800	14	T	C	C	C	754	58	C14orf149	4	4
ZFYVE26	23503	broad.mit.edu	37	14	68275994	68275994	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:68275994C>G	uc001xka.2	-	c.286G>C	c.(286-288)GTT>CTT	p.V96L	ZFYVE26_uc010tsz.1_Non-coding_Transcript|ZFYVE26_uc001xkc.3_Missense_Mutation_p.V96L|ZFYVE26_uc010tta.1_Missense_Mutation_p.V96L	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	96					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	phosphatidylinositol-3-phosphate binding|protein binding|zinc ion binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)										0.371429	82.132471	83.148928	26	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68275994	68275994	18258	14	C	G	G	G	260	20	ZFYVE26	3	3
PCNX	22990	broad.mit.edu	37	14	71444699	71444699	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:71444699G>A	uc001xmo.2	+	c.1645G>A	c.(1645-1647)GTA>ATA	p.V549I	PCNX_uc001xmn.3_Missense_Mutation_p.V549I|PCNX_uc010are.1_Missense_Mutation_p.V549I	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	549						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)										0.22314	65.113408	73.604557	27	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71444699	71444699	12011	14	G	A	A	A	520	40	PCNX	1	1
FOXN3	1112	broad.mit.edu	37	14	89647120	89647120	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:89647120C>A	uc001xxo.3	-	c.842G>T	c.(841-843)CGG>CTG	p.R281L	FOXN3_uc001xxn.3_Missense_Mutation_p.R259L|FOXN3_uc010atk.2_Missense_Mutation_p.R259L	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1	281					DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|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|protein C-terminus 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			ovary(1)|skin(1)	2														0.425	54.754369	54.952954	17	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89647120	89647120	6267	14	C	A	A	A	299	23	FOXN3	1	1
SERPINA3	12	broad.mit.edu	37	14	95088688	95088688	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95088688G>A	uc001ydo.3	+	c.1003G>A	c.(1003-1005)GAG>AAG	p.E335K	SERPINA3_uc001ydr.2_Non-coding_Transcript|SERPINA3_uc001ydq.2_Missense_Mutation_p.E310K|SERPINA3_uc001ydp.2_Missense_Mutation_p.E310K|SERPINA3_uc001yds.2_Missense_Mutation_p.E310K|SERPINA3_uc010avg.2_Missense_Mutation_p.E310K	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	310					acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)	5		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)										0.478873	96.912109	96.941067	34	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95088688	95088688	14578	14	G	A	A	A	585	45	SERPINA3	2	2
OCA2	4948	broad.mit.edu	37	15	28230271	28230271	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:28230271C>G	uc001zbh.3	-	c.1303G>C	c.(1303-1305)GTC>CTC	p.V435L	OCA2_uc010ayv.2_Missense_Mutation_p.V411L	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	435	Helical; (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										0.533333	24.692881	24.706875	8	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28230271	28230271	11220	15	C	G	G	G	247	19	OCA2	3	3
MGA	23269	broad.mit.edu	37	15	42041756	42041756	+	Missense_Mutation	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42041756T>G	uc010ucy.1	+	c.5951T>G	c.(5950-5952)ATA>AGA	p.I1984R	MGA_uc010ucz.1_Missense_Mutation_p.I1775R|MGA_uc010uda.1_Missense_Mutation_p.I600R|MGA_uc001zoi.2_Missense_Mutation_p.I198R	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	1945	Basic motif.				regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)						606				0.375	15.216317	15.445926	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42041756	42041756	9930	15	T	G	G	G	637	49	MGA	4	4
DMXL2	23312	broad.mit.edu	37	15	51741321	51741321	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51741321G>A	uc010ufy.1	-	c.8974C>T	c.(8974-8976)CGA>TGA	p.R2992*	DMXL2_uc002abd.2_Nonsense_Mutation_p.R1083*|DMXL2_uc002abf.2_Nonsense_Mutation_p.R2991*|DMXL2_uc010bfa.2_Nonsense_Mutation_p.R2355*|DMXL2_uc002abc.2_Non-coding_Transcript	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2991						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)	6				all cancers(107;0.00494)										0.263158	24.584996	26.559698	10	28	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	51741321	51741321	4777	15	G	A	A	A	480	37	DMXL2	5	1
DMXL2	23312	broad.mit.edu	37	15	51741341	51741341	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51741341T>A	uc010ufy.1	-	c.8954A>T	c.(8953-8955)CAT>CTT	p.H2985L	DMXL2_uc002abd.2_Missense_Mutation_p.H1076L|DMXL2_uc002abf.2_Missense_Mutation_p.H2984L|DMXL2_uc010bfa.2_Missense_Mutation_p.H2348L|DMXL2_uc002abc.2_Non-coding_Transcript	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2984				H -> Y (in Ref. 1; AAL93215).		cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)	6				all cancers(107;0.00494)										0.421053	51.09501	51.301041	16	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51741341	51741341	4777	15	T	A	A	A	663	51	DMXL2	3	3
FOXB1	27023	broad.mit.edu	37	15	60297294	60297294	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:60297294G>C	uc002agj.1	+	c.132G>C	c.(130-132)ATG>ATC	p.M44I	FOXB1_uc010bgh.1_Intron	NM_012182	NP_036314	Q99853	FOXB1_HUMAN	forkhead box B1	44	Fork-head.				axon target recognition|cell migration in diencephalon|epithelial cell differentiation involved in mammary gland alveolus development|floor plate development|hypothalamus cell migration|inferior colliculus development|lactation|mammillothalamic axonal tract development|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neuron apoptosis|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|telencephalon cell migration|visual learning	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			ovary(1)|central_nervous_system(1)	2														0.5	27.678432	27.678432	10	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60297294	60297294	6234	15	G	C	C	C	611	47	FOXB1	3	3
PIF1	80119	broad.mit.edu	37	15	65108869	65108869	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:65108869G>A	uc002ant.2	-	c.1770C>T	c.(1768-1770)GGC>GGT	p.G590G	PIF1_uc002anr.2_Silent_p.G138G|PIF1_uc002ans.2_Silent_p.G281G|PIF1_uc010uiq.1_Silent_p.G590G	NM_025049	NP_079325	Q9H611	PIF1_HUMAN	DNA helicase homolog PIF1	590	Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity.				negative regulation of telomerase activity|regulation of telomere maintenance	nuclear chromosome, telomeric region	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' DNA/RNA helicase activity|magnesium ion binding|single-stranded DNA-dependent ATP-dependent DNA helicase activity|telomeric DNA binding				0														0.463415	56.255753	56.298813	19	22	KEEP	---	---	---	---	capture		Silent	SNP	65108869	65108869	12307	15	G	A	A	A	535	42	PIF1	2	2
LMAN1L	79748	broad.mit.edu	37	15	75108976	75108976	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75108976A>T	uc002ayt.1	+	c.442A>T	c.(442-444)AGT>TGT	p.S148C	LMAN1L_uc010bkd.2_Missense_Mutation_p.S76C|LMAN1L_uc010ulo.1_Missense_Mutation_p.S40C|LMAN1L_uc010bke.1_Missense_Mutation_p.S148C	NM_021819	NP_068591	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like precursor	148	Lumenal (Potential).|L-type lectin-like.					ER-Golgi intermediate compartment membrane|integral to membrane	sugar binding				0														0.352941	14.514954	14.851889	6	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75108976	75108976	9166	15	A	T	T	T	91	7	LMAN1L	3	3
AGBL1	123624	broad.mit.edu	37	15	86807971	86807971	+	Silent	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:86807971T>C	uc002blz.1	+	c.1431T>C	c.(1429-1431)TCT>TCC	p.S477S	AGBL1_uc002bma.1_Silent_p.S208S|AGBL1_uc002bmb.1_Silent_p.S171S	NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	477					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0														0.4	51.242042	51.634931	18	27	KEEP	---	---	---	---	capture		Silent	SNP	86807971	86807971	377	15	T	C	C	C	704	55	AGBL1	4	4
MYH11	4629	broad.mit.edu	37	16	15811192	15811192	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:15811192C>T	uc002ddx.2	-	c.5330G>A	c.(5329-5331)AGC>AAC	p.S1777N	MYH11_uc002ddv.2_Missense_Mutation_p.S1777N|MYH11_uc002ddw.2_Missense_Mutation_p.S1770N|MYH11_uc002ddy.2_Missense_Mutation_p.S1770N|MYH11_uc010bvg.2_Missense_Mutation_p.S1602N|NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron|MYH11_uc010bvh.2_Missense_Mutation_p.S476N	NM_001040114	NP_001035203	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	1770	Potential.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(4)|skin(2)|lung(1)	7										1257				0.641509	118.363073	119.297316	34	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15811192	15811192	10426	16	C	T	T	T	364	28	MYH11	2	2
ACSM2B	348158	broad.mit.edu	37	16	20548599	20548599	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20548599C>A	uc002dhj.3	-	c.1715G>T	c.(1714-1716)GGA>GTA	p.G572V	ACSM2B_uc002dhk.3_Missense_Mutation_p.G572V	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	572					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2														0.474576	327.401519	327.531777	112	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20548599	20548599	185	16	C	A	A	A	390	30	ACSM2B	2	2
CDR2	1039	broad.mit.edu	37	16	22358637	22358637	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:22358637C>T	uc002dkn.2	-	c.1014G>A	c.(1012-1014)GTG>GTA	p.V338V		NM_001802	NP_001793	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2	338						nucleus	protein binding				0				GBM - Glioblastoma multiforme(48;0.0188)										0.104167	3.138007	10.624604	5	43	KEEP	---	---	---	---	capture		Silent	SNP	22358637	22358637	3301	16	C	T	T	T	366	29	CDR2	2	2
ERN2	10595	broad.mit.edu	37	16	23721868	23721868	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23721868G>T	uc002dma.3	-	c.346C>A	c.(346-348)CCC>ACC	p.P116T	ERN2_uc010bxp.2_Missense_Mutation_p.P116T|ERN2_uc010bxq.1_5'UTR	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	68	Lumenal (Potential).				apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|protein phosphorylation|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)						225				0.455556	235.916688	236.227592	82	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23721868	23721868	5431	16	G	T	T	T	533	41	ERN2	2	2
TBC1D10B	26000	broad.mit.edu	37	16	30376830	30376830	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30376830G>A	uc002dxu.2	-	c.1042C>T	c.(1042-1044)CGG>TGG	p.R348W		NM_015527	NP_056342	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	348						cytoplasm	Rab GTPase activator activity				0			Colorectal(24;0.193)											0.12	10.58	24.716182	12	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30376830	30376830	16121	16	G	A	A	A	519	40	TBC1D10B	1	1
ITGAX	3687	broad.mit.edu	37	16	31371771	31371771	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31371771G>A	uc002ebt.2	+	c.848G>A	c.(847-849)CGC>CAC	p.R283H	ITGAX_uc002ebu.1_Missense_Mutation_p.R283H|ITGAX_uc010vfk.1_5'Flank	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	283	VWFA.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.229885	45.888368	51.688713	20	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31371771	31371771	8193	16	G	A	A	A	494	38	ITGAX	1	1
SALL1	6299	broad.mit.edu	37	16	51174340	51174340	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:51174340G>T	uc010vgs.1	-	c.1793C>A	c.(1792-1794)CCT>CAT	p.P598H	SALL1_uc010vgr.1_Missense_Mutation_p.P501H|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	598					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			ovary(3)	3		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GBM(103;1352 1446 1855 4775 8890)								0.416667	43.017535	43.235929	15	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51174340	51174340	14290	16	G	T	T	T	455	35	SALL1	2	2
CNOT1	23019	broad.mit.edu	37	16	58621300	58621300	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:58621300G>T	uc002env.2	-	c.327C>A	c.(325-327)CCC>CCA	p.P109P	CNOT1_uc002enw.2_Non-coding_Transcript|CNOT1_uc002enu.3_Silent_p.P109P|CNOT1_uc002enx.2_Silent_p.P109P|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	109					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)										0.122807	9.390068	17.32269	7	50	KEEP	---	---	---	---	capture		Silent	SNP	58621300	58621300	3755	16	G	T	T	T	548	43	CNOT1	2	2
CDH11	1009	broad.mit.edu	37	16	64981542	64981542	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:64981542C>G	uc002eoi.2	-	c.2355G>C	c.(2353-2355)TTG>TTC	p.L785F	CDH11_uc010cdn.2_Non-coding_Transcript|CDH11_uc002eoj.2_3'UTR|CDH11_uc010vin.1_Missense_Mutation_p.L659F	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	785	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(7)|ovary(2)	9		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)						239	TSP Lung(24;0.17)			0.518519	95.45526	95.469635	28	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64981542	64981542	3226	16	C	G	G	G	220	17	CDH11	3	3
CTCF	10664	broad.mit.edu	37	16	67660607	67660607	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:67660607G>A	uc002etl.2	+	c.1507G>A	c.(1507-1509)GCT>ACT	p.A503T	CTCF_uc010cek.2_Missense_Mutation_p.A175T|CTCF_uc002etm.1_5'Flank	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	503	C2H2-type 9.				chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		Colon(175;1200 1966 6945 23069 27405)								0.757576	76.714689	78.766764	25	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67660607	67660607	4159	16	G	A	A	A	494	38	CTCF	1	1
PLCG2	5336	broad.mit.edu	37	16	81953109	81953109	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:81953109A>G	uc002fgt.2	+	c.2075A>G	c.(2074-2076)CAT>CGT	p.H692R	PLCG2_uc010chg.1_Missense_Mutation_p.H692R	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	692	SH2 2.				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8										1880				0.156863	12.164888	17.901549	8	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81953109	81953109	12462	16	A	G	G	G	104	8	PLCG2	4	4
CHTF18	63922	broad.mit.edu	37	16	844112	844112	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:844112G>A	uc002ckf.3	+	c.1945G>A	c.(1945-1947)GAC>AAC	p.D649N	CHTF18_uc002cke.3_Missense_Mutation_p.D621N|CHTF18_uc010brf.2_Missense_Mutation_p.D203N|CHTF18_uc002ckg.3_Missense_Mutation_p.D139N	NM_022092	NP_071375	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor	621					cell cycle|DNA replication	nucleus	ATP binding|DNA binding|nucleoside-triphosphatase activity			kidney(1)	1		Hepatocellular(780;0.00335)												0.822222	121.495878	125.895297	37	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	844112	844112	3548	16	G	A	A	A	533	41	CHTF18	2	2
ZC3H18	124245	broad.mit.edu	37	16	88694395	88694395	+	Silent	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:88694395C>G	uc010voz.1	+	c.2409C>G	c.(2407-2409)CCC>CCG	p.P803P	ZC3H18_uc002fky.2_Silent_p.P779P|ZC3H18_uc010chw.2_Intron|ZC3H18_uc002fkz.2_Silent_p.P49P	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	779						nucleus	nucleic acid binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0542)		Ovarian(121;375 2276 20373 38669)								0.2625	48.531635	52.620836	21	59	KEEP	---	---	---	---	capture		Silent	SNP	88694395	88694395	18156	16	C	G	G	G	262	21	ZC3H18	3	3
GRIN2A	2903	broad.mit.edu	37	16	9857330	9857330	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9857330G>T	uc002czo.3	-	c.4071C>A	c.(4069-4071)CTC>CTA	p.L1357L	GRIN2A_uc010uym.1_Silent_p.L1357L|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1357	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.666667	62.806736	63.543562	20	10	KEEP	---	---	---	---	capture		Silent	SNP	9857330	9857330	7058	16	G	T	T	T	418	33	GRIN2A	2	2
MYH4	4622	broad.mit.edu	37	17	10366498	10366498	+	Silent	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10366498T>C	uc002gmn.2	-	c.813A>G	c.(811-813)CTA>CTG	p.L271L		NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	271	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|central_nervous_system(1)	11														0.722222	147.251225	149.653084	39	15	KEEP	---	---	---	---	capture		Silent	SNP	10366498	10366498	10432	17	T	C	C	C	678	53	MYH4	4	4
ZNF18	7566	broad.mit.edu	37	17	11881705	11881705	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11881705G>C	uc002gng.1	-	c.1219C>G	c.(1219-1221)CTC>GTC	p.L407V	ZNF18_uc002gnh.1_Missense_Mutation_p.L407V|ZNF18_uc002gni.1_Missense_Mutation_p.L406V	NM_144680	NP_653281	P17022	ZNF18_HUMAN	zinc finger protein 18	407					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)										0.730769	195.762471	199.50126	57	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11881705	11881705	18338	17	G	C	C	C	442	34	ZNF18	3	3
ZNF624	57547	broad.mit.edu	37	17	16525829	16525829	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16525829T>C	uc010cpi.1	-	c.2371A>G	c.(2371-2373)ACT>GCT	p.T791A		NM_020787	NP_065838	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	791	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		NSCLC(186;1023 2134 13330 38202 39800)								0.695652	112.604389	114.174142	32	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16525829	16525829	18643	17	T	C	C	C	741	57	ZNF624	4	4
EPN2	22905	broad.mit.edu	37	17	19213203	19213203	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:19213203T>A	uc002gvd.3	+	c.772T>A	c.(772-774)TCC>ACC	p.S258T	EPN2_uc010cql.1_5'UTR|EPN2_uc002gve.3_Missense_Mutation_p.S201T|EPN2_uc002gvf.3_5'UTR|EPN2_uc010vyo.1_5'UTR|EPN2_uc002gvg.1_Missense_Mutation_p.S201T|EPN2_uc010vyp.1_Missense_Mutation_p.S201T|EPN2_uc010vyq.1_Missense_Mutation_p.S201T|EPN2_uc002gvh.1_Missense_Mutation_p.S258T	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b	258					endocytosis		lipid binding				0	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)													0.209677	27.964059	32.787966	13	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19213203	19213203	5379	17	T	A	A	A	702	54	EPN2	3	3
SPACA3	124912	broad.mit.edu	37	17	31323984	31323984	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31323984C>T	uc002hhs.1	+	c.467C>T	c.(466-468)CCG>CTG	p.P156L	SPACA3_uc010cte.1_Non-coding_Transcript	NM_173847	NP_776246	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	156	Extracellular (Potential).				cell wall macromolecule catabolic process|defense response to Gram-positive bacterium|monocyte activation|peptidoglycan catabolic process|positive regulation of macrophage activation|positive regulation of phagocytosis|response to virus	acrosomal membrane|extracellular region|integral to membrane|lysosome	bacterial cell surface binding|lysozyme activity|protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;0.193)											0.307692	56.98378	59.122125	20	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31323984	31323984	15474	17	C	T	T	T	299	23	SPACA3	1	1
CCL14	6358	broad.mit.edu	37	17	34311470	34311470	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34311470G>A	uc010wcq.1	-	c.146C>T	c.(145-147)TCA>TTA	p.S49L	CCL16_uc002hkl.2_5'Flank|CCL16_uc002hkm.2_5'Flank|CCL14_uc010wcr.1_Missense_Mutation_p.S33L|CCL14_uc002hkn.2_Non-coding_Transcript|CCL14-CCL15_uc010wcs.1_Non-coding_Transcript|CCL14-CCL15_uc010wct.1_Non-coding_Transcript	NM_032962	NP_116738	Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14 isoform 2	33					cellular calcium ion homeostasis|immune response|positive regulation of cell proliferation	extracellular space	chemokine activity|signal transducer activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.4	36.593543	36.856073	12	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34311470	34311470	3010	17	G	A	A	A	585	45	CCL14	2	2
SMARCE1	6605	broad.mit.edu	37	17	38787077	38787077	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38787077C>G	uc002hux.2	-	c.916G>C	c.(916-918)GAG>CAG	p.E306Q	SMARCE1_uc010wff.1_Missense_Mutation_p.E271Q|SMARCE1_uc010wfg.1_Missense_Mutation_p.E236Q|SMARCE1_uc002huy.2_Missense_Mutation_p.E271Q|SMARCE1_uc010wfh.1_Missense_Mutation_p.E236Q|SMARCE1_uc010wfi.1_Missense_Mutation_p.E288Q	NM_003079	NP_003070	Q969G3	SMCE1_HUMAN	SWI/SNF-related matrix-associated	306	Potential.				chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex	chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity				0		Breast(137;0.000812)												0.306931	86.128942	89.466118	31	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38787077	38787077	15278	17	C	G	G	G	390	30	SMARCE1	3	3
KRT24	192666	broad.mit.edu	37	17	38855764	38855764	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38855764C>G	uc002hvd.2	-	c.1293G>C	c.(1291-1293)TTG>TTC	p.L431F		NM_019016	NP_061889	Q2M2I5	K1C24_HUMAN	keratin 24	431	Rod.|Coil 2.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.00526)				GBM(61;380 1051 14702 23642 31441)								0.3	103.905856	108.164706	36	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38855764	38855764	8776	17	C	G	G	G	324	25	KRT24	3	3
AOC3	8639	broad.mit.edu	37	17	41004383	41004383	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41004383C>T	uc002ibv.2	+	c.1023C>T	c.(1021-1023)CTC>CTT	p.L341L		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	341	Extracellular (Potential).				amine metabolic process|cell adhesion|inflammatory response|oxidation-reduction process	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)	3		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	NSCLC(3;192 220 10664 11501 16477)								0.142857	13.569972	20.446437	8	48	KEEP	---	---	---	---	capture		Silent	SNP	41004383	41004383	738	17	C	T	T	T	392	31	AOC3	1	1
PLEKHM1	9842	broad.mit.edu	37	17	43552468	43552468	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43552468T>A	uc002ija.2	-	c.921A>T	c.(919-921)CAA>CAT	p.Q307H	PLEKHM1_uc010wjm.1_Missense_Mutation_p.Q279H|PLEKHM1_uc002ijb.2_De_novo_Start_OutOfFrame|PLEKHM1_uc010wjn.1_Missense_Mutation_p.Q256H	NM_014798	NP_055613	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M	307					intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)													0.47619	30.748157	30.758555	10	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43552468	43552468	12506	17	T	A	A	A	725	56	PLEKHM1	3	3
SKAP1	8631	broad.mit.edu	37	17	46239860	46239860	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46239860G>T	uc002ini.1	-	c.949C>A	c.(949-951)CGG>AGG	p.R317R	SKAP1_uc002inj.1_Silent_p.R316R|SKAP1_uc010dbd.1_Silent_p.R222R|SKAP1_uc010dbe.1_Silent_p.R317R	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform	317	SH3.				positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding|SH3/SH2 adaptor activity|transcription activator activity				0														0.375	29.272071	29.600145	9	15	KEEP	---	---	---	---	capture		Silent	SNP	46239860	46239860	14850	17	G	T	T	T	519	40	SKAP1	1	1
HOXB1	3211	broad.mit.edu	37	17	46607742	46607742	+	Silent	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46607742G>C	uc002ink.1	-	c.525C>G	c.(523-525)CCC>CCG	p.P175P		NM_002144	NP_002135	P14653	HXB1_HUMAN	homeobox B1	175						nucleus	protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.347826	22.291497	22.762236	8	15	KEEP	---	---	---	---	capture		Silent	SNP	46607742	46607742	7591	17	G	C	C	C	600	47	HOXB1	3	3
SPOP	8405	broad.mit.edu	37	17	47696724	47696725	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:47696724_47696725CC>AA	uc010dbk.2	-	c.223_224GG>TT	c.(223-225)GGG>TTG	p.G75L	SPOP_uc002ipb.2_Missense_Mutation_p.G75L|SPOP_uc002ipc.2_Missense_Mutation_p.G75L|SPOP_uc002ipd.2_Missense_Mutation_p.G75L|SPOP_uc002ipe.2_Missense_Mutation_p.G75L|SPOP_uc002ipf.2_Missense_Mutation_p.G75L|SPOP_uc002ipg.2_Missense_Mutation_p.G75L	NM_003563	NP_003554	O43791	SPOP_HUMAN	speckle-type POZ protein	75	MATH.|Required for nuclear localization.				mRNA processing	nucleus	protein binding			ovary(1)	1											Prostate(2;0.17)			0.25	21.779092	23.810529	9	27	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	47696724	47696725	15597	17	CC	AA	AA	AA	286	22	SPOP	2	2
ANKFN1	162282	broad.mit.edu	37	17	54555015	54555015	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:54555015G>T	uc002iun.1	+	c.1949G>T	c.(1948-1950)AGA>ATA	p.R650I		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	650										large_intestine(1)|ovary(1)	2														0.310345	50.428099	52.286683	18	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54555015	54555015	628	17	G	T	T	T	455	35	ANKFN1	2	2
LRRC37A3	374819	broad.mit.edu	37	17	62856473	62856473	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62856473G>A	uc002jey.2	-	c.3791C>T	c.(3790-3792)GCC>GTC	p.A1264V	LRRC37A3_uc010wqg.1_Missense_Mutation_p.A382V|LRRC37A3_uc002jex.1_Missense_Mutation_p.A241V|LRRC37A3_uc010wqf.1_Missense_Mutation_p.A302V|LRRC37A3_uc010dek.1_Missense_Mutation_p.A270V	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1264	Extracellular (Potential).					integral to membrane					0														0.333333	39.467873	40.656802	16	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62856473	62856473	9368	17	G	A	A	A	546	42	LRRC37A3	2	2
PSMD12	5718	broad.mit.edu	37	17	65362551	65362551	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:65362551G>T	uc002jfy.2	-	c.85C>A	c.(85-87)CCC>ACC	p.P29T	PSMD12_uc002jga.2_Missense_Mutation_p.P29T|PSMD12_uc002jfz.2_5'UTR|PSMD12_uc010det.1_Missense_Mutation_p.P29T	NM_002816	NP_002807	O00232	PSD12_HUMAN	proteasome 26S non-ATPase subunit 12 isoform 1	29					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)													0.25	7.383777	8.301289	4	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65362551	65362551	13148	17	G	T	T	T	572	44	PSMD12	2	2
SDK2	54549	broad.mit.edu	37	17	71412116	71412116	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:71412116C>T	uc010dfm.2	-	c.2202G>A	c.(2200-2202)GGG>GGA	p.G734G	SDK2_uc010dfn.2_Silent_p.G413G	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	734	Extracellular (Potential).|Fibronectin type-III 2.				cell adhesion	integral to membrane				ovary(2)	2														0.333333	7.647778	7.856496	3	6	KEEP	---	---	---	---	capture		Silent	SNP	71412116	71412116	14455	17	C	T	T	T	327	26	SDK2	2	2
POLR2A	5430	broad.mit.edu	37	17	7402375	7402375	+	Silent	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7402375T>C	uc002ghf.3	+	c.1353T>C	c.(1351-1353)TGT>TGC	p.C451C	POLR2A_uc002ghe.2_Silent_p.C451C	NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	451					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)												0.727273	256.718357	261.846681	80	30	KEEP	---	---	---	---	capture		Silent	SNP	7402375	7402375	12642	17	T	C	C	C	764	59	POLR2A	4	4
TP53	7157	broad.mit.edu	37	17	7577559	7577559	+	Missense_Mutation	SNP	G	A	A	rs28934573		TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577559G>A	uc002gim.2	-	c.722C>T	c.(721-723)TCC>TTC	p.S241F	TP53_uc002gig.1_Missense_Mutation_p.S241F|TP53_uc002gih.2_Missense_Mutation_p.S241F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.S109F|TP53_uc010cng.1_Missense_Mutation_p.S109F|TP53_uc002gii.1_Missense_Mutation_p.S109F|TP53_uc010cnh.1_Missense_Mutation_p.S241F|TP53_uc010cni.1_Missense_Mutation_p.S241F|TP53_uc002gij.2_Missense_Mutation_p.S241F|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.S148F|TP53_uc002gio.2_Missense_Mutation_p.S109F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	241	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		S -> A (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> C (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).|S -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.S241F(72)|p.S241C(24)|p.S241Y(7)|p.0?(6)|p.C242fs*5(6)|p.S241del(5)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.S241Y(DMS53-Tumor)|p.S241Y(KMM1-Tumor)|p.S241Y(KALS1-Tumor)|p.S241C(EVSAT-Tumor)|p.S241C(BFTC909-Tumor)|p.S241Y(HCC78-Tumor)|p.S241Y(ES2-Tumor)|p.S241Y(HCT15-Tumor)|p.C238fs(SW1417-Tumor)|p.S241F(HEC251-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.705882	80.812862	82.102823	24	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577559	7577559	16923	17	G	A	A	A	533	41	TP53	2	2
LGALS3BP	3959	broad.mit.edu	37	17	76968265	76968265	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:76968265T>A	uc002jwh.2	-	c.1151A>T	c.(1150-1152)CAC>CTC	p.H384L	LGALS3BP_uc002jwi.2_Missense_Mutation_p.H190L|LGALS3BP_uc010dhr.2_Missense_Mutation_p.H190L	NM_005567	NP_005558	Q08380	LG3BP_HUMAN	galectin 3 binding protein	384					cell adhesion|cellular defense response	extracellular space|membrane|proteinaceous extracellular matrix	protein binding|scavenger receptor activity			central_nervous_system(3)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GBM(89;1105 1755 18102 21513)						OREG0024787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.555556	112.189737	112.356569	35	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76968265	76968265	9069	17	T	A	A	A	767	59	LGALS3BP	3	3
KDM6B	23135	broad.mit.edu	37	17	7752487	7752487	+	Missense_Mutation	SNP	G	A	A	rs71371820		TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7752487G>A	uc002giw.1	+	c.2881G>A	c.(2881-2883)GAG>AAG	p.E961K	KDM6B_uc002gix.2_Missense_Mutation_p.E263K	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	961					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.488372	65.672553	65.677635	21	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7752487	7752487	8444	17	G	A	A	A	533	41	KDM6B	2	2
KDM6B	23135	broad.mit.edu	37	17	7752588	7752588	+	Silent	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7752588G>C	uc002giw.1	+	c.2982G>C	c.(2980-2982)GTG>GTC	p.V994V	KDM6B_uc002gix.2_Silent_p.V296V	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	994					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.6	15.746028	15.833677	6	4	KEEP	---	---	---	---	capture		Silent	SNP	7752588	7752588	8444	17	G	C	C	C	600	47	KDM6B	3	3
KDM6B	23135	broad.mit.edu	37	17	7752684	7752684	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7752684G>A	uc002giw.1	+	c.3078G>A	c.(3076-3078)GAG>GAA	p.E1026E	KDM6B_uc002gix.2_Silent_p.E328E	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1026					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.481481	42.289918	42.296842	13	14	KEEP	---	---	---	---	capture		Silent	SNP	7752684	7752684	8444	17	G	A	A	A	451	35	KDM6B	2	2
KDM6B	23135	broad.mit.edu	37	17	7752915	7752915	+	Silent	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7752915G>C	uc002giw.1	+	c.3309G>C	c.(3307-3309)CTG>CTC	p.L1103L	KDM6B_uc002gix.2_Silent_p.L405L	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1103					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.465116	67.897858	67.943257	20	23	KEEP	---	---	---	---	capture		Silent	SNP	7752915	7752915	8444	17	G	C	C	C	574	45	KDM6B	3	3
KDM6B	23135	broad.mit.edu	37	17	7753196	7753196	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7753196G>A	uc002giw.1	+	c.3498G>A	c.(3496-3498)GTG>GTA	p.V1166V	KDM6B_uc002gix.2_Silent_p.V468V	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1166					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.383621	239.147761	241.925105	89	143	KEEP	---	---	---	---	capture		Silent	SNP	7753196	7753196	8444	17	G	A	A	A	574	45	KDM6B	2	2
KDM6B	23135	broad.mit.edu	37	17	7753205	7753205	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7753205G>T	uc002giw.1	+	c.3507G>T	c.(3505-3507)AAG>AAT	p.K1169N	KDM6B_uc002gix.2_Missense_Mutation_p.K471N	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1169					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.377682	238.773226	241.855348	88	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7753205	7753205	8444	17	G	T	T	T	425	33	KDM6B	2	2
KDM6B	23135	broad.mit.edu	37	17	7753218	7753218	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7753218G>C	uc002giw.1	+	c.3520G>C	c.(3520-3522)GAG>CAG	p.E1174Q	KDM6B_uc002gix.2_Missense_Mutation_p.E476Q	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1174					inflammatory response|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			pancreas(1)	1														0.388646	269.572219	272.041672	89	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7753218	7753218	8444	17	G	C	C	C	533	41	KDM6B	3	3
ENPP7	339221	broad.mit.edu	37	17	77705081	77705081	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77705081C>T	uc002jxa.2	+	c.180C>T	c.(178-180)GAC>GAT	p.D60D		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	60					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)											0.192308	10.368648	12.661076	5	21	KEEP	---	---	---	---	capture		Silent	SNP	77705081	77705081	5328	17	C	T	T	T	246	19	ENPP7	1	1
DSG4	147409	broad.mit.edu	37	18	28993162	28993162	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28993162G>C	uc002kwr.2	+	c.2784G>C	c.(2782-2784)GAG>GAC	p.E928D	DSG4_uc002kwq.2_Missense_Mutation_p.E909D	NM_001134453	NP_001127925	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 1 preproprotein	909	Cytoplasmic (Potential).|Desmoglein repeat 1.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.182796	37.727404	46.507856	17	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28993162	28993162	4963	18	G	C	C	C	425	33	DSG4	3	3
C18orf34	374864	broad.mit.edu	37	18	30992034	30992034	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:30992034C>A	uc010xbr.1	-	c.19G>T	c.(19-21)GTT>TTT	p.V7F	C18orf34_uc002kxn.2_Missense_Mutation_p.V7F|C18orf34_uc010dmf.1_Missense_Mutation_p.V7F|C18orf34_uc002kxo.2_Missense_Mutation_p.V7F|C18orf34_uc002kxp.2_Missense_Mutation_p.V7F	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	7										ovary(1)	1														0.26087	15.94478	17.131779	6	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30992034	30992034	1963	18	C	A	A	A	260	20	C18orf34	2	2
DTNA	1837	broad.mit.edu	37	18	32391994	32391994	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:32391994G>T	uc010dmn.1	+	c.520G>T	c.(520-522)GTT>TTT	p.V174F	DTNA_uc002kxu.2_Missense_Mutation_p.V174F|DTNA_uc010xbx.1_Missense_Mutation_p.V174F|DTNA_uc002kxv.3_Missense_Mutation_p.V174F|DTNA_uc002kxw.2_Missense_Mutation_p.V174F|DTNA_uc002kxx.2_Missense_Mutation_p.V174F|DTNA_uc010dmj.2_Missense_Mutation_p.V174F|DTNA_uc002kxz.2_Missense_Mutation_p.V174F|DTNA_uc002kxy.2_Missense_Mutation_p.V174F|DTNA_uc010dmk.1_Non-coding_Transcript|DTNA_uc010dml.2_Missense_Mutation_p.V174F|DTNA_uc002kyb.3_Missense_Mutation_p.V174F|DTNA_uc010dmm.2_Missense_Mutation_p.V174F	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	174	Interaction with MAGEE1 (By similarity).				neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0														0.454545	46.021391	46.080683	15	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32391994	32391994	4973	18	G	T	T	T	468	36	DTNA	2	2
TCEB3B	51224	broad.mit.edu	37	18	44559841	44559841	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:44559841G>C	uc002lcr.1	-	c.1795C>G	c.(1795-1797)CAG>GAG	p.Q599E	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	599	Activation domain (By similarity).				transcription from RNA polymerase II promoter	integral to membrane|nucleus	DNA binding|transcription elongation regulator activity			ovary(2)|large_intestine(1)|pancreas(1)	4														0.333333	57.04864	58.368829	18	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44559841	44559841	16208	18	G	C	C	C	624	48	TCEB3B	3	3
DCC	1630	broad.mit.edu	37	18	51025876	51025876	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:51025876G>A	uc002lfe.1	+	c.4107G>A	c.(4105-4107)CAG>CAA	p.Q1369Q	DCC_uc010dpf.1_Silent_p.Q1002Q	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	1369	Cytoplasmic (Potential).				apoptosis|induction of apoptosis	cytosol|integral to membrane				ovary(6)|large_intestine(1)|central_nervous_system(1)|skin(1)	9		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)										0.21875	15.707879	18.040363	7	25	KEEP	---	---	---	---	capture		Silent	SNP	51025876	51025876	4453	18	G	A	A	A	438	34	DCC	2	2
POLI	11201	broad.mit.edu	37	18	51820115	51820115	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:51820115G>T	uc002lfj.3	+	c.1501G>T	c.(1501-1503)GAG>TAG	p.E501*	POLI_uc010xds.1_Nonsense_Mutation_p.E422*|POLI_uc002lfk.3_Nonsense_Mutation_p.E398*|POLI_uc010dpg.2_Nonsense_Mutation_p.E97*	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota	501					DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)										0.5	12.762288	12.762288	5	5	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	51820115	51820115	12631	18	G	T	T	T	533	41	POLI	5	2
SERPINB12	89777	broad.mit.edu	37	18	61223420	61223420	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61223420A>G	uc010xeo.1	+	c.28A>G	c.(28-30)AAA>GAA	p.K10E	SERPINB12_uc010xen.1_Missense_Mutation_p.K10E	NM_080474	NP_536722	Q96P63	SPB12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	10					negative regulation of protein catabolic process|regulation of proteolysis	cytoplasm	enzyme binding|serine-type endopeptidase inhibitor activity				0														0.217105	71.554342	82.733675	33	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61223420	61223420	14587	18	A	G	G	G	65	5	SERPINB12	4	4
LAMA1	284217	broad.mit.edu	37	18	7080458	7080458	+	Splice_Site_SNP	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:7080458T>C	uc002knm.2	-	c.62_splice	c.e2-1	p.G21_splice	LAMA1_uc010wzj.1_Splice_Site_SNP	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.235294	9.191747	10.28101	4	13	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	7080458	7080458	8928	18	T	C	C	C	715	55	LAMA1	5	4
PQLC1	80148	broad.mit.edu	37	18	77693994	77693994	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:77693994C>A	uc002lnl.2	-	c.366G>T	c.(364-366)AAG>AAT	p.K122N	PQLC1_uc010dre.2_Missense_Mutation_p.K39N|PQLC1_uc002lnk.2_Intron|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1 isoform 1	122						integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)										0.272727	7.920268	8.432314	3	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77693994	77693994	12854	18	C	A	A	A	311	24	PQLC1	2	2
RAVER1	125950	broad.mit.edu	37	19	10433905	10433905	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10433905G>A	uc002moa.2	-	c.1045C>T	c.(1045-1047)CAG>TAG	p.Q349*		NM_133452	NP_597709	Q8IY67	RAVR1_HUMAN	RAVER1	332	Interaction with PTBP1 (By similarity).					cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)											0.5	21.392496	21.392496	8	8	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10433905	10433905	13555	19	G	A	A	A	598	46	RAVER1	5	2
POLR2E	5434	broad.mit.edu	37	19	1095300	1095300	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1095300C>T	uc002lre.3	-	c.15G>A	c.(13-15)GAG>GAA	p.E5E	POLR2E_uc010xgf.1_Non-coding_Transcript	NM_002695	NP_002686	P19388	RPAB1_HUMAN	DNA directed RNA polymerase II polypeptide E	5					interspecies interaction between organisms|mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity				0		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)										0.346154	56.035004	57.121337	18	34	KEEP	---	---	---	---	capture		Silent	SNP	1095300	1095300	12646	19	C	T	T	T	311	24	POLR2E	2	2
SMARCA4	6597	broad.mit.edu	37	19	11170531	11170531	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11170531G>T	uc010dxo.2	+	c.4834G>T	c.(4834-4836)GAG>TAG	p.E1612*	SMARCA4_uc002mqf.3_Nonsense_Mutation_p.E1580*|SMARCA4_uc010dxp.2_Nonsense_Mutation_p.E1580*|SMARCA4_uc010dxq.2_Nonsense_Mutation_p.E1547*|SMARCA4_uc010dxr.2_Nonsense_Mutation_p.E1546*|SMARCA4_uc002mqj.3_Nonsense_Mutation_p.E1550*|SMARCA4_uc010dxs.2_Nonsense_Mutation_p.E1549*|SMARCA4_uc002mqh.3_Nonsense_Mutation_p.E670*	NM_001128849	NP_001122321	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1580	Poly-Glu.				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			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				0.625	26.813318	27.024536	10	6	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	11170531	11170531	15268	19	G	T	T	T	429	33	SMARCA4	5	2
LDLR	3949	broad.mit.edu	37	19	11200278	11200279	+	Missense_Mutation	DNP	GG	CC	CC			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11200278_11200279GG>CC	uc002mqk.3	+	c.54_55GG>CC	c.(52-57)GCGGCG>GCCCCG	p.A19P	LDLR_uc010xlk.1_Missense_Mutation_p.A19P|LDLR_uc010xll.1_Missense_Mutation_p.A19P|LDLR_uc010xlm.1_5'UTR|LDLR_uc010xln.1_Missense_Mutation_p.A19P|LDLR_uc010xlo.1_Missense_Mutation_p.A19P	NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	19					cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)	2		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	GBM(18;201 575 7820 21545)				1109				0.333333	8.524256	8.744535	3	6	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	11200278	11200279	9028	19	GG	CC	CC	CC	496	39	LDLR	3	3
CYP4F3	4051	broad.mit.edu	37	19	15760829	15760829	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15760829G>T	uc002nbj.2	+	c.754G>T	c.(754-756)GAT>TAT	p.D252Y	CYP4F3_uc010xok.1_Missense_Mutation_p.D252Y|CYP4F3_uc010xol.1_Missense_Mutation_p.D252Y|CYP4F3_uc010xom.1_Missense_Mutation_p.D103Y|CYP4F3_uc002nbk.2_Missense_Mutation_p.D252Y|CYP4F3_uc010xon.1_5'UTR	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,	252					leukotriene metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3														0.601942	191.969376	192.912147	62	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15760829	15760829	4355	19	G	T	T	T	585	45	CYP4F3	2	2
JAK3	3718	broad.mit.edu	37	19	17949156	17949156	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17949156G>A	uc002nhn.3	-	c.1485C>T	c.(1483-1485)CCC>CCT	p.P495P	JAK3_uc010ebh.2_Non-coding_Transcript|JAK3_uc002nho.2_Silent_p.P495P|JAK3_uc010xpx.1_3'UTR	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	495					B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(36)|lung(3)|ovary(3)|stomach(2)|breast(2)	46								2		364				0.702381	208.874172	211.970683	59	25	KEEP	---	---	---	---	capture		Silent	SNP	17949156	17949156	8243	19	G	A	A	A	600	47	JAK3	2	2
NDUFA13	51079	broad.mit.edu	37	19	19646177	19646177	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19646177G>A	uc010xqy.1	+	c.707G>A	c.(706-708)CGC>CAC	p.R236H	YJEFN3_uc002nmt.1_Missense_Mutation_p.R154H|YJEFN3_uc010ecf.1_Missense_Mutation_p.R104H|YJEFN3_uc002nmu.1_Non-coding_Transcript|CILP2_uc002nmv.3_5'Flank|CILP2_uc002nmw.3_5'Flank	NM_015965	NP_057049	Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	Error:Variant_position_missing_in_Q9P0J0_after_alignment					apoptotic nuclear change|induction of apoptosis by extracellular signals|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|negative regulation of translation|protein import into nucleus|reactive oxygen species metabolic process|respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain complex I|nucleoplasm	ATP binding|NADH dehydrogenase (ubiquinone) activity|protein binding				0					NADH(DB00157)					42				0.315789	15.765442	16.327017	6	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19646177	19646177	10662	19	G	A	A	A	494	38	NDUFA13	1	1
CILP2	148113	broad.mit.edu	37	19	19655656	19655656	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19655656G>T	uc002nmw.3	+	c.2320G>T	c.(2320-2322)GCC>TCC	p.A774S	CILP2_uc002nmv.3_Missense_Mutation_p.A768S	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	768				A -> G (in Ref. 1; AAN17826).		proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1														0.454545	16.074133	16.093884	5	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19655656	19655656	3564	19	G	T	T	T	494	38	CILP2	1	1
ZNF208	7757	broad.mit.edu	37	19	22154536	22154536	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22154536A>T	uc002nqp.2	-	c.2916T>A	c.(2914-2916)CTT>CTA	p.L972L	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)	5		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.681818	195.222874	197.807951	60	28	KEEP	---	---	---	---	capture		Silent	SNP	22154536	22154536	18357	19	A	T	T	T	158	13	ZNF208	3	3
ZNF382	84911	broad.mit.edu	37	19	37117262	37117262	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37117262A>G	uc002oek.2	+	c.463A>G	c.(463-465)AGC>GGC	p.S155G	ZNF382_uc010efa.2_Missense_Mutation_p.S106G|ZNF382_uc010efb.2_Missense_Mutation_p.S154G|ZNF382_uc002oel.2_Missense_Mutation_p.S154G	NM_032825	NP_116214	Q96SR6	ZN382_HUMAN	zinc finger protein 382	155	Represses transcription (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)											0.162338	56.174728	72.871204	25	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37117262	37117262	18465	19	A	G	G	G	39	3	ZNF382	4	4
ZNF573	126231	broad.mit.edu	37	19	38230451	38230451	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38230451C>G	uc002ohe.2	-	c.940G>C	c.(940-942)GGT>CGT	p.G314R	ZNF573_uc010efs.2_Missense_Mutation_p.G227R|ZNF573_uc002ohd.2_Missense_Mutation_p.G312R|ZNF573_uc002ohf.2_Missense_Mutation_p.G256R|ZNF573_uc002ohg.2_Missense_Mutation_p.G226R	NM_152360	NP_689573	Q86YE8	ZN573_HUMAN	zinc finger protein 573	294	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)											0.440945	164.106949	164.50331	56	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38230451	38230451	18600	19	C	G	G	G	312	24	ZNF573	3	3
IRGC	56269	broad.mit.edu	37	19	44223928	44223928	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44223928T>A	uc002oxh.2	+	c.1218T>A	c.(1216-1218)GAT>GAA	p.D406E		NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	406						membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)	1		Prostate(69;0.0435)				Colon(189;350 2037 11447 13433 38914)								0.590909	45.1815	45.341387	13	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44223928	44223928	8141	19	T	A	A	A	660	51	IRGC	3	3
ZNF235	9310	broad.mit.edu	37	19	44792868	44792868	+	Silent	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44792868A>G	uc002oza.3	-	c.720T>C	c.(718-720)GAT>GAC	p.D240D	ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Silent_p.D236D|ZNF235_uc010xwx.1_Silent_p.D154D	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog	240					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)												0.414286	92.179031	92.645843	29	41	KEEP	---	---	---	---	capture		Silent	SNP	44792868	44792868	18379	19	A	G	G	G	50	4	ZNF235	4	4
CBLC	23624	broad.mit.edu	37	19	45303666	45303666	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45303666C>G	uc002ozs.2	+	c.1391C>G	c.(1390-1392)GCT>GGT	p.A464G	CBLC_uc010ejt.2_Missense_Mutation_p.A418G	NM_012116	NP_036248	Q9ULV8	CBLC_HUMAN	Cas-Br-M (murine) ecotropic retroviral	464					cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)										OREG0025543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.416667	55.381508	55.674418	20	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45303666	45303666	2821	19	C	G	G	G	364	28	CBLC	3	3
PRR12	57479	broad.mit.edu	37	19	50099342	50099342	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50099342G>T	uc002poo.3	+	c.1750G>T	c.(1750-1752)GGA>TGA	p.G584*		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	348	A.T hook 1.|Pro-rich.						DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)										0.3	78.435718	81.99592	30	70	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	50099342	50099342	13027	19	G	T	T	T	455	35	PRR12	5	2
IL4I1	259307	broad.mit.edu	37	19	50397696	50397696	+	Silent	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50397696C>A	uc002pqu.1	-	c.462G>T	c.(460-462)GGG>GGT	p.G154G	IL4I1_uc002pqv.1_Silent_p.G141G|IL4I1_uc010eno.1_Silent_p.G140G|IL4I1_uc002pqw.1_Silent_p.G140G|IL4I1_uc002pqt.1_Silent_p.G132G	NM_172374	NP_758962	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 2	132					oxidation-reduction process	lysosome	L-amino-acid oxidase activity			ovary(1)	1		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)										0.314286	54.454448	56.587309	22	48	KEEP	---	---	---	---	capture		Silent	SNP	50397696	50397696	7998	19	C	A	A	A	327	26	IL4I1	2	2
KLK8	11202	broad.mit.edu	37	19	51499412	51499412	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51499412C>G	uc002puq.1	-	c.821G>C	c.(820-822)GGC>GCC	p.G274A	KLK8_uc002pur.1_Missense_Mutation_p.G229A|KLK8_uc002pus.1_Missense_Mutation_p.G88A|KLK8_uc002put.1_3'UTR|KLK8_uc002puu.1_Missense_Mutation_p.G229A|KLK9_uc002puv.1_Non-coding_Transcript	NM_144505	NP_653088	O60259	KLK8_HUMAN	kallikrein 8 isoform 2	229	Peptidase S1.				cell death|keratinocyte proliferation|memory|negative regulation of axon regeneration|negative regulation of myelination|neuron projection morphogenesis|proteolysis|regulation of synapse organization|response to wounding	cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)										0.424779	149.387794	149.916792	48	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51499412	51499412	8724	19	C	G	G	G	338	26	KLK8	3	3
CEACAM18	729767	broad.mit.edu	37	19	51984864	51984864	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51984864A>T	uc002pwv.1	+	c.801A>T	c.(799-801)ATA>ATT	p.I267I		NM_001080405	NP_001073874	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion	267						integral to membrane				skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)										0.375	44.816854	45.36487	15	25	KEEP	---	---	---	---	capture		Silent	SNP	51984864	51984864	3322	19	A	T	T	T	189	15	CEACAM18	3	3
FPR2	2358	broad.mit.edu	37	19	52272196	52272196	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52272196G>T	uc002pxr.2	+	c.285G>T	c.(283-285)TGG>TGT	p.W95C	FPR2_uc002pxs.3_Missense_Mutation_p.W95C|FPR2_uc010epf.2_Missense_Mutation_p.W95C	NM_001005738	NP_001005738	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	95	Extracellular (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1														0.405882	201.985573	203.314922	69	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52272196	52272196	6285	19	G	T	T	T	572	44	FPR2	2	2
FPR3	2359	broad.mit.edu	37	19	52327526	52327526	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52327526C>T	uc002pxt.1	+	c.525C>T	c.(523-525)TAC>TAT	p.Y175Y		NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2	175	Extracellular (Potential).				cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity				0														0.305263	162.567889	169.002568	58	132	KEEP	---	---	---	---	capture		Silent	SNP	52327526	52327526	6286	19	C	T	T	T	259	20	FPR3	2	2
NLRP12	91662	broad.mit.edu	37	19	54313990	54313990	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54313990C>A	uc002qcj.3	-	c.923G>T	c.(922-924)GGA>GTA	p.G308V	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qch.3_Missense_Mutation_p.G308V|NLRP12_uc002qci.3_Missense_Mutation_p.G308V|NLRP12_uc002qck.3_Non-coding_Transcript|NLRP12_uc010eqx.2_Missense_Mutation_p.G308V	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	308	NACHT.				activation of caspase activity|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|lung(1)	5	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)										0.4	59.5056	59.964963	22	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54313990	54313990	10877	19	C	A	A	A	390	30	NLRP12	2	2
PRKCG	5582	broad.mit.edu	37	19	54401741	54401741	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54401741G>T	uc010yeg.1	+	c.1140G>T	c.(1138-1140)AAG>AAT	p.K380N	PRKCG_uc010yef.1_3'UTR|PRKCG_uc002qcq.1_Missense_Mutation_p.K380N|PRKCG_uc010yeh.1_Missense_Mutation_p.K267N	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma	380	Protein kinase.	ATP (By similarity).			activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|protein phosphorylation|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)						505				0.405797	74.022301	74.571309	28	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54401741	54401741	12955	19	G	T	T	T	425	33	PRKCG	2	2
LILRA1	11024	broad.mit.edu	37	19	55106301	55106301	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55106301G>A	uc002qgh.1	+	c.242G>A	c.(241-243)GGC>GAC	p.G81D	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Missense_Mutation_p.G81D	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	81	Ig-like C2-type 1.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0348)										0.485437	151.856256	151.874482	50	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55106301	55106301	9110	19	G	A	A	A	546	42	LILRA1	2	2
EPN1	29924	broad.mit.edu	37	19	56196893	56196893	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56196893C>T	uc002qlx.2	+	c.693C>T	c.(691-693)GGC>GGT	p.G231G	EPN1_uc002qlw.2_Silent_p.G120G|EPN1_uc002qlv.2_Silent_p.G120G|EPN1_uc010etd.2_Silent_p.G120G	NM_001130071	NP_001123543	Q9Y6I3	EPN1_HUMAN	epsin 1 isoform a	120	ENTH.				endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|cytoplasm|nucleus|plasma membrane	lipid binding				0		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)										0.428571	8.686291	8.702626	3	4	KEEP	---	---	---	---	capture		Silent	SNP	56196893	56196893	5378	19	C	T	T	T	340	27	EPN1	1	1
NLRP5	126206	broad.mit.edu	37	19	56544081	56544081	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56544081C>T	uc002qmj.2	+	c.2381C>T	c.(2380-2382)ACA>ATA	p.T794I	NLRP5_uc002qmi.2_Missense_Mutation_p.T775I	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	794	LRR 3.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)										0.405797	79.277456	79.814788	28	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56544081	56544081	10883	19	C	T	T	T	221	17	NLRP5	2	2
ZIM2	23619	broad.mit.edu	37	19	57286693	57286693	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57286693G>C	uc002qnr.2	-	c.947C>G	c.(946-948)ACG>AGG	p.T316R	ZIM2_uc010ygq.1_Missense_Mutation_p.T112R|ZIM2_uc010ygr.1_Missense_Mutation_p.T112R|ZIM2_uc002qnq.2_Missense_Mutation_p.T316R|ZIM2_uc010etp.2_Missense_Mutation_p.T316R|ZIM2_uc010ygs.1_Missense_Mutation_p.T316R	NM_015363	NP_056178	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	316					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)										0.139535	23.568848	34.33892	12	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57286693	57286693	18275	19	G	C	C	C	520	40	ZIM2	3	3
ZNF8	7554	broad.mit.edu	37	19	58806789	58806789	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58806789G>A	uc002qry.1	+	c.1615G>A	c.(1615-1617)GCT>ACT	p.A539T	ZNF8_uc002qrz.2_Non-coding_Transcript	NM_021089	NP_066575	P17098	ZNF8_HUMAN	zinc finger protein 8	539					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)										0.278261	78.801013	83.859149	32	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58806789	58806789	18765	19	G	A	A	A	546	42	ZNF8	2	2
CCL25	6370	broad.mit.edu	37	19	8121327	8121327	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8121327T>A	uc002mjd.2	+	c.269T>A	c.(268-270)CTG>CAG	p.L90Q	CCL25_uc002mjc.3_Missense_Mutation_p.L90Q|CCL25_uc010dvy.1_Intron	NM_005624	NP_005615	O15444	CCL25_HUMAN	small inducible cytokine A25 precursor	90					chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response	extracellular space|soluble fraction	CCR10 chemokine receptor binding|chemokine activity|hormone activity				0														0.363636	23.193165	23.553418	8	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8121327	8121327	3022	19	T	A	A	A	715	55	CCL25	3	3
COL11A1	1301	broad.mit.edu	37	1	103449747	103449747	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:103449747C>A	uc001dum.2	-	c.2539G>T	c.(2539-2541)GGA>TGA	p.G847*	COL11A1_uc001duk.2_Missense_Mutation_p.R25S|COL11A1_uc001dul.2_Nonsense_Mutation_p.G835*|COL11A1_uc001dun.2_Nonsense_Mutation_p.G796*|COL11A1_uc009weh.2_Nonsense_Mutation_p.G719*	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	835	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|central_nervous_system(1)|pancreas(1)	11		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)										0.272727	14.908055	15.891193	6	16	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	103449747	103449747	3805	1	C	A	A	A	286	22	COL11A1	5	2
SARS	6301	broad.mit.edu	37	1	109774338	109774338	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109774338C>T	uc001dwv.1	+	c.677C>T	c.(676-678)CCC>CTC	p.P226L	SARS_uc001dwt.1_Missense_Mutation_p.P226L|SARS_uc001dwu.1_Missense_Mutation_p.P226L|SARS_uc001dww.1_Missense_Mutation_p.P159L|SARS_uc001dwx.1_Missense_Mutation_p.P178L|SARS_uc009wfa.1_Missense_Mutation_p.P226L|SARS_uc001dwy.1_Missense_Mutation_p.P51L|SARS_uc001dwz.1_Missense_Mutation_p.P51L	NM_006513	NP_006504	P49591	SYSC_HUMAN	seryl-tRNA synthetase	226					seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)									0.596154	99.427499	99.847847	31	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109774338	109774338	14325	1	C	T	T	T	286	22	SARS	2	2
DENND2D	79961	broad.mit.edu	37	1	111743052	111743052	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:111743052G>A	uc001eak.1	-	c.30C>T	c.(28-30)TTC>TTT	p.F10F	DENND2D_uc001eal.1_Intron	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	10										ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)										0.444444	12.298684	12.322919	4	5	KEEP	---	---	---	---	capture		Silent	SNP	111743052	111743052	4610	1	G	A	A	A	581	45	DENND2D	2	2
SYT6	148281	broad.mit.edu	37	1	114680557	114680557	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:114680557G>T	uc001eev.2	-	c.376C>A	c.(376-378)CTC>ATC	p.L126I		NM_205848	NP_995320	Q5T7P8	SYT6_HUMAN	synaptotagmin VI	211	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)										0.26087	31.879806	34.260125	12	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114680557	114680557	15999	1	G	T	T	T	442	34	SYT6	2	2
SPAG17	200162	broad.mit.edu	37	1	118609489	118609489	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118609489C>A	uc001ehk.2	-	c.2419G>T	c.(2419-2421)GTT>TTT	p.V807F		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	807						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)										0.213115	31.955056	36.583603	13	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118609489	118609489	15482	1	C	A	A	A	221	17	SPAG17	2	2
DVL1	1855	broad.mit.edu	37	1	1277441	1277441	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1277441C>T	uc001aer.3	-	c.458G>A	c.(457-459)CGC>CAC	p.R153H	DVL1_uc002quu.2_5'Flank|DVL1_uc009vka.2_5'Flank|DVL1_uc001aeu.1_5'UTR	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1	153					canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)						137				0.5	6.450068	6.450068	2	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1277441	1277441	5021	1	C	T	T	T	351	27	DVL1	1	1
SSU72	29101	broad.mit.edu	37	1	1500234	1500234	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1500234G>T	uc001agd.2	-	c.143C>A	c.(142-144)GCT>GAT	p.A48D	SSU72_uc009vkg.1_Missense_Mutation_p.A48D|SSU72_uc001age.1_Missense_Mutation_p.A48D	NM_014188	NP_054907	Q9NP77	SSU72_HUMAN	Ssu72 RNA polymerase II CTD phosphatase homolog	48					mRNA processing	cytoplasm|nucleus	phosphoprotein phosphatase activity				0	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)						170				0.467742	86.262357	86.319032	29	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1500234	1500234	15718	1	G	T	T	T	442	34	SSU72	2	2
SETDB1	9869	broad.mit.edu	37	1	150933451	150933451	+	Silent	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:150933451T>G	uc001evu.2	+	c.2913T>G	c.(2911-2913)CCT>CCG	p.P971P	SETDB1_uc001evv.2_Silent_p.P971P|SETDB1_uc009wmg.1_Silent_p.P971P	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	971	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)							452				0.106383	4.087598	18.564977	10	84	KEEP	---	---	---	---	capture		Silent	SNP	150933451	150933451	14627	1	T	G	G	G	717	56	SETDB1	4	4
GATAD2B	57459	broad.mit.edu	37	1	153789997	153789997	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153789997C>A	uc001fdb.3	-	c.751G>T	c.(751-753)GCT>TCT	p.A251S		NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	251					regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)											0.344828	28.341717	28.958144	10	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153789997	153789997	6525	1	C	A	A	A	364	28	GATAD2B	2	2
FCRL3	115352	broad.mit.edu	37	1	157660129	157660129	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157660129T>A	uc001fqz.3	-	c.1606A>T	c.(1606-1608)ACA>TCA	p.T536S	FCRL3_uc001fqx.3_Non-coding_Transcript|FCRL3_uc001fqy.3_Non-coding_Transcript|FCRL3_uc009wsn.2_Non-coding_Transcript|FCRL3_uc009wso.2_Non-coding_Transcript|FCRL3_uc001fra.2_Missense_Mutation_p.T262S|FCRL3_uc001frb.2_Missense_Mutation_p.T536S|FCRL3_uc001frc.1_Missense_Mutation_p.T536S	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	536	Ig-like C2-type 6.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)													0.470588	124.095193	124.158928	40	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157660129	157660129	6033	1	T	A	A	A	741	57	FCRL3	3	3
FCRL2	79368	broad.mit.edu	37	1	157739907	157739907	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157739907G>T	uc001fre.2	-	c.344C>A	c.(343-345)TCC>TAC	p.S115Y	FCRL2_uc001frd.2_5'Flank|FCRL2_uc010phz.1_Missense_Mutation_p.S115Y|FCRL2_uc009wsp.2_Intron|FCRL2_uc010pia.1_Missense_Mutation_p.S115Y	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	115	Extracellular (Potential).|Ig-like C2-type 2.				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)											0.315789	28.16864	29.326573	12	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157739907	157739907	6032	1	G	T	T	T	533	41	FCRL2	2	2
FCRL1	115350	broad.mit.edu	37	1	157773709	157773709	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157773709C>A	uc001frg.2	-	c.245G>T	c.(244-246)GGG>GTG	p.G82V	FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Missense_Mutation_p.G82V|FCRL1_uc001fri.2_Missense_Mutation_p.G82V|FCRL1_uc001frj.2_Non-coding_Transcript	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor	82	Extracellular (Potential).|Ig-like C2-type 1.					integral to membrane|plasma membrane	receptor activity			ovary(3)	3	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GBM(54;482 1003 11223 30131 35730)								0.105263	8.352995	25.985296	12	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157773709	157773709	6031	1	C	A	A	A	286	22	FCRL1	2	2
OR10R2	343406	broad.mit.edu	37	1	158450117	158450117	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158450117G>T	uc010pik.1	+	c.450G>T	c.(448-450)CTG>CTT	p.L150L		NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	150	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)	2	all_hematologic(112;0.0378)													0.267016	128.266032	137.620573	51	140	KEEP	---	---	---	---	capture		Silent	SNP	158450117	158450117	11323	1	G	T	T	T	587	46	OR10R2	2	2
SPTA1	6708	broad.mit.edu	37	1	158612648	158612648	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158612648G>A	uc001fst.1	-	c.4561C>T	c.(4561-4563)CCC>TCC	p.P1521S		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1521	Spectrin 15.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.116505	13.961179	28.836582	12	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158612648	158612648	15630	1	G	A	A	A	546	42	SPTA1	2	2
SPTA1	6708	broad.mit.edu	37	1	158624419	158624419	+	Silent	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158624419C>G	uc001fst.1	-	c.3018G>C	c.(3016-3018)CTG>CTC	p.L1006L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1006	SH3.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.388889	43.99192	44.362869	14	22	KEEP	---	---	---	---	capture		Silent	SNP	158624419	158624419	15630	1	C	G	G	G	314	25	SPTA1	3	3
SPTA1	6708	broad.mit.edu	37	1	158636289	158636289	+	Splice_Site_SNP	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158636289T>C	uc001fst.1	-	c.2039_splice	c.e16-1	p.G680_splice		NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.333333	18.57998	19.176432	8	16	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	158636289	158636289	15630	1	T	C	C	C	715	55	SPTA1	5	4
NOS1AP	9722	broad.mit.edu	37	1	162124198	162124198	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:162124198G>T	uc001gbv.2	+	c.109G>T	c.(109-111)GTA>TTA	p.V37L	NOS1AP_uc010pkr.1_Missense_Mutation_p.V37L|NOS1AP_uc010pks.1_Non-coding_Transcript|NOS1AP_uc001gbw.2_Missense_Mutation_p.V37L	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor	37	PID.				regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)	2	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)											0.259259	19.363807	20.748261	7	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	162124198	162124198	10945	1	G	T	T	T	520	40	NOS1AP	1	1
DDR2	4921	broad.mit.edu	37	1	162729653	162729653	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:162729653G>T	uc001gcf.2	+	c.739G>T	c.(739-741)GAA>TAA	p.E247*	DDR2_uc001gcg.2_Nonsense_Mutation_p.E247*	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2	247	Extracellular (Potential).				cell adhesion|protein phosphorylation	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			NSCLC(161;314 2006 8283 19651 23192)				497				0.5	82.922171	82.922171	27	27	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	162729653	162729653	4508	1	G	T	T	T	585	45	DDR2	5	2
ADCY10	55811	broad.mit.edu	37	1	167825402	167825402	+	Splice_Site_SNP	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167825402C>T	uc001ger.2	-	c.2171_splice	c.e17+1	p.S724_splice	ADCY10_uc009wvk.2_Splice_Site_SNP_p.S632_splice|ADCY10_uc010plj.1_Splice_Site_SNP_p.S571_splice|ADCY10_uc009wvl.2_Splice_Site_SNP_p.S723_splice	NM_018417	NP_060887			adenylate cyclase 10						intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3														0.424242	123.825913	124.322419	42	57	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	167825402	167825402	294	1	C	T	T	T	247	19	ADCY10	5	1
NADK	65220	broad.mit.edu	37	1	1687735	1687735	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1687735C>T	uc001aie.2	-	c.982G>A	c.(982-984)GGA>AGA	p.G328R	NADK_uc009vkw.2_Missense_Mutation_p.G183R|NADK_uc001aic.2_Missense_Mutation_p.G183R|NADK_uc001aid.3_Missense_Mutation_p.G183R|NADK_uc010nyv.1_Missense_Mutation_p.G151R|NADK_uc009vkx.1_Missense_Mutation_p.G61R	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	183					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)										0.195652	22.248304	26.219908	9	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1687735	1687735	10533	1	C	T	T	T	286	22	NADK	2	2
SLC9A11	284525	broad.mit.edu	37	1	173486708	173486708	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173486708C>A	uc001giz.2	-	c.2875G>T	c.(2875-2877)GAA>TAA	p.E959*	SLC9A11_uc009wwe.2_Nonsense_Mutation_p.E517*	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	959	cNMP.				sodium ion transport	integral to membrane	solute:hydrogen antiporter activity			ovary(2)	2														0.252632	59.961934	65.236777	24	71	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	173486708	173486708	15208	1	C	A	A	A	377	29	SLC9A11	5	2
SLC9A11	284525	broad.mit.edu	37	1	173516881	173516881	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173516881T>A	uc001giz.2	-	c.1504A>T	c.(1504-1506)ACA>TCA	p.T502S	SLC9A11_uc009wwe.2_Missense_Mutation_p.T60S|SLC9A11_uc010pmq.1_Non-coding_Transcript	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	502					sodium ion transport	integral to membrane	solute:hydrogen antiporter activity			ovary(2)	2														0.272727	30.170071	32.227584	12	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173516881	173516881	15208	1	T	A	A	A	780	60	SLC9A11	3	3
TNR	7143	broad.mit.edu	37	1	175331943	175331944	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:175331943_175331944CC>AA	uc001gkp.1	-	c.2709_2710GG>TT	c.(2707-2712)GTGGGA>GTTTGA	p.G904*	TNR_uc009wwu.1_Nonsense_Mutation_p.G904*	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	904	Fibronectin type-III 7.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)													0.243243	42.436982	46.965242	18	56	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	175331943	175331944	16879	1	CC	AA	AA	AA	286	22	TNR	5	2
PAPPA2	60676	broad.mit.edu	37	1	176564366	176564366	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176564366G>T	uc001gkz.2	+	c.1626G>T	c.(1624-1626)GTG>GTT	p.V542V	PAPPA2_uc001gky.1_Silent_p.V542V|PAPPA2_uc009www.2_Non-coding_Transcript	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	542	Metalloprotease.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|lung(1)|breast(1)	14														0.431818	58.518044	58.696464	19	25	KEEP	---	---	---	---	capture		Silent	SNP	176564366	176564366	11850	1	G	T	T	T	574	45	PAPPA2	2	2
C1orf49	84066	broad.mit.edu	37	1	178489836	178489836	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:178489836C>G	uc001glt.1	+	c.370C>G	c.(370-372)CAG>GAG	p.Q124E	C1orf49_uc001glu.1_Missense_Mutation_p.Q124E|C1orf49_uc001glv.1_Non-coding_Transcript|C1orf49_uc001glw.1_Missense_Mutation_p.Q132E	NM_032126	NP_115502	Q5T0J7	CA049_HUMAN	hypothetical protein LOC84066	124						microtubule cytoskeleton					0														0.461538	20.050065	20.066638	6	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178489836	178489836	2115	1	C	G	G	G	325	25	C1orf49	3	3
TDRD5	163589	broad.mit.edu	37	1	179587773	179587773	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179587773C>A	uc010pnp.1	+	c.871C>A	c.(871-873)CCT>ACT	p.P291T	TDRD5_uc001gnf.1_Missense_Mutation_p.P291T|TDRD5_uc001gnh.1_5'UTR	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	291					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														0.333333	48.456684	49.711974	17	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179587773	179587773	16260	1	C	A	A	A	234	18	TDRD5	2	2
CACNA1E	777	broad.mit.edu	37	1	181549852	181549852	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181549852T>A	uc001gow.2	+	c.891T>A	c.(889-891)TTT>TTA	p.F297L	CACNA1E_uc009wxr.2_Missense_Mutation_p.F204L|CACNA1E_uc009wxs.2_Missense_Mutation_p.F204L	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	297	I.|Extracellular (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.521739	117.506988	117.535804	36	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	181549852	181549852	2658	1	T	A	A	A	816	63	CACNA1E	3	3
GLUL	2752	broad.mit.edu	37	1	182357841	182357841	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:182357841T>C	uc001gpa.1	-	c.32A>G	c.(31-33)AAA>AGA	p.K11R	GLUL_uc001gpb.1_Missense_Mutation_p.K11R|GLUL_uc001gpc.1_Missense_Mutation_p.K11R|GLUL_uc001gpd.1_Missense_Mutation_p.K11R	NM_001033056	NP_001028228	P15104	GLNA_HUMAN	glutamine synthetase	11					cell proliferation|glutamine biosynthetic process|neurotransmitter uptake	cytosol|Golgi apparatus|mitochondrion	ATP binding|glutamate decarboxylase activity|glutamate-ammonia ligase activity|identical protein binding				0					Asparaginase(DB00023)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)|L-Methionine(DB00134)									0.16129	43.31432	56.858726	20	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	182357841	182357841	6746	1	T	C	C	C	832	64	GLUL	4	4
PRG4	10216	broad.mit.edu	37	1	186277271	186277271	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186277271C>A	uc001gru.3	+	c.2420C>A	c.(2419-2421)ACC>AAC	p.T807N	PRG4_uc001grt.3_Missense_Mutation_p.T766N|PRG4_uc009wyl.2_Missense_Mutation_p.T714N|PRG4_uc009wym.2_Missense_Mutation_p.T673N|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	807	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|53; approximate.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity				0														0.215054	93.767791	107.76589	40	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186277271	186277271	12924	1	C	A	A	A	234	18	PRG4	2	2
UBR4	23352	broad.mit.edu	37	1	19525042	19525042	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19525042T>C	uc001bbi.2	-	c.641A>G	c.(640-642)CAG>CGG	p.Q214R		NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	214					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)										0.365385	55.407916	56.237896	19	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19525042	19525042	17462	1	T	C	C	C	715	55	UBR4	4	4
CFHR4	10877	broad.mit.edu	37	1	196871560	196871560	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196871560G>T	uc001gtp.2	+	c.71G>T	c.(70-72)TGT>TTT	p.C24F	CFHR4_uc001gto.2_Missense_Mutation_p.C24F|CFHR4_uc009wyy.2_Missense_Mutation_p.C23F	NM_006684	NM_006684	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor	24	Sushi 1.					extracellular region	lipid transporter activity			ovary(1)|pancreas(1)	2														0.528846	178.733679	178.809578	55	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196871560	196871560	3420	1	G	T	T	T	624	48	CFHR4	2	2
PTPRC	5788	broad.mit.edu	37	1	198711119	198711119	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:198711119G>T	uc001gur.1	+	c.2519G>T	c.(2518-2520)AGC>ATC	p.S840I	PTPRC_uc001gus.1_Missense_Mutation_p.S792I|PTPRC_uc001gut.1_Missense_Mutation_p.S679I	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	840	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815				0.4	29.264942	29.476921	10	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	198711119	198711119	13254	1	G	T	T	T	442	34	PTPRC	2	2
HTR6	3362	broad.mit.edu	37	1	19992706	19992706	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19992706G>T	uc001bcl.2	+	c.460G>T	c.(460-462)GCC>TCC	p.A154S		NM_000871	NP_000862	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6	154	Helical; Name=4; (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	histamine receptor activity|protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Granisetron(DB00889)|Ondansetron(DB00904)|Sertindole(DB06144)	Esophageal Squamous(168;1879 2619 6848 21062)								0.405405	44.92227	45.210042	15	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19992706	19992706	7751	1	G	T	T	T	494	38	HTR6	1	1
TMCO4	255104	broad.mit.edu	37	1	20009765	20009765	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:20009765T>A	uc001bcn.2	-	c.1673A>T	c.(1672-1674)CAG>CTG	p.Q558L	TMCO4_uc001bcm.2_Missense_Mutation_p.Q389L|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	558						integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)										0.418919	95.471955	95.879574	31	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20009765	20009765	16528	1	T	A	A	A	715	55	TMCO4	3	3
LAD1	3898	broad.mit.edu	37	1	201355596	201355596	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201355596G>T	uc001gwm.2	-	c.893C>A	c.(892-894)TCT>TAT	p.S298Y	LAD1_uc009wzu.1_Missense_Mutation_p.S320Y	NM_005558	NP_005549	O00515	LAD1_HUMAN	ladinin 1	298						basement membrane	structural molecule activity				0														0.183099	25.452584	32.13361	13	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	201355596	201355596	8922	1	G	T	T	T	429	33	LAD1	2	2
LAD1	3898	broad.mit.edu	37	1	201358337	201358337	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201358337C>A	uc001gwm.2	-	c.133G>T	c.(133-135)GCT>TCT	p.A45S	LAD1_uc009wzu.1_Missense_Mutation_p.A67S	NM_005558	NP_005549	O00515	LAD1_HUMAN	ladinin 1	45						basement membrane	structural molecule activity				0														0.507692	94.15704	94.160121	33	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	201358337	201358337	8922	1	C	A	A	A	338	26	LAD1	2	2
CHIT1	1118	broad.mit.edu	37	1	203192741	203192741	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:203192741T>A	uc001gzn.2	-	c.362A>T	c.(361-363)AAC>ATC	p.N121I	FMOD_uc010pqi.1_Intron|CHIT1_uc001gzm.1_Non-coding_Transcript|CHIT1_uc009xal.1_5'Flank|CHIT1_uc009xam.1_Non-coding_Transcript|CHIT1_uc009xan.1_Non-coding_Transcript|CHIT1_uc001gzo.2_Missense_Mutation_p.N112I	NM_003465	NP_003456	Q13231	CHIT1_HUMAN	chitotriosidase precursor	121					chitin catabolic process|immune response|response to bacterium	extracellular space|lysosome	cation binding|chitin binding|endochitinase activity				0														0.453608	127.552021	127.73725	44	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	203192741	203192741	3480	1	T	A	A	A	780	60	CHIT1	3	3
OPTC	26254	broad.mit.edu	37	1	203467947	203467947	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:203467947C>A	uc001gzu.1	+	c.509C>A	c.(508-510)GCC>GAC	p.A170D		NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	opticin precursor	170	LRR 1.					proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.109)											0.5	58.122682	58.122682	19	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	203467947	203467947	11294	1	C	A	A	A	338	26	OPTC	2	2
IL10	3586	broad.mit.edu	37	1	206945736	206945736	+	Silent	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206945736C>A	uc001hen.1	-	c.45G>T	c.(43-45)GGG>GGT	p.G15G		NM_000572	NP_000563	P22301	IL10_HUMAN	interleukin 10 precursor	15			G -> R (in a family affected by Crohn disease; decreases secretion thereby reducing the anti-inflammatory effect).		anti-apoptosis|B cell differentiation|B cell proliferation|cell-cell signaling|cytoplasmic sequestering of NF-kappaB|inflammatory response|leukocyte chemotaxis|negative regulation of B cell proliferation|negative regulation of cytokine secretion involved in immune response|negative regulation of interferon-alpha biosynthetic process|negative regulation of interleukin-6 production|negative regulation of membrane protein ectodomain proteolysis|negative regulation of MHC class II biosynthetic process|negative regulation of T cell proliferation|positive regulation of B cell apoptosis|positive regulation of cytokine secretion|positive regulation of gene-specific transcription|positive regulation of sequence-specific DNA binding transcription factor activity|receptor biosynthetic process|regulation of isotype switching|response to glucocorticoid stimulus|type 2 immune response	extracellular space	cytokine activity|growth factor activity|interleukin-10 receptor binding				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)											0.12766	7.718015	14.070404	6	41	KEEP	---	---	---	---	capture		Silent	SNP	206945736	206945736	7920	1	C	A	A	A	275	22	IL10	2	2
CENPF	1063	broad.mit.edu	37	1	214818865	214818865	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:214818865G>A	uc001hkm.2	+	c.5952G>A	c.(5950-5952)ATG>ATA	p.M1984I		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2080	Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)	12				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		Colon(80;575 1284 11000 14801 43496)								0.424242	40.056611	40.218377	14	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	214818865	214818865	3364	1	G	A	A	A	585	45	CENPF	2	2
HHIPL2	79802	broad.mit.edu	37	1	222696210	222696210	+	Silent	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222696210T>C	uc001hnh.1	-	c.1908A>G	c.(1906-1908)CTA>CTG	p.L636L		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	636					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)										0.37234	110.657988	112.018569	35	59	KEEP	---	---	---	---	capture		Silent	SNP	222696210	222696210	7378	1	T	C	C	C	782	61	HHIPL2	4	4
HIST3H3	8290	broad.mit.edu	37	1	228612717	228612717	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228612717G>A	uc001hsx.1	-	c.310C>T	c.(310-312)CTG>TTG	p.L104L		NM_003493	NP_003484	Q16695	H31T_HUMAN	histone cluster 3, H3	104					nucleosome assembly|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0		Prostate(94;0.0724)												0.373134	71.387472	72.321257	25	42	KEEP	---	---	---	---	capture		Silent	SNP	228612717	228612717	7475	1	G	A	A	A	438	34	HIST3H3	2	2
COG2	22796	broad.mit.edu	37	1	230795245	230795245	+	Silent	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:230795245T>C	uc001htw.2	+	c.108T>C	c.(106-108)TGT>TGC	p.C36C	COG2_uc001htx.2_Silent_p.C36C|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	36					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)												0.396825	84.769374	85.35372	25	38	KEEP	---	---	---	---	capture		Silent	SNP	230795245	230795245	3796	1	T	C	C	C	738	57	COG2	4	4
EPHB2	2048	broad.mit.edu	37	1	23191570	23191570	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23191570G>T	uc009vqj.1	+	c.1168G>T	c.(1168-1170)GAG>TAG	p.E390*	EPHB2_uc001bge.2_Nonsense_Mutation_p.E390*|EPHB2_uc001bgf.2_Nonsense_Mutation_p.E390*|EPHB2_uc010odu.1_Nonsense_Mutation_p.E390*	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	390	Extracellular (Potential).|Fibronectin type-III 1.				axon guidance|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)						437				0.307692	43.185261	44.897537	16	36	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	23191570	23191570	5368	1	G	T	T	T	481	37	EPHB2	5	1
NID1	4811	broad.mit.edu	37	1	236212142	236212142	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236212142C>A	uc001hxo.2	-	c.373G>T	c.(373-375)GAC>TAC	p.D125Y	NID1_uc009xgd.2_Missense_Mutation_p.D125Y	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	125	NIDO.				bioluminescence|cell-matrix adhesion|protein-chromophore linkage	basement membrane|membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)									0.146341	6.510857	11.469409	6	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	236212142	236212142	10815	1	C	A	A	A	416	32	NID1	2	2
RYR2	6262	broad.mit.edu	37	1	237551449	237551449	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237551449G>T	uc001hyl.1	+	c.739G>T	c.(739-741)GTC>TTC	p.V247F		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	247	Cytoplasmic (By similarity).|MIR 3.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.28	19.613444	20.701931	7	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237551449	237551449	14249	1	G	T	T	T	624	48	RYR2	2	2
RYR2	6262	broad.mit.edu	37	1	237789019	237789019	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237789019G>T	uc001hyl.1	+	c.6081G>T	c.(6079-6081)GGG>GGT	p.G2027G		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2027	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.454545	56.905635	56.981001	20	24	KEEP	---	---	---	---	capture		Silent	SNP	237789019	237789019	14249	1	G	T	T	T	535	42	RYR2	2	2
RYR2	6262	broad.mit.edu	37	1	237972319	237972319	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237972319G>A	uc001hyl.1	+	c.14417G>A	c.(14416-14418)TGT>TAT	p.C4806Y	RYR2_uc010pyb.1_Missense_Mutation_p.C239Y	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4806					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.184932	53.785397	67.343746	27	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237972319	237972319	14249	1	G	A	A	A	624	48	RYR2	2	2
ZP4	57829	broad.mit.edu	37	1	238048522	238048522	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:238048522G>A	uc001hym.2	-	c.1254C>T	c.(1252-1254)AGC>AGT	p.S418S	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	418	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)								0.354839	29.210035	29.788218	11	20	KEEP	---	---	---	---	capture		Silent	SNP	238048522	238048522	18822	1	G	A	A	A	594	46	ZP4	2	2
FH	2271	broad.mit.edu	37	1	241661252	241661252	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241661252T>C	uc001hyx.2	-	c.1409A>G	c.(1408-1410)AAG>AGG	p.K470R		NM_000143	NP_000134	P07954	FUMH_HUMAN	fumarate hydratase precursor	470					fumarate metabolic process|tricarboxylic acid cycle	cell junction|mitochondrial matrix|tricarboxylic acid cycle enzyme complex	fumarate hydratase activity			lung(3)|ovary(1)	4	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		Melanoma(148;1573 2486 7381 46575)				119				0.133333	13.753936	21.612263	8	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241661252	241661252	6112	1	T	C	C	C	728	56	FH	4	4
OR2C3	81472	broad.mit.edu	37	1	247695586	247695586	+	Silent	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247695586C>G	uc009xgy.2	-	c.228G>C	c.(226-228)ACG>ACC	p.T76T	C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron|LOC148824_uc001idd.2_5'Flank	NM_198074	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C,	76	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)											0.190476	8.187196	10.069488	4	17	KEEP	---	---	---	---	capture		Silent	SNP	247695586	247695586	11399	1	C	G	G	G	392	31	OR2C3	3	3
OR2L3	391192	broad.mit.edu	37	1	248224182	248224182	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248224182C>A	uc001idx.1	+	c.199C>A	c.(199-201)CTC>ATC	p.L67I	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	67	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)											0.3	210.901626	220.224599	78	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248224182	248224182	11414	1	C	A	A	A	312	24	OR2L3	2	2
OR2M5	127059	broad.mit.edu	37	1	248309310	248309310	+	Silent	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248309310C>A	uc010pze.1	+	c.861C>A	c.(859-861)CCC>CCA	p.P287P		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)											0.423729	62.220179	62.52779	25	34	KEEP	---	---	---	---	capture		Silent	SNP	248309310	248309310	11419	1	C	A	A	A	275	22	OR2M5	2	2
OR2T4	127074	broad.mit.edu	37	1	248525191	248525191	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248525191G>T	uc001ieh.1	+	c.309G>T	c.(307-309)ATG>ATT	p.M103I		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	103	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.12931	40.705861	71.798933	30	202	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248525191	248525191	11433	1	G	T	T	T	611	47	OR2T4	2	2
OR2T27	403239	broad.mit.edu	37	1	248814155	248814155	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248814155C>A	uc010pzo.1	-	c.31G>T	c.(31-33)GAC>TAC	p.D11Y		NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,	11	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.166667	7.015507	8.909954	3	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248814155	248814155	11427	1	C	A	A	A	403	31	OR2T27	1	1
OR14I1	401994	broad.mit.edu	37	1	248844994	248844994	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248844994C>T	uc001ieu.1	-	c.612G>A	c.(610-612)TTG>TTA	p.L204L		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.352941	34.893083	35.540002	12	22	KEEP	---	---	---	---	capture		Silent	SNP	248844994	248844994	11353	1	C	T	T	T	272	21	OR14I1	2	2
AHDC1	27245	broad.mit.edu	37	1	27874644	27874644	+	Nonsense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27874644G>C	uc009vsy.2	-	c.3983C>G	c.(3982-3984)TCA>TGA	p.S1328*	AHDC1_uc009vsz.1_Nonsense_Mutation_p.S1328*	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1328							DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)										0.142857	15.668051	22.545304	8	48	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	27874644	27874644	415	1	G	C	C	C	585	45	AHDC1	5	3
MACF1	23499	broad.mit.edu	37	1	39801748	39801748	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:39801748C>A	uc010oiu.1	+	c.4808C>A	c.(4807-4809)TCC>TAC	p.S1603Y	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	1786	Potential.				cell cycle arrest	cytoplasm|cytoskeleton	actin filament binding|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)	14	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)											0.146341	9.534443	14.454226	6	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39801748	39801748	9521	1	C	A	A	A	390	30	MACF1	2	2
CHD5	26038	broad.mit.edu	37	1	6215697	6215697	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:6215697G>A	uc001amb.1	-	c.468C>T	c.(466-468)CAC>CAT	p.H156H		NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	156					chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|zinc ion binding			breast(3)|central_nervous_system(3)|ovary(1)|lung(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)						2304				0.184211	13.127472	16.664549	7	31	KEEP	---	---	---	---	capture		Silent	SNP	6215697	6215697	3462	1	G	A	A	A	620	48	CHD5	2	2
GPR153	387509	broad.mit.edu	37	1	6313779	6313779	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:6313779A>G	uc001amp.1	-	c.785T>C	c.(784-786)CTG>CCG	p.L262P		NM_207370	NP_997253	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	262	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)										0.288462	34.988338	37.086508	15	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6313779	6313779	6934	1	A	G	G	G	91	7	GPR153	4	4
LRRC7	57554	broad.mit.edu	37	1	70478698	70478698	+	Silent	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70478698C>A	uc001dep.2	+	c.1062C>A	c.(1060-1062)TCC>TCA	p.S354S	LRRC7_uc009wbg.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	354	LRR 15.					centrosome|focal adhesion|nucleolus	protein binding			ovary(8)|breast(2)|central_nervous_system(2)|liver(1)	13										783				0.098765	6.766011	19.783598	8	73	KEEP	---	---	---	---	capture		Silent	SNP	70478698	70478698	9396	1	C	A	A	A	262	21	LRRC7	2	2
C1orf173	127254	broad.mit.edu	37	1	75037223	75037223	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75037223C>A	uc001dgg.2	-	c.4171G>T	c.(4171-4173)GAT>TAT	p.D1391Y		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1391	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.151515	22.659183	34.179583	15	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75037223	75037223	2081	1	C	A	A	A	390	30	C1orf173	2	2
FNBP1L	54874	broad.mit.edu	37	1	94014930	94014930	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:94014930A>C	uc001dpw.2	+	c.1424A>C	c.(1423-1425)GAT>GCT	p.D475A	FNBP1L_uc001dpv.2_Missense_Mutation_p.D475A|FNBP1L_uc010otk.1_Missense_Mutation_p.D353A|FNBP1L_uc010otl.1_Missense_Mutation_p.D103A	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1	533	Interaction with DNM1.|Interaction with CDC42.				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)										0.423077	38.822171	38.956102	11	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94014930	94014930	6208	1	A	C	C	C	156	12	FNBP1L	4	4
GGTLC1	92086	broad.mit.edu	37	20	23967133	23967133	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23967133T>A	uc002wts.2	-	c.116A>T	c.(115-117)CAC>CTC	p.H39L	GGTLC1_uc002wtu.2_Missense_Mutation_p.H39L	NM_178312	NP_842564	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	39							gamma-glutamyltransferase activity			ovary(1)	1														0.473684	55.455924	55.477878	18	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23967133	23967133	6633	20	T	A	A	A	767	59	GGTLC1	3	3
TGM6	343641	broad.mit.edu	37	20	2411636	2411636	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2411636G>A	uc002wfy.1	+	c.1930G>A	c.(1930-1932)GAG>AAG	p.E644K	TGM6_uc010gal.1_Intron	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	644					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)	3					L-Glutamine(DB00130)									0.386792	120.764026	121.949474	41	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2411636	2411636	16362	20	G	A	A	A	533	41	TGM6	2	2
XKR7	343702	broad.mit.edu	37	20	30584572	30584572	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30584572G>T	uc002wxe.2	+	c.1052G>T	c.(1051-1053)TGC>TTC	p.C351F		NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related	351						integral to membrane				ovary(1)|breast(1)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)											0.368421	41.439473	42.018006	14	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30584572	30584572	18017	20	G	T	T	T	598	46	XKR7	2	2
PTPRT	11122	broad.mit.edu	37	20	40790092	40790092	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40790092G>T	uc010ggj.2	-	c.2639C>A	c.(2638-2640)CCC>CAC	p.P880H	PTPRT_uc002xkg.2_Missense_Mutation_p.P861H|PTPRT_uc010ggi.2_Missense_Mutation_p.P64H	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	861	Cytoplasmic (Potential).				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.37037	76.582452	77.794006	30	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40790092	40790092	13270	20	G	T	T	T	559	43	PTPRT	2	2
SERINC3	10955	broad.mit.edu	37	20	43138621	43138621	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43138621T>A	uc002xme.2	-	c.524A>T	c.(523-525)CAG>CTG	p.Q175L	SERINC3_uc002xmf.1_Missense_Mutation_p.Q175L|SERINC3_uc010ggs.1_Missense_Mutation_p.Q168L|SERINC3_uc010zwp.1_Missense_Mutation_p.Q120L	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1	175	Helical; (Potential).					integral to membrane|plasma membrane	protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)											0.294118	71.957843	75.172689	25	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43138621	43138621	14569	20	T	A	A	A	715	55	SERINC3	3	3
PREX1	57580	broad.mit.edu	37	20	47273727	47273727	+	Splice_Site_SNP	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47273727C>T	uc002xtw.1	-	c.1975_splice	c.e18-1	p.V659_splice	PREX1_uc002xtv.1_5'Flank	NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)									OREG0026010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.282051	31.407899	33.072676	11	28	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	47273727	47273727	12919	20	C	T	T	T	312	24	PREX1	5	2
PREX1	57580	broad.mit.edu	37	20	47361594	47361594	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47361594G>C	uc002xtw.1	-	c.382C>G	c.(382-384)CAG>GAG	p.Q128E		NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	128	DH.				actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)											0.194286	82.464461	97.654241	34	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47361594	47361594	12919	20	G	C	C	C	585	45	PREX1	3	3
PTGIS	5740	broad.mit.edu	37	20	48129765	48129765	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:48129765G>T	uc002xut.2	-	c.1058C>A	c.(1057-1059)GCT>GAT	p.A353D	PTGIS_uc010zyi.1_Missense_Mutation_p.A214D	NM_000961	NP_000952	Q16647	PTGIS_HUMAN	prostaglandin I2 synthase	353					hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|prostaglandin-I synthase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)									0.145833	12.214184	17.985848	7	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48129765	48129765	13207	20	G	T	T	T	442	34	PTGIS	2	2
SPATA2	9825	broad.mit.edu	37	20	48525018	48525018	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:48525018G>C	uc010gie.2	-	c.10C>G	c.(10-12)CCC>GCC	p.P4A	SPATA2_uc002xuw.2_Missense_Mutation_p.P4A|SPATA2_uc010zyn.1_Intron	NM_001135773	NP_001129245	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	4					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus				central_nervous_system(1)	1	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)											0.444444	49.495897	49.592368	16	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48525018	48525018	15513	20	G	C	C	C	546	42	SPATA2	3	3
ZNF217	7764	broad.mit.edu	37	20	52193535	52193535	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:52193535C>T	uc002xwq.3	-	c.1768G>A	c.(1768-1770)GCT>ACT	p.A590T	ZNF217_uc010gij.1_Missense_Mutation_p.A582T	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	590					regulation of transcription, DNA-dependent	histone deacetylase complex	promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			skin(2)|large_intestine(1)|lung(1)|ovary(1)	5	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)						p.A590T(HEC6-Tumor)	185				0.300813	96.23976	100.536097	37	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52193535	52193535	18363	20	C	T	T	T	351	27	ZNF217	1	1
SYCP2	10388	broad.mit.edu	37	20	58461889	58461889	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:58461889T>C	uc002yaz.2	-	c.2365A>G	c.(2365-2367)AGA>GGA	p.R789G		NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	789					cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)											0.166667	17.622237	22.027002	7	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58461889	58461889	15953	20	T	C	C	C	700	54	SYCP2	4	4
DIDO1	11083	broad.mit.edu	37	20	61542492	61542492	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61542492C>A	uc002ydr.1	-	c.473G>T	c.(472-474)GGC>GTC	p.G158V	DIDO1_uc002yds.1_Missense_Mutation_p.G158V|DIDO1_uc002ydt.1_Missense_Mutation_p.G158V|DIDO1_uc002ydu.1_Missense_Mutation_p.G158V|DIDO1_uc002ydv.1_Missense_Mutation_p.G158V|DIDO1_uc002ydw.1_Missense_Mutation_p.G158V|DIDO1_uc002ydx.1_Missense_Mutation_p.G158V|DIDO1_uc011aao.1_Missense_Mutation_p.G158V	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	158					apoptosis	cytoplasm|nucleus	zinc ion binding			ovary(3)	3	Breast(26;5.68e-08)					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)								0.71831	161.641093	164.679961	51	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61542492	61542492	4701	20	C	A	A	A	338	26	DIDO1	2	2
COL20A1	57642	broad.mit.edu	37	20	61950436	61950436	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61950436C>A	uc011aau.1	+	c.2690C>A	c.(2689-2691)CCA>CAA	p.P897Q	COL20A1_uc011aav.1_Missense_Mutation_p.P718Q	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	897	TSP N-terminal.				cell adhesion	collagen|extracellular space	structural molecule activity				0	all_cancers(38;1.39e-10)													0.428571	34.986294	35.112457	12	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61950436	61950436	3817	20	C	A	A	A	273	21	COL20A1	2	2
GMEB2	26205	broad.mit.edu	37	20	62226975	62226975	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62226975C>A	uc002yfp.1	-	c.607G>T	c.(607-609)GCC>TCC	p.A203S	GMEB2_uc002yfo.1_Missense_Mutation_p.A125S|GMEB2_uc002yfq.1_Missense_Mutation_p.A203S	NM_012384	NP_036516	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding	203					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding|RNA polymerase II transcription factor activity				0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)											0.4375	18.318421	18.373464	7	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62226975	62226975	6757	20	C	A	A	A	351	27	GMEB2	1	1
SAMD10	140700	broad.mit.edu	37	20	62608630	62608630	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62608630G>A	uc002yhm.2	-	c.221C>T	c.(220-222)GCC>GTC	p.A74V	SAMD10_uc002yhn.2_Non-coding_Transcript	NM_080621	NP_542188	Q9BYL1	SAM10_HUMAN	sterile alpha motif domain containing 10	74											0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)													0.41791	81.828693	82.211135	28	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62608630	62608630	14295	20	G	A	A	A	546	42	SAMD10	2	2
USP25	29761	broad.mit.edu	37	21	17202921	17202921	+	Splice_Site_SNP	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:17202921G>A	uc011aby.1	+	c.1764_splice	c.e15+1	p.Q588_splice	USP25_uc002yjy.1_Splice_Site_SNP_p.Q588_splice|USP25_uc002yjz.1_Splice_Site_SNP_p.Q588_splice|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)										0.516129	50.001133	50.008227	16	15	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	17202921	17202921	17619	21	G	A	A	A	468	36	USP25	5	2
RNF160	26046	broad.mit.edu	37	21	30308959	30308959	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:30308959G>C	uc002ymr.2	-	c.4681C>G	c.(4681-4683)CAC>GAC	p.H1561D		NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	1515							ligase activity|zinc ion binding				0														0.12253	49.875149	85.196583	31	222	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30308959	30308959	13932	21	G	C	C	C	585	45	RNF160	3	3
CLDN14	23562	broad.mit.edu	37	21	37833476	37833476	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:37833476A>T	uc002yvk.1	-	c.518T>A	c.(517-519)CTC>CAC	p.L173H	CLDN14_uc002yvn.1_Missense_Mutation_p.L173H|CLDN14_uc002yvo.1_Missense_Mutation_p.L173H|CLDN14_uc002yvl.1_Missense_Mutation_p.L173H|CLDN14_uc002yvm.1_Missense_Mutation_p.L173H	NM_012130	NP_036262	O95500	CLD14_HUMAN	claudin 14	173	Helical; (Potential).				calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0														0.804878	95.642378	99.176173	33	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37833476	37833476	3611	21	A	T	T	T	143	11	CLDN14	3	3
DSCR6	53820	broad.mit.edu	37	21	38380502	38380502	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:38380502G>T	uc002yvv.2	+	c.150G>T	c.(148-150)GAG>GAT	p.E50D	DSCR6_uc011aec.1_5'UTR|DSCR6_uc010gnd.2_5'UTR	NM_018962	NP_061835	P57055	DSCR6_HUMAN	Down syndrome critical region protein 6	50						nucleus				breast(1)	1		Myeloproliferative disorder(46;0.0632)				Colon(134;194 1731 2725 51652 51982)								0.8	53.510285	55.183885	16	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38380502	38380502	4957	21	G	T	T	T	438	34	DSCR6	2	2
C21orf33	8209	broad.mit.edu	37	21	45563153	45563153	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45563153C>G	uc002zec.3	+	c.588C>G	c.(586-588)CAC>CAG	p.H196Q	C21orf33_uc002zed.3_Missense_Mutation_p.H165Q	NM_004649	NP_004640	P30042	ES1_HUMAN	es1 protein isoform Ia precursor	196						mitochondrion				ovary(1)	1				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)										0.181818	13.295017	16.385162	6	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45563153	45563153	2205	21	C	G	G	G	246	19	C21orf33	3	3
GAB4	128954	broad.mit.edu	37	22	17444635	17444635	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:17444635G>T	uc002zlw.2	-	c.1561C>A	c.(1561-1563)CTG>ATG	p.L521M		NM_001037814	NP_001032903	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member	521										large_intestine(1)|ovary(1)	2		all_epithelial(15;0.112)|Lung NSC(13;0.248)												0.888889	24.566768	25.844927	8	1	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17444635	17444635	6402	22	G	T	T	T	451	35	GAB4	2	2
ASCC2	84164	broad.mit.edu	37	22	30221692	30221692	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30221692C>A	uc003agr.2	-	c.159G>T	c.(157-159)GAG>GAT	p.E53D	ASCC2_uc003ags.2_Non-coding_Transcript|ASCC2_uc003agt.2_Missense_Mutation_p.E53D|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit	53					regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)											0.538462	109.728051	109.811669	35	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30221692	30221692	1050	22	C	A	A	A	311	24	ASCC2	2	2
APOL2	23780	broad.mit.edu	37	22	36629211	36629211	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36629211T>A	uc011amm.1	-	c.334A>T	c.(334-336)ACC>TCC	p.T112S	APOL2_uc003aoz.2_5'UTR|APOL2_uc003apa.2_5'UTR	NM_145637	NP_663612	Q9BQE5	APOL2_HUMAN	apolipoprotein L2	Error:Variant_position_missing_in_Q9BQE5_after_alignment					acute-phase response|cholesterol metabolic process|lipid transport|lipoprotein metabolic process|maternal process involved in female pregnancy|multicellular organismal development	endoplasmic reticulum membrane|extracellular region	high-density lipoprotein particle binding|lipid binding|receptor binding				0														0.61039	160.947661	161.773391	47	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36629211	36629211	817	22	T	A	A	A	755	59	APOL2	3	3
SELO	83642	broad.mit.edu	37	22	50646965	50646965	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50646965G>T	uc011arr.1	+	c.759G>T	c.(757-759)AGG>AGT	p.R253S	SELO_uc010hap.2_Missense_Mutation_p.R64S|SELO_uc003bjy.2_5'UTR|SELO_uc003bjz.2_5'Flank	NM_031454	NP_113642	Q9BVL4	SELO_HUMAN	selenoprotein O	253				R -> RGWGQVWPVDASGLPSR (in Ref. 3; AAH20510).							0		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)										0.357143	28.649334	29.149431	10	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50646965	50646965	14504	22	G	T	T	T	568	44	SELO	2	2
CNTNAP5	129684	broad.mit.edu	37	2	125281892	125281892	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125281892A>T	uc010flu.2	+	c.1340A>T	c.(1339-1341)AAT>ATT	p.N447I	CNTNAP5_uc002tno.2_Missense_Mutation_p.N446I	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	446	Laminin G-like 2.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.55814	77.301497	77.428122	24	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125281892	125281892	3788	2	A	T	T	T	52	4	CNTNAP5	3	3
UGGT1	56886	broad.mit.edu	37	2	128855128	128855128	+	Missense_Mutation	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128855128T>G	uc002tps.2	+	c.184T>G	c.(184-186)TTA>GTA	p.L62V	UGGT1_uc010fme.1_Missense_Mutation_p.V8G|UGGT1_uc002tpr.2_Missense_Mutation_p.L38V	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	62					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1														0.39726	89.156751	89.859982	29	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128855128	128855128	17499	2	T	G	G	G	777	60	UGGT1	4	4
TUBA3D	113457	broad.mit.edu	37	2	132235885	132235885	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:132235885C>A	uc002tsu.3	+	c.152C>A	c.(151-153)ACG>AAG	p.T51K		NM_080386	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	51					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)		Ovarian(137;2059 2432 35543 39401)								0.307692	35.491299	36.773714	12	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132235885	132235885	17302	2	C	A	A	A	247	19	TUBA3D	1	1
TUBA3D	113457	broad.mit.edu	37	2	132238318	132238318	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:132238318T>A	uc002tsu.3	+	c.1052T>A	c.(1051-1053)TTT>TAT	p.F351Y		NM_080386	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	351					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)		Ovarian(137;2059 2432 35543 39401)								0.157895	16.338586	22.699738	9	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132238318	132238318	17302	2	T	A	A	A	832	64	TUBA3D	3	3
LRP1B	53353	broad.mit.edu	37	2	141032006	141032006	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141032006C>A	uc002tvj.1	-	c.13129G>T	c.(13129-13131)GAT>TAT	p.D4377Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4377	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)			p.D4377Y(MEWO-Tumor)	2546	TSP Lung(27;0.18)			0.145833	10.692849	16.483124	7	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141032006	141032006	9328	2	C	A	A	A	416	32	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141108485	141108485	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141108485C>A	uc002tvj.1	-	c.11773G>T	c.(11773-11775)GGG>TGG	p.G3925W		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3925	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.259259	51.025997	55.29109	21	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141108485	141108485	9328	2	C	A	A	A	312	24	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141294231	141294231	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141294231C>A	uc002tvj.1	-	c.7561G>T	c.(7561-7563)GGT>TGT	p.G2521C		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2521	Extracellular (Potential).|LDL-receptor class A 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.320755	47.987749	49.483994	17	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141294231	141294231	9328	2	C	A	A	A	273	21	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141707803	141707803	+	Splice_Site_SNP	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141707803C>T	uc002tvj.1	-	c.3136_splice	c.e20+1	p.E1046_splice	LRP1B_uc010fnl.1_Splice_Site_SNP_p.E228_splice	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.3	16.742076	17.456885	6	14	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	141707803	141707803	9328	2	C	T	T	T	234	18	LRP1B	5	2
NR4A2	4929	broad.mit.edu	37	2	157184934	157184934	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:157184934C>A	uc002tyz.3	-	c.976G>T	c.(976-978)GTT>TTT	p.V326F	NR4A2_uc002tyx.3_Missense_Mutation_p.V263F|NR4A2_uc010zcf.1_Missense_Mutation_p.V326F|NR4A2_uc010zcg.1_5'Flank	NM_006186	NP_006177	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	326	Nuclear receptor.				cellular response to extracellular stimulus|dopaminergic neuron differentiation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus	nucleoplasm	sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3														0.339623	51.449011	52.646726	18	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157184934	157184934	11038	2	C	A	A	A	221	17	NR4A2	2	2
FAP	2191	broad.mit.edu	37	2	163075642	163075642	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:163075642G>T	uc002ucd.2	-	c.538C>A	c.(538-540)CCT>ACT	p.P180T	FAP_uc010zct.1_Missense_Mutation_p.P155T|FAP_uc010fpd.2_Intron|FAP_uc010fpe.1_Missense_Mutation_p.P147T	NM_004460	NP_004451	Q12884	SEPR_HUMAN	fibroblast activation protein, alpha subunit	180	Extracellular (Potential).				endothelial cell migration|negative regulation of extracellular matrix disassembly|proteolysis	cell junction|integral to membrane|invadopodium membrane|lamellipodium membrane	dipeptidyl-peptidase activity|metalloendopeptidase activity|protein homodimerization activity|serine-type endopeptidase activity			ovary(3)	3														0.477612	94.897578	94.918152	32	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	163075642	163075642	5909	2	G	T	T	T	572	44	FAP	2	2
KCNH7	90134	broad.mit.edu	37	2	163361085	163361085	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:163361085A>T	uc002uch.1	-	c.996T>A	c.(994-996)ATT>ATA	p.I332I	KCNH7_uc002uci.2_Silent_p.I325I	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	332	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)	3					Ibutilide(DB00308)	GBM(196;1492 2208 17507 24132 45496)								0.442105	118.830721	119.108979	42	53	KEEP	---	---	---	---	capture		Silent	SNP	163361085	163361085	8342	2	A	T	T	T	112	9	KCNH7	3	3
SCN9A	6335	broad.mit.edu	37	2	167145088	167145088	+	Silent	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:167145088A>G	uc010fpl.2	-	c.1173T>C	c.(1171-1173)TTT>TTC	p.F391F	SCN9A_uc002udr.1_Silent_p.F262F|SCN9A_uc002uds.1_Silent_p.F262F|SCN9A_uc002udt.1_Silent_p.F262F	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	391	I.|Helical; Name=S6 of repeat I; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.411765	67.10388	67.464679	21	30	KEEP	---	---	---	---	capture		Silent	SNP	167145088	167145088	14407	2	A	G	G	G	11	1	SCN9A	4	4
CHRNA1	1134	broad.mit.edu	37	2	175622695	175622695	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:175622695C>T	uc002ujd.2	-	c.288G>A	c.(286-288)TTG>TTA	p.L96L	CHRNA1_uc002uje.2_Intron|CHRNA1_uc002ujf.3_Intron	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a	96	Extracellular.				muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)	3														0.444444	36.696379	36.768992	12	15	KEEP	---	---	---	---	capture		Silent	SNP	175622695	175622695	3515	2	C	T	T	T	220	17	CHRNA1	2	2
CHN1	1123	broad.mit.edu	37	2	175742647	175742647	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:175742647T>C	uc002uji.2	-	c.470A>G	c.(469-471)TAC>TGC	p.Y157C	CHN1_uc010zeq.1_Missense_Mutation_p.Y157C|CHN1_uc002ujj.2_Intron	NM_001822	NP_001813	P15882	CHIN_HUMAN	chimerin (chimaerin) 1 isoform a	157					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)							265				0.45	153.767333	153.984204	45	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175742647	175742647	3496	2	T	C	C	C	741	57	CHN1	4	4
TTN	7273	broad.mit.edu	37	2	179423169	179423169	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179423169C>T	uc010zfg.1	-	c.79313G>A	c.(79312-79314)AGA>AAA	p.R26438K	TTN_uc010zfh.1_Missense_Mutation_p.R20133K|TTN_uc010zfi.1_Missense_Mutation_p.R20066K|TTN_uc010zfj.1_Missense_Mutation_p.R19941K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3211										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				0.386364	50.217134	50.729679	17	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179423169	179423169	17290	2	C	T	T	T	416	32	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179553472	179553472	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179553472T>C	uc010zfg.1	-	c.28397A>G	c.(28396-28398)AAG>AGG	p.K9466R	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.K6127R|TTN_uc010fre.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	800										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				0.396226	71.063626	71.563212	21	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179553472	179553472	17290	2	T	C	C	C	728	56	TTN	4	4
TTN	7273	broad.mit.edu	37	2	179579124	179579124	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179579124T>C	uc010zfg.1	-	c.22645A>G	c.(22645-22647)ACC>GCC	p.T7549A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.T4210A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3480										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				0.175676	28.682472	36.107018	13	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179579124	179579124	17290	2	T	C	C	C	780	60	TTN	4	4
DNAH7	56171	broad.mit.edu	37	2	196698983	196698983	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:196698983C>G	uc002utj.3	-	c.9047G>C	c.(9046-9048)AGT>ACT	p.S3016T		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3016	AAA 5 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(2)	2														0.40678	79.493146	79.939851	24	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196698983	196698983	4789	2	C	G	G	G	260	20	DNAH7	3	3
PGAP1	80055	broad.mit.edu	37	2	197708759	197708759	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:197708759T>C	uc002utw.2	-	c.2378A>G	c.(2377-2379)CAT>CGT	p.H793R	PGAP1_uc002utx.2_Missense_Mutation_p.H619R|PGAP1_uc010fsi.2_Missense_Mutation_p.H67R	NM_024989	NP_079265	Q75T13	PGAP1_HUMAN	GPI deacylase	793	Cytoplasmic (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4														0.348837	37.117312	37.981709	15	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197708759	197708759	12200	2	T	C	C	C	663	51	PGAP1	4	4
BZW1	9689	broad.mit.edu	37	2	201683039	201683039	+	Nonsense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:201683039C>T	uc010zhg.1	+	c.838C>T	c.(838-840)CAG>TAG	p.Q280*	BZW1_uc002uwc.2_Nonsense_Mutation_p.Q248*|BZW1_uc010zhh.1_Nonsense_Mutation_p.Q248*	NM_014670	NP_055485	Q7L1Q6	BZW1_HUMAN	basic leucine zipper and W2 domains 1	248	W2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	protein binding				0														0.439024	54.730025	54.864922	18	23	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	201683039	201683039	1612	2	C	T	T	T	377	29	BZW1	5	2
ALS2	57679	broad.mit.edu	37	2	202582933	202582933	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:202582933C>A	uc002uyo.2	-	c.3703G>T	c.(3703-3705)GGA>TGA	p.G1235*	ALS2_uc010ftl.2_Non-coding_Transcript	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	1235	MORN 8.				cell death|endosome organization|positive regulation of Rac GTPase activity|positive regulation of Rac protein signal transduction|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(4)|lung(1)|breast(1)	6										498				0.32	43.142723	44.551259	16	34	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	202582933	202582933	553	2	C	A	A	A	286	22	ALS2	5	2
HS1BP3	64342	broad.mit.edu	37	2	20818972	20818972	+	Silent	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:20818972C>A	uc002rdw.1	-	c.954G>T	c.(952-954)CTG>CTT	p.L318L		NM_022460	NP_071905	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	318					cell communication		phosphatidylinositol binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.516129	47.295445	47.302277	16	15	KEEP	---	---	---	---	capture		Silent	SNP	20818972	20818972	7655	2	C	A	A	A	262	21	HS1BP3	2	2
DOCK10	55619	broad.mit.edu	37	2	225635348	225635348	+	Silent	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:225635348T>A	uc010fwz.1	-	c.6219A>T	c.(6217-6219)CCA>CCT	p.P2073P	DOCK10_uc002vob.2_Silent_p.P2067P|DOCK10_uc002voa.2_Silent_p.P729P	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2073	DHR-2.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)										0.368421	67.561841	68.428654	21	36	KEEP	---	---	---	---	capture		Silent	SNP	225635348	225635348	4869	2	T	A	A	A	808	63	DOCK10	3	3
COL4A4	1286	broad.mit.edu	37	2	227924926	227924926	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:227924926G>T	uc010zlt.1	-	c.2090C>A	c.(2089-2091)CCT>CAT	p.P697H		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	697	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|breast(1)|pancreas(1)	10		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)										0.373737	104.230906	105.623457	37	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	227924926	227924926	3831	2	G	T	T	T	455	35	COL4A4	2	2
TM4SF20	79853	broad.mit.edu	37	2	228235653	228235653	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228235653G>A	uc002vpb.2	-	c.227C>T	c.(226-228)GCG>GTG	p.A76V		NM_024795	NP_079071	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	76	Cytoplasmic (Potential).					integral to membrane|plasma membrane					0		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)										0.327684	296.752916	306.089666	116	238	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228235653	228235653	16499	2	G	A	A	A	494	38	TM4SF20	1	1
KIF1A	547	broad.mit.edu	37	2	241697805	241697805	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241697805G>T	uc010fzk.2	-	c.2554C>A	c.(2554-2556)CGC>AGC	p.R852S	KIF1A_uc002vzy.2_Missense_Mutation_p.R843S|KIF1A_uc002vzz.1_Missense_Mutation_p.R852S	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	843					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)										0.481481	40.17476	40.18271	13	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241697805	241697805	8594	2	G	T	T	T	507	39	KIF1A	1	1
C2orf44	80304	broad.mit.edu	37	2	24261821	24261821	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:24261821A>C	uc002rep.2	-	c.544T>G	c.(544-546)TAT>GAT	p.Y182D	C2orf44_uc010eya.2_Missense_Mutation_p.Y182D	NM_025203	NP_079479	Q9H6R7	CB044_HUMAN	hypothetical protein LOC80304 isoform 1	182	WD 2.						protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.255814	32.906189	35.230331	11	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24261821	24261821	2256	2	A	C	C	C	169	13	C2orf44	4	4
TSSC1	7260	broad.mit.edu	37	2	3196338	3196338	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:3196338C>A	uc002qxj.2	-	c.836G>T	c.(835-837)CGC>CTC	p.R279L	TSSC1_uc002qxi.2_Non-coding_Transcript	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	279	WD 4.						protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		Colon(140;1261 1762 4183 34270 49743)								0.363636	47.573365	48.298454	16	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3196338	3196338	17219	2	C	A	A	A	351	27	TSSC1	1	1
BIRC6	57448	broad.mit.edu	37	2	32640830	32640830	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32640830A>G	uc010ezu.2	+	c.2471A>G	c.(2470-2472)TAT>TGT	p.Y824C		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	824					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.53125	50.535101	50.55986	17	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32640830	32640830	1463	2	A	G	G	G	208	16	BIRC6	4	4
PRKD3	23683	broad.mit.edu	37	2	37513418	37513418	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:37513418G>T	uc002rqd.2	-	c.812C>A	c.(811-813)CCA>CAA	p.P271Q	PRKD3_uc002rqf.1_Missense_Mutation_p.P271Q	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	271	Phorbol-ester/DAG-type 2.				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)				569				0.210526	17.175761	20.126676	8	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37513418	37513418	12963	2	G	T	T	T	611	47	PRKD3	2	2
ABCG5	64240	broad.mit.edu	37	2	44053560	44053560	+	Silent	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44053560C>A	uc002rtn.2	-	c.735G>T	c.(733-735)GTG>GTT	p.V245V	ABCG5_uc002rtm.2_Intron|ABCG5_uc002rto.2_Intron|ABCG5_uc002rtp.2_Intron	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5	245	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|intestinal cholesterol absorption|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.345455	54.61176	55.770116	19	36	KEEP	---	---	---	---	capture		Silent	SNP	44053560	44053560	72	2	C	A	A	A	262	21	ABCG5	2	2
PLEK	5341	broad.mit.edu	37	2	68607461	68607461	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:68607461G>C	uc002sen.3	+	c.44G>C	c.(43-45)GGG>GCG	p.G15A	PLEK_uc010fde.2_Missense_Mutation_p.G15A	NM_002664	NP_002655	P08567	PLEK_HUMAN	pleckstrin	15	PH 1.				actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding			ovary(1)	1		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)										0.5	51.510257	51.510257	16	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68607461	68607461	12479	2	G	C	C	C	559	43	PLEK	3	3
CLEC4F	165530	broad.mit.edu	37	2	71043795	71043796	+	Missense_Mutation	DNP	CC	AG	AG			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71043795_71043796CC>AG	uc002shf.2	-	c.717_718GG>CT	c.(715-720)CAGGCT>CACTCT	p.239_240QA>HS	CLEC4F_uc010yqv.1_Missense_Mutation_p.239_240QA>HS	NM_173535	NP_775806	Q8N1N0	CLC4F_HUMAN	C-type lectin, superfamily member 13	239_240	Extracellular (Potential).				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(5)	5						Colon(107;10 2157 6841 26035)								0.622951	122.69031	123.527553	38	23	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	71043795	71043796	3654	2	CC	AG	AG	AG	338	26	CLEC4F	2	2
ZNF638	27332	broad.mit.edu	37	2	71590292	71590292	+	Silent	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71590292T>C	uc002shx.2	+	c.1389T>C	c.(1387-1389)GAT>GAC	p.D463D	ZNF638_uc010fec.2_Silent_p.D569D|ZNF638_uc010yqw.1_Silent_p.D42D|ZNF638_uc002shw.2_Silent_p.D463D|ZNF638_uc002shy.2_Silent_p.D463D|ZNF638_uc002shz.2_Silent_p.D463D|ZNF638_uc002sia.2_Silent_p.D463D|ZNF638_uc002sib.1_Silent_p.D463D|ZNF638_uc010fed.2_5'Flank	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	463					RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)	3														0.4	49.145575	49.450937	14	21	KEEP	---	---	---	---	capture		Silent	SNP	71590292	71590292	18650	2	T	C	C	C	673	52	ZNF638	4	4
DYSF	8291	broad.mit.edu	37	2	71741006	71741006	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71741006G>T	uc010fen.2	+	c.714G>T	c.(712-714)GCG>GCT	p.A238A	DYSF_uc010feg.2_Silent_p.A237A|DYSF_uc010feh.2_Silent_p.A206A|DYSF_uc002sig.3_Silent_p.A206A|DYSF_uc010yqx.1_Non-coding_Transcript|DYSF_uc010fee.2_Silent_p.A206A|DYSF_uc010fef.2_Silent_p.A237A|DYSF_uc002sie.2_Silent_p.A206A|DYSF_uc010fei.2_Silent_p.A237A|DYSF_uc010fek.2_Silent_p.A238A|DYSF_uc010fej.2_Silent_p.A207A|DYSF_uc010fel.2_Silent_p.A207A|DYSF_uc010feo.2_Silent_p.A238A|DYSF_uc010fem.2_Silent_p.A207A|DYSF_uc002sif.2_Silent_p.A207A	NM_001130987	NP_001124459	O75923	DYSF_HUMAN	dysferlin isoform 1	206	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.470588	46.039665	46.06837	16	18	KEEP	---	---	---	---	capture		Silent	SNP	71741006	71741006	5045	2	G	T	T	T	483	38	DYSF	1	1
CYP26B1	56603	broad.mit.edu	37	2	72360229	72360229	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:72360229C>T	uc002sih.1	-	c.1069G>A	c.(1069-1071)GTC>ATC	p.V357I	CYP26B1_uc010yra.1_Missense_Mutation_p.V340I|CYP26B1_uc010yrb.1_Missense_Mutation_p.V282I	NM_019885	NP_063938	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily b,	357					cell fate determination|embryonic limb morphogenesis|male meiosis|negative regulation of retinoic acid receptor signaling pathway|oxidation-reduction process|proximal/distal pattern formation|retinoic acid catabolic process|spermatogenesis|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding				0														0.170732	13.240661	17.412911	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72360229	72360229	4321	2	C	T	T	T	247	19	CYP26B1	1	1
SLC4A5	57835	broad.mit.edu	37	2	74491340	74491340	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74491340G>A	uc002sko.1	-	c.649C>T	c.(649-651)CGC>TGC	p.R217C	SLC4A5_uc002skl.2_Non-coding_Transcript|SLC4A5_uc002skn.2_Missense_Mutation_p.R217C|SLC4A5_uc010ffc.1_Missense_Mutation_p.R217C|SLC4A5_uc002skp.1_Missense_Mutation_p.R153C|SLC4A5_uc002sks.1_Missense_Mutation_p.R217C	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a	217	Cytoplasmic (Potential).					apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity	p.R217C(1)		ovary(5)|central_nervous_system(1)|skin(1)	7														0.170732	13.852999	18.014943	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74491340	74491340	15154	2	G	A	A	A	507	39	SLC4A5	1	1
SEMA4F	10505	broad.mit.edu	37	2	74902162	74902162	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74902162G>T	uc002sna.1	+	c.1149G>T	c.(1147-1149)GAG>GAT	p.E383D	SEMA4F_uc010ffq.1_Missense_Mutation_p.E350D|SEMA4F_uc010ffr.1_5'UTR|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Missense_Mutation_p.E228D	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor	383	Sema.|Extracellular (Potential).				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)	3												OREG0014721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.533333	76.601918	76.645316	24	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74902162	74902162	14521	2	G	T	T	T	451	35	SEMA4F	2	2
REG1B	5968	broad.mit.edu	37	2	79313628	79313628	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:79313628G>T	uc002sny.2	-	c.186C>A	c.(184-186)CTC>CTA	p.L62L	REG1B_uc010ffv.1_Silent_p.L62L|REG1B_uc010ffw.2_3'UTR	NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor	62	C-type lectin.				cell proliferation	extracellular region	sugar binding			central_nervous_system(1)	1														0.389474	101.239384	102.25935	37	58	KEEP	---	---	---	---	capture		Silent	SNP	79313628	79313628	13680	2	G	T	T	T	418	33	REG1B	2	2
C2orf51	200523	broad.mit.edu	37	2	88828634	88828634	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:88828634C>A	uc002stb.1	+	c.185C>A	c.(184-186)CCC>CAC	p.P62H		NM_152670	NP_689883	Q96LM6	TSC21_HUMAN	chromosome 2 open reading frame 51	62						nucleus					0														0.217391	22.524684	25.912805	10	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88828634	88828634	2261	2	C	A	A	A	286	22	C2orf51	2	2
SNRNP200	23020	broad.mit.edu	37	2	96943347	96943347	+	Nonsense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:96943347C>T	uc002svu.2	-	c.5861G>A	c.(5860-5862)TGG>TAG	p.W1954*	SNRNP200_uc002svt.2_Nonsense_Mutation_p.W564*|SNRNP200_uc010yuj.1_Non-coding_Transcript	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1954	SEC63 2.				cis assembly of pre-catalytic spliceosome|response to stimulus|visual perception	catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|large_intestine(1)|skin(1)	7														0.377049	70.83549	71.634844	23	38	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	96943347	96943347	15352	2	C	T	T	T	273	21	SNRNP200	5	2
C3orf24	115795	broad.mit.edu	37	3	10146346	10146346	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10146346C>G	uc003buz.2	-	c.113G>C	c.(112-114)TGC>TCC	p.C38S	C3orf24_uc003bva.1_Missense_Mutation_p.C38S	NM_173472	NP_775743	Q96PS1	CC024_HUMAN	hypothetical protein LOC115795	38											0				OV - Ovarian serous cystadenocarcinoma(96;0.196)						5				0.648649	80.305001	81.024597	24	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10146346	10146346	2310	3	C	G	G	G	325	25	C3orf24	3	3
BBX	56987	broad.mit.edu	37	3	107491504	107491504	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:107491504G>T	uc010hpr.2	+	c.936G>T	c.(934-936)ATG>ATT	p.M312I	BBX_uc003dwk.3_Missense_Mutation_p.M312I|BBX_uc003dwl.3_Intron|BBX_uc010hps.1_Missense_Mutation_p.M333I|BBX_uc003dwm.3_Missense_Mutation_p.M312I|BBX_uc003dwo.3_5'Flank	NM_001142568	NP_001136040	Q8WY36	BBX_HUMAN	HMG-BOX transcription factor BBX isoform 1	312					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)	3			OV - Ovarian serous cystadenocarcinoma(3;0.112)											0.384615	71.729183	72.497025	25	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107491504	107491504	1364	3	G	T	T	T	611	47	BBX	2	2
SLC9A10	285335	broad.mit.edu	37	3	111927123	111927123	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:111927123T>A	uc003dyu.2	-	c.1888A>T	c.(1888-1890)ATC>TTC	p.I630F	SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Missense_Mutation_p.I582F	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	630	Helical; (Potential).|Ion transport-like.				cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5														0.431694	242.095239	242.835508	79	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111927123	111927123	15207	3	T	A	A	A	676	52	SLC9A10	3	3
CCDC80	151887	broad.mit.edu	37	3	112356904	112356904	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112356904C>A	uc003dzf.2	-	c.1849G>T	c.(1849-1851)GGG>TGG	p.G617W	CCDC80_uc011bhv.1_Missense_Mutation_p.G617W|CCDC80_uc003dzg.2_Missense_Mutation_p.G617W|CCDC80_uc003dzh.1_Missense_Mutation_p.G617W	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	617										ovary(2)	2														0.406542	254.30457	255.930441	87	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112356904	112356904	2978	3	C	A	A	A	286	22	CCDC80	2	2
SEC22A	26984	broad.mit.edu	37	3	122928165	122928165	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122928165G>C	uc003ege.2	+	c.101G>C	c.(100-102)AGA>ACA	p.R34T	SEC22A_uc003egf.2_Missense_Mutation_p.R34T	NM_012430	NP_036562	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A	34	Cytoplasmic (Potential).|Longin.				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)										0.141026	20.066776	29.778177	11	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122928165	122928165	14474	3	G	C	C	C	429	33	SEC22A	3	3
ADCY5	111	broad.mit.edu	37	3	123003553	123003553	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123003553C>T	uc003egh.1	-	c.3688G>A	c.(3688-3690)GCC>ACC	p.A1230T	ADCY5_uc003egg.1_Missense_Mutation_p.A888T	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	1230	Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)										0.118056	15.465686	36.133019	17	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123003553	123003553	298	3	C	T	T	T	325	25	ADCY5	2	2
IFT122	55764	broad.mit.edu	37	3	129185898	129185898	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:129185898G>T	uc003eml.2	+	c.882G>T	c.(880-882)AGG>AGT	p.R294S	IFT122_uc003emm.2_Missense_Mutation_p.R243S|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Missense_Mutation_p.R93S|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_Intron	NM_052985	NP_443711	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 1	243					camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)	1														0.276596	32.556239	34.667208	13	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129185898	129185898	7856	3	G	T	T	T	555	43	IFT122	2	2
NEK11	79858	broad.mit.edu	37	3	130992400	130992400	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130992400A>T	uc003eny.2	+	c.1700A>T	c.(1699-1701)AAG>ATG	p.K567M	NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Missense_Mutation_p.K385M|NEK11_uc010htn.2_Non-coding_Transcript|NEK11_uc011blk.1_Missense_Mutation_p.K383M|NEK11_uc011bll.1_Missense_Mutation_p.K462M	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1	567					cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade|protein phosphorylation	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|central_nervous_system(1)	5										271				0.636364	68.982634	69.522146	21	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130992400	130992400	10722	3	A	T	T	T	39	3	NEK11	3	3
DNAJC13	23317	broad.mit.edu	37	3	132169588	132169588	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:132169588A>C	uc003eor.2	+	c.434A>C	c.(433-435)AAC>ACC	p.N145T	DNAJC13_uc010htq.1_Missense_Mutation_p.N145T	NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	145							heat shock protein binding			breast(1)	1														0.571429	150.54266	150.896641	44	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132169588	132169588	4815	3	A	C	C	C	26	2	DNAJC13	4	4
STAG1	10274	broad.mit.edu	37	3	136240070	136240070	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:136240070T>C	uc003era.1	-	c.661A>G	c.(661-663)ACA>GCA	p.T221A	STAG1_uc003erb.1_Missense_Mutation_p.T221A|STAG1_uc003erc.1_De_novo_Start_OutOfFrame|STAG1_uc010hua.1_Missense_Mutation_p.T84A|STAG1_uc003erd.2_Missense_Mutation_p.T124A|STAG1_uc003ere.2_Missense_Mutation_p.T221A	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	221					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2														0.19697	32.94978	38.586317	13	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136240070	136240070	15760	3	T	C	C	C	741	57	STAG1	4	4
CLSTN2	64084	broad.mit.edu	37	3	140282871	140282871	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:140282871G>T	uc003etn.2	+	c.2551G>T	c.(2551-2553)GGT>TGT	p.G851C		NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	851	Helical; (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						GBM(45;858 913 3709 36904 37282)								0.185185	61.969726	77.018714	30	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140282871	140282871	3700	3	G	T	T	T	559	43	CLSTN2	2	2
MED12L	116931	broad.mit.edu	37	3	151105632	151105633	+	Missense_Mutation	DNP	CG	TT	TT			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151105632_151105633CG>TT	uc003eyp.2	+	c.5018_5019CG>TT	c.(5017-5019)CCG>CTT	p.P1673L	MED12L_uc011bnz.1_Missense_Mutation_p.P1533L|MED12L_uc003eyy.1_Missense_Mutation_p.P836L	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1673					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	RNA polymerase II transcription mediator activity			ovary(4)|large_intestine(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)							59				0.510638	78.407985	78.413006	24	23	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	151105632	151105633	9818	3	CG	TT	TT	TT	299	23	MED12L	1	1
SLITRK3	22865	broad.mit.edu	37	3	164906953	164906953	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164906953G>A	uc003fej.3	-	c.1666C>T	c.(1666-1668)CAG>TAG	p.Q556*	SLITRK3_uc003fek.2_Nonsense_Mutation_p.Q556*	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	556	Extracellular (Potential).					integral to membrane				ovary(6)|pancreas(1)	7														0.634615	114.388368	115.216898	33	19	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	164906953	164906953	15242	3	G	A	A	A	611	47	SLITRK3	5	2
SAMD7	344658	broad.mit.edu	37	3	169644740	169644740	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:169644740A>T	uc003fgd.2	+	c.690A>T	c.(688-690)GAA>GAT	p.E230D	SAMD7_uc003fge.2_Missense_Mutation_p.E230D|SAMD7_uc011bpo.1_Missense_Mutation_p.E131D	NM_182610	NP_872416	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	230										skin(1)	1	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)											0.232143	29.477658	33.136336	13	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169644740	169644740	14304	3	A	T	T	T	37	3	SAMD7	3	3
PLCL2	23228	broad.mit.edu	37	3	17051999	17051999	+	Silent	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:17051999A>G	uc011awc.1	+	c.1137A>G	c.(1135-1137)AAA>AAG	p.K379K	PLCL2_uc010het.1_Intron|PLCL2_uc011awd.1_Silent_p.K261K	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	387					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)	2														0.522727	77.925843	77.945604	23	21	KEEP	---	---	---	---	capture		Silent	SNP	17051999	17051999	12466	3	A	G	G	G	50	4	PLCL2	4	4
NLGN1	22871	broad.mit.edu	37	3	173993119	173993119	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:173993119G>A	uc003fio.1	+	c.661G>A	c.(661-663)GGC>AGC	p.G221S	NLGN1_uc010hww.1_Missense_Mutation_p.G261S|NLGN1_uc003fip.1_Missense_Mutation_p.G221S	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	238	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of excitatory postsynaptic membrane potential|regulation of N-methyl-D-aspartate selective glutamate receptor activity|regulation of synaptic transmission|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	carboxylesterase activity|cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	6	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)											0.57732	194.730381	195.241545	56	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173993119	173993119	10864	3	G	A	A	A	455	35	NLGN1	2	2
EIF4G1	1981	broad.mit.edu	37	3	184042135	184042135	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:184042135G>A	uc010hxx.2	+	c.2640G>A	c.(2638-2640)ACG>ACA	p.T880T	EIF4G1_uc003fno.1_Silent_p.T814T|EIF4G1_uc010hxw.1_Silent_p.T709T|EIF4G1_uc003fnp.2_Silent_p.T873T|EIF4G1_uc003fnt.2_Silent_p.T584T|EIF4G1_uc003fnq.2_Silent_p.T786T|EIF4G1_uc003fnr.2_Silent_p.T709T|EIF4G1_uc003fns.2_Silent_p.T833T|EIF4G1_uc010hxy.2_Silent_p.T880T|EIF4G1_uc003fnv.3_Silent_p.T874T|EIF4G1_uc003fnu.3_Silent_p.T873T|EIF4G1_uc003fnw.2_Silent_p.T880T|EIF4G1_uc003fnx.2_Silent_p.T678T|EIF4G1_uc003fny.3_Silent_p.T677T|SNORD66_uc003fnz.2_5'Flank	NM_004953	NP_004944	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	873	eIF3/EIF4A-binding.				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				0.177778	16.273308	20.67292	8	37	KEEP	---	---	---	---	capture		Silent	SNP	184042135	184042135	5227	3	G	A	A	A	496	39	EIF4G1	1	1
OSTN	344901	broad.mit.edu	37	3	190930341	190930341	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:190930341C>G	uc011bsn.1	+	c.20C>G	c.(19-21)GCA>GGA	p.A7G		NM_198184	NP_937827	P61366	OSTN_HUMAN	osteocrin precursor	7					cell differentiation|multicellular organismal development|ossification		hormone activity			pancreas(1)	1	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)										0.5	63.511315	63.511315	19	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190930341	190930341	11711	3	C	G	G	G	325	25	OSTN	3	3
ATP13A5	344905	broad.mit.edu	37	3	193023452	193023452	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:193023452C>G	uc011bsq.1	-	c.2574G>C	c.(2572-2574)TTG>TTC	p.L858F		NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5	858					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|large_intestine(2)	7	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)						699				0.2125	44.381706	50.463481	17	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	193023452	193023452	1146	3	C	G	G	G	376	29	ATP13A5	3	3
SCN11A	11280	broad.mit.edu	37	3	38908896	38908896	+	Silent	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38908896T>A	uc011ays.1	-	c.3867A>T	c.(3865-3867)GTA>GTT	p.V1289V		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	1289	Helical; Name=S6 of repeat III; (By similarity).|III.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)									0.641026	81.583851	82.266282	25	14	KEEP	---	---	---	---	capture		Silent	SNP	38908896	38908896	14395	3	T	A	A	A	678	53	SCN11A	3	3
TTC21A	199223	broad.mit.edu	37	3	39167012	39167012	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39167012T>C	uc003cje.2	+	c.1405T>C	c.(1405-1407)TGC>CGC	p.C469R	TTC21A_uc003cjc.2_Missense_Mutation_p.C469R|TTC21A_uc003cjd.2_Non-coding_Transcript|TTC21A_uc011ayx.1_Missense_Mutation_p.C420R	NM_001105513	NP_001098983	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 1	469							binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)										0.516667	84.803306	84.817103	31	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39167012	39167012	17241	3	T	C	C	C	715	55	TTC21A	4	4
CAV3	859	broad.mit.edu	37	3	8787303	8787303	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:8787303A>T	uc003bra.2	+	c.206A>T	c.(205-207)AAG>ATG	p.K69M	C3orf32_uc003bqz.2_5'Flank|CAV3_uc003brb.2_Missense_Mutation_p.K69M	NM_001234	NP_001225	P56539	CAV3_HUMAN	caveolin 3	69	Cytoplasmic (Potential).|Required for interaction with DAG1.				cell growth|elevation of cytosolic calcium ion concentration|muscle organ development|negative regulation of cardiac muscle hypertrophy|negative regulation of cell size|negative regulation of MAP kinase activity|negative regulation of sarcomere organization|positive regulation of microtubule polymerization|regulation of skeletal muscle contraction|regulation of ventricular cardiomyocyte membrane repolarization|T-tubule organization	caveola|dystrophin-associated glycoprotein complex|Golgi membrane|neuromuscular junction|T-tubule	protein C-terminus binding|protein complex binding|protein complex scaffold|sodium channel regulator activity				0														0.653846	50.256106	50.792885	17	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8787303	8787303	2814	3	A	T	T	T	39	3	CAV3	3	3
WDR1	9948	broad.mit.edu	37	4	10099383	10099383	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:10099383G>A	uc003gmf.2	-	c.510C>T	c.(508-510)TGC>TGT	p.C170C	WDR1_uc003gmg.2_Intron	NM_017491	NP_059830	O75083	WDR1_HUMAN	WD repeat-containing protein 1 isoform 1	170	WD 3.				platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)										0.7	44.855959	45.570209	14	6	KEEP	---	---	---	---	capture		Silent	SNP	10099383	10099383	17845	4	G	A	A	A	490	38	WDR1	1	1
LEF1	51176	broad.mit.edu	37	4	109002741	109002741	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109002741C>A	uc003hyt.1	-	c.722_splice	c.e6+1	p.R241_splice	LEF1_uc011cfj.1_Intron|LEF1_uc011cfk.1_Intron|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Splice_Site_SNP|LEF1_uc003hyw.1_5'Flank	NM_016269	NP_057353			lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of caspase activity|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of gene-specific transcription|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|promoter binding|transcription activator activity|transcription repressor activity			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)										0.533333	26.701077	26.715575	8	7	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	109002741	109002741	9038	4	C	A	A	A	234	18	LEF1	5	2
MAP9	79884	broad.mit.edu	37	4	156289877	156289877	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:156289877T>C	uc003ios.2	-	c.569A>G	c.(568-570)GAG>GGG	p.E190G	MAP9_uc011cin.1_Missense_Mutation_p.E189G|MAP9_uc010iqa.1_Non-coding_Transcript|MAP9_uc003iot.1_Missense_Mutation_p.E189G|MAP9_uc010iqb.1_Missense_Mutation_p.E117G	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein	190	Potential.				cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)										0.677966	146.018423	147.67712	40	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156289877	156289877	9653	4	T	C	C	C	702	54	MAP9	4	4
WWC2	80014	broad.mit.edu	37	4	184233492	184233492	+	Splice_Site_SNP	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:184233492A>T	uc010irx.2	+	c.3385_splice	c.e22-2	p.A1129_splice	WWC2_uc003ivk.3_Splice_Site_SNP_p.A924_splice|WWC2_uc003ivl.3_Splice_Site_SNP|WWC2_uc010iry.2_Splice_Site_SNP_p.A811_splice|WWC2_uc003ivn.3_Splice_Site_SNP_p.A644_splice|WWC2_uc010irz.2_Splice_Site_SNP_p.A470_splice|WWC2_uc003ivo.3_Splice_Site_SNP_p.A257_splice	NM_024949	NP_079225			WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)										0.583333	95.907664	96.198844	28	20	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	184233492	184233492	17986	4	A	T	T	T	91	7	WWC2	5	3
TUBB4Q	56604	broad.mit.edu	37	4	190904504	190904505	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:190904504_190904505GG>AT	uc011clg.1	-	c.475_476CC>AT	c.(475-477)CCA>ATA	p.P159I		NM_020040	NP_064424	Q99867	TBB4Q_HUMAN	tubulin, beta polypeptide 4, member Q	160					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;4.1e-31)|Epithelial(3;1.44e-30)|OV - Ovarian serous cystadenocarcinoma(60;2.03e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00839)|READ - Rectum adenocarcinoma(43;0.155)										0.484848	47.503926	47.51016	16	17	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	190904504	190904505	17314	4	GG	AT	AT	AT	611	47	TUBB4Q	2	2
POLN	353497	broad.mit.edu	37	4	2129883	2129883	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2129883C>G	uc003ger.2	-	c.1939G>C	c.(1939-1941)GAA>CAA	p.E647Q	POLN_uc010icg.1_Missense_Mutation_p.E95Q|POLN_uc010ich.1_Missense_Mutation_p.E179Q	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu	647					DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)											0.7	51.558027	52.272656	14	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2129883	2129883	12635	4	C	G	G	G	390	30	POLN	3	3
STIM2	57620	broad.mit.edu	37	4	27010119	27010119	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:27010119G>T	uc003gsh.3	+	c.1504G>T	c.(1504-1506)GAT>TAT	p.D502Y	STIM2_uc003gsg.3_Missense_Mutation_p.D494Y|STIM2_uc010iex.2_Missense_Mutation_p.D494Y|STIM2_uc010iey.2_Missense_Mutation_p.D118Y	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	407	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)	1		Breast(46;0.0503)												0.529412	27.174499	27.187191	9	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27010119	27010119	15804	4	G	T	T	T	429	33	STIM2	2	2
EPHA5	2044	broad.mit.edu	37	4	66467388	66467388	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:66467388C>G	uc011cah.1	-	c.881G>C	c.(880-882)GGA>GCA	p.G294A	EPHA5_uc003hcx.2_Missense_Mutation_p.G225A|EPHA5_uc003hcy.2_Missense_Mutation_p.G294A|EPHA5_uc003hcz.2_Missense_Mutation_p.G294A|EPHA5_uc011cai.1_Missense_Mutation_p.G294A|EPHA5_uc003hda.2_Missense_Mutation_p.G294A	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	294	Extracellular (Potential).|Cys-rich.				cAMP-mediated signaling|ephrin receptor signaling pathway|neuron development|protein phosphorylation	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(12)|ovary(2)|central_nervous_system(1)	15										537	TSP Lung(17;0.13)			0.458333	38.650838	38.682884	11	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66467388	66467388	5363	4	C	G	G	G	390	30	EPHA5	3	3
TMPRSS11B	132724	broad.mit.edu	37	4	69097043	69097043	+	Silent	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:69097043T>G	uc003hdw.3	-	c.564A>C	c.(562-564)GGA>GGC	p.G188G		NM_182502	NP_872308	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	188	Peptidase S1.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1														0.466667	24.72454	24.738981	7	8	KEEP	---	---	---	---	capture		Silent	SNP	69097043	69097043	16780	4	T	G	G	G	795	62	TMPRSS11B	4	4
MUC7	4589	broad.mit.edu	37	4	71347098	71347098	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71347098G>T	uc011cat.1	+	c.637G>T	c.(637-639)GCT>TCT	p.A213S	MUC7_uc011cau.1_Missense_Mutation_p.A213S|MUC7_uc003hfj.2_Missense_Mutation_p.A213S	NM_001145006	NP_001138478	Q8TAX7	MUC7_HUMAN	mucin 7, secreted precursor	213	3.|Thr-rich.					extracellular region	protein binding			ovary(2)|central_nervous_system(1)	3			Lung(101;0.211)											0.483333	77.595517	77.612717	29	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71347098	71347098	10375	4	G	T	T	T	442	34	MUC7	2	2
WDR36	134430	broad.mit.edu	37	5	110428264	110428264	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:110428264A>T	uc003kpd.2	+	c.278A>T	c.(277-279)AAG>ATG	p.K93M	WDR36_uc010jbu.2_Non-coding_Transcript	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	93					response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)	1		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)										0.641026	79.084999	79.769643	25	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110428264	110428264	17863	5	A	T	T	T	39	3	WDR36	3	3
TSSK1B	83942	broad.mit.edu	37	5	112770281	112770281	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112770281C>A	uc003kqm.2	-	c.256G>T	c.(256-258)GTC>TTC	p.V86F	MCC_uc003kql.3_Intron	NM_032028	NP_114417	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1	86	Protein kinase.				cell differentiation|multicellular organismal development|protein phosphorylation|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|skin(1)	3		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)						32				0.633333	61.230462	61.69904	19	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112770281	112770281	17221	5	C	A	A	A	234	18	TSSK1B	2	2
AQPEP	206338	broad.mit.edu	37	5	115350132	115350132	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:115350132A>C	uc003kro.2	+	c.2358A>C	c.(2356-2358)AAA>AAC	p.K786N	AQPEP_uc003krp.2_Non-coding_Transcript|AQPEP_uc003krq.2_Non-coding_Transcript|AQPEP_uc003krr.2_Non-coding_Transcript|AQPEP_uc003krs.2_Non-coding_Transcript	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	786	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0														0.382979	57.16872	57.721988	18	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115350132	115350132	845	5	A	C	C	C	24	2	AQPEP	4	4
DNAH5	1767	broad.mit.edu	37	5	13830206	13830206	+	Nonsense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:13830206T>A	uc003jfd.2	-	c.6178A>T	c.(6178-6180)AAA>TAA	p.K2060*		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2060	AAA 1 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.394366	84.3825	85.076512	28	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	13830206	13830206	4787	5	T	A	A	A	819	63	DNAH5	5	3
CXXC5	51523	broad.mit.edu	37	5	139060874	139060874	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:139060874G>A	uc010jfg.1	+	c.766G>A	c.(766-768)GGC>AGC	p.G256S	CXXC5_uc003let.2_Missense_Mutation_p.G256S	NM_016463	NP_057547	Q7LFL8	CXXC5_HUMAN	CXXC finger 5	256	CXXC-type.				positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|nucleus	DNA binding|signal transducer activity|zinc ion binding			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.720588	160.980918	163.958079	49	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139060874	139060874	4259	5	G	A	A	A	507	39	CXXC5	1	1
PCDHB14	56122	broad.mit.edu	37	5	140603219	140603219	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140603219C>G	uc003ljb.2	+	c.142C>G	c.(142-144)CTA>GTA	p.L48V	PCDHB14_uc011dal.1_Intron	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	48	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			Ovarian(141;50 1831 27899 33809 37648)								0.113208	8.34705	16.140125	6	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140603219	140603219	11959	5	C	G	G	G	415	32	PCDHB14	3	3
HTR4	3360	broad.mit.edu	37	5	147863923	147863923	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:147863923T>C	uc003lpm.2	-	c.1096A>G	c.(1096-1098)AGA>GGA	p.R366G	HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpn.2_Intron|HTR4_uc010jgv.2_Intron	NM_001040173	NP_001035263	Q13639	5HT4R_HUMAN	serotonin 5-HT4 receptor isoform i	359	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)	GBM(120;370 1604 14007 17804 41573)								0.628571	66.969768	67.45796	22	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147863923	147863923	7749	5	T	C	C	C	713	55	HTR4	4	4
SLC36A1	206358	broad.mit.edu	37	5	150856278	150856278	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150856278A>T	uc003luc.2	+	c.950A>T	c.(949-951)AAT>ATT	p.N317I	GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Missense_Mutation_p.N317I|SLC36A1_uc010jhw.1_Missense_Mutation_p.N317I	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	317	Extracellular (Potential).				cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	Melanoma(151;1534 1860 12947 32979 37872)								0.685714	80.366082	81.42927	24	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150856278	150856278	15090	5	A	T	T	T	52	4	SLC36A1	3	3
FAT2	2196	broad.mit.edu	37	5	150945342	150945342	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150945342C>T	uc003lue.3	-	c.3151G>A	c.(3151-3153)GTG>ATG	p.V1051M	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Missense_Mutation_p.V1051M	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1051	Cadherin 9.|Extracellular (Potential).				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)											0.162791	11.294273	15.947821	7	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150945342	150945342	5926	5	C	T	T	T	234	18	FAT2	2	2
GABRA6	2559	broad.mit.edu	37	5	161116290	161116290	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:161116290G>A	uc003lyu.2	+	c.477G>A	c.(475-477)AGG>AGA	p.R159R	GABRA6_uc003lyv.2_5'Flank	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	159	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)			0.7	154.7551	157.24254	49	21	KEEP	---	---	---	---	capture		Silent	SNP	161116290	161116290	6416	5	G	A	A	A	542	42	GABRA6	2	2
CDH18	1016	broad.mit.edu	37	5	19473547	19473547	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:19473547C>A	uc003jgc.2	-	c.2161G>T	c.(2161-2163)GCA>TCA	p.A721S	CDH18_uc003jgd.2_Missense_Mutation_p.A721S|CDH18_uc011cnm.1_3'UTR	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	721	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.58	178.686043	179.258895	58	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19473547	19473547	3232	5	C	A	A	A	338	26	CDH18	2	2
CDH6	1004	broad.mit.edu	37	5	31316316	31316316	+	Missense_Mutation	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31316316T>G	uc003jhe.1	+	c.1392T>G	c.(1390-1392)AAT>AAG	p.N464K	CDH6_uc003jhd.1_Missense_Mutation_p.N464K	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	464	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|large_intestine(1)	5														0.118421	15.523236	26.389645	9	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31316316	31316316	3243	5	T	G	G	G	634	49	CDH6	4	4
TARS	6897	broad.mit.edu	37	5	33457373	33457373	+	Silent	SNP	G	C	C	rs113811412		TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33457373G>C	uc011coc.1	+	c.912G>C	c.(910-912)ACG>ACC	p.T304T	TARS_uc011cob.1_Silent_p.T271T|TARS_uc010iup.1_Silent_p.T224T|TARS_uc003jhy.2_Silent_p.T283T|TARS_uc003jhz.2_Silent_p.T179T|TARS_uc011cod.1_Silent_p.T162T	NM_152295	NP_689508	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	283					threonyl-tRNA aminoacylation	cytosol	ATP binding|protein homodimerization activity|threonine-tRNA ligase activity			ovary(2)	2					L-Threonine(DB00156)									0.275862	92.467353	97.704431	32	84	KEEP	---	---	---	---	capture		Silent	SNP	33457373	33457373	16081	5	G	C	C	C	509	40	TARS	3	3
ADAMTS12	81792	broad.mit.edu	37	5	33588881	33588881	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33588881C>T	uc003jia.1	-	c.2688G>A	c.(2686-2688)GCG>GCA	p.A896A	ADAMTS12_uc010iuq.1_Silent_p.A811A	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	896	TSP type-1 3.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7												OREG0016553	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.102273	6.667498	20.493852	9	79	KEEP	---	---	---	---	capture		Silent	SNP	33588881	33588881	258	5	C	T	T	T	392	31	ADAMTS12	1	1
C5orf42	65250	broad.mit.edu	37	5	37183179	37183179	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:37183179A>C	uc011cpa.1	-	c.5104T>G	c.(5104-5106)TCA>GCA	p.S1702A	C5orf42_uc011coy.1_Missense_Mutation_p.S203A|C5orf42_uc003jks.2_Non-coding_Transcript|C5orf42_uc011coz.1_Missense_Mutation_p.S777A|C5orf42_uc011cpb.1_Missense_Mutation_p.S583A	NM_023073	NP_075561	B7ZLV7	B7ZLV7_HUMAN	hypothetical protein LOC65250	615										ovary(4)|breast(2)	6	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)											0.101266	7.446736	20.052071	8	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37183179	37183179	2399	5	A	C	C	C	156	12	C5orf42	4	4
PRKAA1	5562	broad.mit.edu	37	5	40764924	40764924	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:40764924C>G	uc003jmb.2	-	c.1283G>C	c.(1282-1284)AGT>ACT	p.S428T	PRKAA1_uc003jmc.2_Missense_Mutation_p.S413T	NM_206907	NP_996790	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic	413					activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)					149				0.148649	22.775943	31.5409	11	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40764924	40764924	12936	5	C	G	G	G	260	20	PRKAA1	3	3
ADAMTS16	170690	broad.mit.edu	37	5	5306811	5306811	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:5306811G>A	uc003jdl.2	+	c.3381G>A	c.(3379-3381)AGG>AGA	p.R1127R		NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1127	TSP type-1 6.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.176471	13.731818	17.08339	6	28	KEEP	---	---	---	---	capture		Silent	SNP	5306811	5306811	262	5	G	A	A	A	555	43	ADAMTS16	2	2
GZMA	3001	broad.mit.edu	37	5	54401361	54401361	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:54401361G>T	uc003jpm.2	+	c.130G>T	c.(130-132)GTC>TTC	p.V44F		NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor	44	Peptidase S1.				cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|pancreas(1)	3		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)												0.351351	32.924008	33.662337	13	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54401361	54401361	7195	5	G	T	T	T	572	44	GZMA	2	2
KIAA0947	23379	broad.mit.edu	37	5	5473822	5473822	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:5473822G>T	uc003jdm.3	+	c.6374G>T	c.(6373-6375)TGC>TTC	p.C2125F		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	2125										ovary(1)|central_nervous_system(1)	2														0.534884	75.539195	75.586392	23	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5473822	5473822	8509	5	G	T	T	T	598	46	KIAA0947	2	2
BDP1	55814	broad.mit.edu	37	5	70813227	70813227	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:70813227C>G	uc003kbp.1	+	c.4939C>G	c.(4939-4941)CAG>GAG	p.Q1647E	BDP1_uc003kbo.2_Missense_Mutation_p.Q1647E	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	1647					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)										0.692308	129.315849	131.028677	36	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70813227	70813227	1417	5	C	G	G	G	377	29	BDP1	3	3
F2R	2149	broad.mit.edu	37	5	76028843	76028843	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:76028843G>T	uc003ken.3	+	c.793G>T	c.(793-795)GGC>TGC	p.G265C		NM_001992	NP_001983	P25116	PAR1_HUMAN	coagulation factor II receptor precursor	265	Extracellular (Potential).				activation of caspase activity|anatomical structure morphogenesis|connective tissue replacement involved in inflammatory response wound healing|negative regulation of cell proliferation|platelet activation|platelet dense granule organization|positive regulation of blood coagulation|positive regulation of cell migration|positive regulation of collagen biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JAK-STAT cascade|positive regulation of MAPKKK cascade|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of transcription, DNA-dependent|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	caveola|extracellular region|Golgi apparatus|integral to plasma membrane|platelet dense tubular network	receptor binding|thrombin receptor activity			ovary(3)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)									0.647059	134.89756	136.189277	44	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76028843	76028843	5537	5	G	T	T	T	455	35	F2R	2	2
LNPEP	4012	broad.mit.edu	37	5	96315308	96315308	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:96315308A>T	uc003kmv.1	+	c.486A>T	c.(484-486)CCA>CCT	p.P162P	LNPEP_uc003kmw.1_Silent_p.P148P	NM_005575	NP_005566	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase isoform 1	162	Extracellular (Potential).				cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)										0.74026	199.59015	203.61164	57	20	KEEP	---	---	---	---	capture		Silent	SNP	96315308	96315308	9193	5	A	T	T	T	93	8	LNPEP	3	3
SIM1	6492	broad.mit.edu	37	6	100838549	100838549	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:100838549C>T	uc003pqj.3	-	c.1989G>A	c.(1987-1989)TCG>TCA	p.S663S	SIM1_uc010kcu.2_Silent_p.S663S	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	663	Single-minded C-terminal.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)										0.222222	66.205323	74.50309	26	91	KEEP	---	---	---	---	capture		Silent	SNP	100838549	100838549	14818	6	C	T	T	T	288	23	SIM1	1	1
PDSS2	57107	broad.mit.edu	37	6	107533454	107533454	+	Silent	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:107533454C>G	uc003prt.2	-	c.735G>C	c.(733-735)TCG>TCC	p.S245S	PDSS2_uc011eak.1_Silent_p.S109S|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Silent_p.S245S	NM_020381	NP_065114	Q86YH6	DLP1_HUMAN	prenyl diphosphate synthase, subunit 2	245					isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)										0.211268	35.493121	40.962503	15	56	KEEP	---	---	---	---	capture		Silent	SNP	107533454	107533454	12115	6	C	G	G	G	392	31	PDSS2	3	3
GPRC6A	222545	broad.mit.edu	37	6	117128030	117128030	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117128030G>A	uc003pxj.1	-	c.838C>T	c.(838-840)CAA>TAA	p.Q280*	GPRC6A_uc003pxk.1_Intron|GPRC6A_uc003pxl.1_Nonsense_Mutation_p.Q280*	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,	280	Extracellular (Potential).				response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)										0.363636	21.614328	21.965582	8	14	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	117128030	117128030	7004	6	G	A	A	A	598	46	GPRC6A	5	2
FOXQ1	94234	broad.mit.edu	37	6	1313599	1313599	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:1313599G>T	uc003mtl.3	+	c.660G>T	c.(658-660)GCG>GCT	p.A220A		NM_033260	NP_150285	Q9C009	FOXQ1_HUMAN	forkhead box Q1	220					DNA fragmentation involved in apoptotic nuclear change|embryo development|hair follicle morphogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of caspase activity|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	caspase regulator activity|DNA bending activity|double-stranded DNA binding|estrogen receptor 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|ubiquitin conjugating enzyme binding				0	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)										0.4	13.594878	13.739319	6	9	KEEP	---	---	---	---	capture		Silent	SNP	1313599	1313599	6276	6	G	T	T	T	483	38	FOXQ1	1	1
STX7	8417	broad.mit.edu	37	6	132785215	132785215	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:132785215C>A	uc003qdg.2	-	c.611_splice	c.e9-1	p.D204_splice	STX7_uc011ecg.1_Splice_Site_SNP|STX7_uc011ech.1_Splice_Site_SNP_p.Y29_splice	NM_003569	NP_003560			syntaxin 7						intracellular protein transport|post-Golgi vesicle-mediated transport	early endosome membrane|integral to membrane	SNAP receptor activity				0	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)										0.371795	83.760184	84.884298	29	49	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	132785215	132785215	15870	6	C	A	A	A	416	32	STX7	5	2
TAAR5	9038	broad.mit.edu	37	6	132909899	132909899	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:132909899G>T	uc003qdk.2	-	c.927C>A	c.(925-927)TAC>TAA	p.Y309*		NM_003967	NP_003958	O14804	TAAR5_HUMAN	trace amine associated receptor 5	309	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity				0	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)										0.4	52.535353	52.930262	18	27	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	132909899	132909899	16012	6	G	T	T	T	568	44	TAAR5	5	2
ALDH8A1	64577	broad.mit.edu	37	6	135239557	135239557	+	Missense_Mutation	SNP	T	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:135239557T>A	uc003qew.2	-	c.1460A>T	c.(1459-1461)CAC>CTC	p.H487L	ALDH8A1_uc003qex.2_Missense_Mutation_p.H433L|ALDH8A1_uc010kgh.2_Missense_Mutation_p.H265L|ALDH8A1_uc011ecx.1_Missense_Mutation_p.H437L	NM_022568	NP_072090	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8A1 isoform 1	487					oxidation-reduction process|retinal metabolic process	cytoplasm	retinal dehydrogenase activity			ovary(2)|pancreas(1)	3	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)										0.40625	37.755988	38.003922	13	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135239557	135239557	508	6	T	A	A	A	767	59	ALDH8A1	3	3
MYB	4602	broad.mit.edu	37	6	135521439	135521439	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:135521439C>T	uc003qfh.2	+	c.1836C>T	c.(1834-1836)CCC>CCT	p.P612P	MYB_uc003qfc.2_Silent_p.P491P|MYB_uc003qfi.2_Silent_p.P596P|MYB_uc010kgi.2_Silent_p.P491P|MYB_uc003qfq.2_Silent_p.P609P|MYB_uc010kgj.2_Silent_p.P456P|MYB_uc003qfo.2_Silent_p.P406P|MYB_uc003qfu.2_Silent_p.P488P|MYB_uc003qfl.2_Non-coding_Transcript|MYB_uc003qfv.2_Non-coding_Transcript|MYB_uc003qfz.2_Non-coding_Transcript|MYB_uc003qfx.2_Non-coding_Transcript|MYB_uc003qga.2_Non-coding_Transcript|MYB_uc003qgb.2_Non-coding_Transcript|MYB_uc010kgk.2_Non-coding_Transcript|MYB_uc003qfd.2_Non-coding_Transcript|MYB_uc003qfe.2_Non-coding_Transcript|MYB_uc003qfg.2_Non-coding_Transcript|MYB_uc003qff.2_Non-coding_Transcript|MYB_uc003qfj.2_Non-coding_Transcript|MYB_uc003qfm.2_Non-coding_Transcript|MYB_uc003qfp.2_Non-coding_Transcript|MYB_uc003qfn.2_Non-coding_Transcript|MYB_uc003qfk.2_Non-coding_Transcript|MYB_uc003qfr.2_Non-coding_Transcript|MYB_uc003qfs.2_Silent_p.P117P|MYB_uc003qft.2_Non-coding_Transcript|MYB_uc003qfw.2_Silent_p.P303P|MYB_uc003qfy.2_Non-coding_Transcript|MYB_uc003qgc.2_Non-coding_Transcript|MYB_uc003qfb.1_Silent_p.P491P	NM_001130173	NP_001123645	P10242	MYB_HUMAN	v-myb myeloblastosis viral oncogene homolog	520					blood coagulation|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear matrix	DNA binding|protein binding|specific transcriptional repressor activity|transcription activator activity			lung(1)	1	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)						299				0.358491	53.786422	54.729698	19	34	KEEP	---	---	---	---	capture		Silent	SNP	135521439	135521439	10402	6	C	T	T	T	301	24	MYB	2	2
PEX7	5191	broad.mit.edu	37	6	137191109	137191109	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:137191109C>G	uc003qhd.2	+	c.715C>G	c.(715-717)CTT>GTT	p.L239V	PEX7_uc010kgx.2_Non-coding_Transcript	NM_000288	NP_000279	O00628	PEX7_HUMAN	peroxisomal biogenesis factor 7	239					ether lipid biosynthetic process|protein import into peroxisome matrix|response to stimulus|visual perception	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)										0.135678	48.219998	73.780868	27	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137191109	137191109	12173	6	C	G	G	G	416	32	PEX7	3	3
UTRN	7402	broad.mit.edu	37	6	144999682	144999682	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:144999682G>T	uc003qkt.2	+	c.7620G>T	c.(7618-7620)TGG>TGT	p.W2540C		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	2540	Spectrin 17.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(3)|pancreas(1)	4		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)										0.666667	31.653972	32.022788	10	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144999682	144999682	17668	6	G	T	T	T	533	41	UTRN	2	2
UTRN	7402	broad.mit.edu	37	6	145051568	145051568	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:145051568G>A	uc003qkt.2	+	c.7885G>A	c.(7885-7887)GAT>AAT	p.D2629N		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	2629	Spectrin 18.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(3)|pancreas(1)	4		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)										0.282051	54.404434	57.743461	22	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145051568	145051568	17668	6	G	A	A	A	585	45	UTRN	2	2
STXBP5	134957	broad.mit.edu	37	6	147588262	147588262	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:147588262C>A	uc003qlz.2	+	c.673C>A	c.(673-675)CTC>ATC	p.L225I	STXBP5_uc010khz.1_Missense_Mutation_p.L225I|STXBP5_uc003qlx.2_Non-coding_Transcript|STXBP5_uc003qly.2_5'UTR	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	225	WD 4.				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)										0.34	95.008665	97.276684	34	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147588262	147588262	15876	6	C	A	A	A	312	24	STXBP5	2	2
AKAP12	9590	broad.mit.edu	37	6	151674269	151674269	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:151674269C>T	uc011eep.1	+	c.4743C>T	c.(4741-4743)CAC>CAT	p.H1581H	AKAP12_uc003qoe.2_Silent_p.H1581H|AKAP12_uc003qof.2_Silent_p.H1483H|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Silent_p.H1476H	NM_005100	NP_005091	Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12 isoform 1	1581					G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|pancreas(1)|lung(1)|skin(1)	7		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		Melanoma(141;1616 1805 10049 24534 51979)				196				0.188679	21.432399	26.229161	10	43	KEEP	---	---	---	---	capture		Silent	SNP	151674269	151674269	451	6	C	T	T	T	246	19	AKAP12	1	1
ESR1	2099	broad.mit.edu	37	6	152419965	152419965	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:152419965C>A	uc010kio.2	+	c.1658C>A	c.(1657-1659)GCG>GAG	p.A553E	ESR1_uc003qom.3_Missense_Mutation_p.A551E|ESR1_uc010kin.2_Missense_Mutation_p.A551E|ESR1_uc010kip.2_Missense_Mutation_p.A550E|ESR1_uc003qon.3_Missense_Mutation_p.A551E|ESR1_uc003qoo.3_Missense_Mutation_p.A551E|ESR1_uc010kiq.2_Missense_Mutation_p.A149E|ESR1_uc010kir.2_Missense_Mutation_p.A290E|ESR1_uc011eet.1_Non-coding_Transcript|ESR1_uc011eeu.1_Non-coding_Transcript|ESR1_uc011eev.1_Missense_Mutation_p.A136E|ESR1_uc011eew.1_3'UTR|ESR1_uc011eex.1_Missense_Mutation_p.A226E|ESR1_uc011eey.1_3'UTR	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4	551	Steroid-binding.|Interaction with AKAP13.				positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)	2		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)					249				0.333333	32.879068	33.769284	12	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152419965	152419965	5449	6	C	A	A	A	351	27	ESR1	1	1
MAS1	4142	broad.mit.edu	37	6	160328457	160328457	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160328457G>T	uc003qsz.2	+	c.470G>T	c.(469-471)TGG>TTG	p.W157L		NM_002377	NP_002368	P04201	MAS_HUMAN	MAS1 oncogene	157	Helical; Name=4; (Potential).				anatomical structure morphogenesis|cell proliferation|protein kinase C signaling cascade	integral to plasma membrane	angiotensin type II receptor activity			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)										0.333333	112.385588	115.264067	39	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160328457	160328457	9704	6	G	T	T	T	611	47	MAS1	2	2
PLG	5340	broad.mit.edu	37	6	161135923	161135923	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161135923C>G	uc003qtm.3	+	c.645C>G	c.(643-645)CAC>CAG	p.H215Q		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	215	Kringle 2.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)									0.21875	17.708061	20.040639	7	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161135923	161135923	12512	6	C	G	G	G	246	19	PLG	3	3
NUP153	9972	broad.mit.edu	37	6	17688767	17688767	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:17688767A>T	uc011dje.1	-	c.194T>A	c.(193-195)GTA>GAA	p.V65E	NUP153_uc003ncd.1_Missense_Mutation_p.V65E|NUP153_uc010jpl.1_Missense_Mutation_p.V65E	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	65					carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(2)|ovary(1)|skin(1)	4	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)							1004				0.227273	74.599464	83.597751	30	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17688767	17688767	11160	6	A	T	T	T	182	14	NUP153	3	3
ZNF165	7718	broad.mit.edu	37	6	28056916	28056916	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28056916G>A	uc003nkg.2	+	c.1126G>A	c.(1126-1128)GAA>AAA	p.E376K	ZNF165_uc003nkh.2_Missense_Mutation_p.E376K|ZNF165_uc003nki.3_Missense_Mutation_p.E376K|ZSCAN12P1_uc003nkj.3_5'Flank	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165	376	C2H2-type 3.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.320755	46.756103	48.268897	17	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28056916	28056916	18331	6	G	A	A	A	585	45	ZNF165	2	2
PGBD1	84547	broad.mit.edu	37	6	28269749	28269749	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28269749A>T	uc003nky.2	+	c.2118A>T	c.(2116-2118)CCA>CCT	p.P706P	PGBD1_uc003nkz.2_Silent_p.P706P	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	706					regulation of transcription, DNA-dependent|viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4														0.358974	123.305449	125.35909	42	75	KEEP	---	---	---	---	capture		Silent	SNP	28269749	28269749	12203	6	A	T	T	T	80	7	PGBD1	3	3
OR2J2	26707	broad.mit.edu	37	6	29141566	29141566	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29141566G>T	uc011dlm.1	+	c.154G>T	c.(154-156)GTG>TTG	p.V52L		NM_030905	NP_112167	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J,	52	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.174129	76.792307	96.903388	35	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29141566	29141566	11409	6	G	T	T	T	520	40	OR2J2	1	1
ZFP57	346171	broad.mit.edu	37	6	29640292	29640292	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29640292G>C	uc011dlw.1	-	c.1596C>G	c.(1594-1596)ATC>ATG	p.I532M	ZFP57_uc003nnl.3_Missense_Mutation_p.I512M	NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog	448					DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)	3														0.188679	48.934946	58.551061	20	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29640292	29640292	18239	6	G	C	C	C	421	33	ZFP57	3	3
MUC21	394263	broad.mit.edu	37	6	30955259	30955259	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30955259C>G	uc003nsh.2	+	c.1307C>G	c.(1306-1308)ACC>AGC	p.T436S	MUC21_uc003nsi.1_Non-coding_Transcript	NM_001010909	NP_001010909	Q5SSG8	MUC21_HUMAN	mucin 21 precursor	436	Ser-rich.|28.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(1)	1														0.075	1.103317	23.316953	9	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30955259	30955259	10371	6	C	G	G	G	234	18	MUC21	3	3
HLA-DOA	3111	broad.mit.edu	37	6	32976019	32976019	+	Nonsense_Mutation	SNP	G	T	T	rs41556712		TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32976019G>T	uc003ocr.2	-	c.102C>A	c.(100-102)TAC>TAA	p.Y34*	HLA-DOA_uc010juj.2_Nonsense_Mutation_p.Y4*|HLA-DOA_uc010jui.2_Nonsense_Mutation_p.Y34*	NM_002119	NP_002110	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO	34	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0														0.431818	58.820316	58.997933	19	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	32976019	32976019	7491	6	G	T	T	T	516	40	HLA-DOA	5	1
COL11A2	1302	broad.mit.edu	37	6	33156808	33156809	+	Missense_Mutation	DNP	CC	GA	GA			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33156808_33156809CC>GA	uc003ocx.1	-	c.389_390GG>TC	c.(388-390)CGG>CTC	p.R130L	COL11A2_uc003ocy.1_Missense_Mutation_p.R130L|COL11A2_uc003ocz.1_Missense_Mutation_p.R130L|COL11A2_uc003oda.2_Missense_Mutation_p.R130L	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	130	TSP N-terminal.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(1)	4						Melanoma(1;90 116 3946 5341 17093)								0.179856	55.783488	69.284826	25	114	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	33156808	33156809	3806	6	CC	GA	GA	GA	327	26	COL11A2	3	3
SRPK1	6732	broad.mit.edu	37	6	35842080	35842080	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:35842080A>C	uc003olj.2	-	c.515T>G	c.(514-516)CTG>CGG	p.L172R	SRPK1_uc011dtg.1_Missense_Mutation_p.L156R|SRPK1_uc003olh.2_Missense_Mutation_p.L65R|SRPK1_uc003oli.2_Missense_Mutation_p.L65R	NM_003137	NP_003128	Q96SB4	SRPK1_HUMAN	SFRS protein kinase 1	172	Protein kinase.				cell differentiation|chromosome segregation|innate immune response|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|protein phosphorylation|regulation of mRNA processing|RNA splicing	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						NSCLC(31;67 978 16289 24856 26454)				211				0.222222	10.290423	11.567994	4	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35842080	35842080	15673	6	A	C	C	C	91	7	SRPK1	4	4
DNAH8	1769	broad.mit.edu	37	6	38758183	38758183	+	Splice_Site_SNP	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:38758183T>C	uc003ooe.1	+	c.2130_splice	c.e18+2	p.K710_splice		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.2	14.975347	17.949485	7	28	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	38758183	38758183	4790	6	T	C	C	C	741	57	DNAH8	5	4
LRFN2	57497	broad.mit.edu	37	6	40399544	40399544	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:40399544G>A	uc003oph.1	-	c.1309C>T	c.(1309-1311)CTG>TTG	p.L437L		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	437	Fibronectin type-III.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.171429	26.255836	33.399723	12	58	KEEP	---	---	---	---	capture		Silent	SNP	40399544	40399544	9311	6	G	A	A	A	451	35	LRFN2	2	2
PGC	5225	broad.mit.edu	37	6	41708341	41708341	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41708341C>A	uc003ora.1	-	c.655G>T	c.(655-657)GGC>TGC	p.G219C		NM_002630	NP_002621	P20142	PEPC_HUMAN	progastricsin (pepsinogen C) precursor	219					digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)											0.481481	149.942739	149.971042	52	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41708341	41708341	12208	6	C	A	A	A	286	22	PGC	2	2
PRPH2	5961	broad.mit.edu	37	6	42689590	42689590	+	Silent	SNP	G	T	T	rs76989855	by1000genomes	TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42689590G>T	uc003osk.2	-	c.483C>A	c.(481-483)ATC>ATA	p.I161I		NM_000322	NP_000313	P23942	PRPH2_HUMAN	peripherin 2	161	Lumenal (Potential).				cell adhesion|response to stimulus|visual perception	integral to membrane				ovary(4)|central_nervous_system(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)											0.6	237.05507	238.192736	78	52	KEEP	---	---	---	---	capture		Silent	SNP	42689590	42689590	13020	6	G	T	T	T	473	37	PRPH2	1	1
CAPN11	11131	broad.mit.edu	37	6	44150872	44150872	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:44150872C>G	uc003owt.1	+	c.2034C>G	c.(2032-2034)AAC>AAG	p.N678K	CAPN11_uc011dvn.1_3'UTR	NM_007058	NP_008989	Q9UMQ6	CAN11_HUMAN	calpain 11	678	Domain IV.				proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)											0.297619	73.31668	76.410414	25	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44150872	44150872	2741	6	C	G	G	G	220	17	CAPN11	3	3
CDC5L	988	broad.mit.edu	37	6	44371573	44371573	+	Silent	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:44371573A>G	uc003oxl.2	+	c.567A>G	c.(565-567)AGA>AGG	p.R189R		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	189	Potential.				cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)	5	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)							515				0.244898	30.670617	33.581271	12	37	KEEP	---	---	---	---	capture		Silent	SNP	44371573	44371573	3211	6	A	G	G	G	141	11	CDC5L	4	4
FAM83B	222584	broad.mit.edu	37	6	54735153	54735153	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:54735153G>A	uc003pck.2	+	c.109G>A	c.(109-111)GAA>AAA	p.E37K		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	37										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)													0.564516	215.849321	216.305042	70	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54735153	54735153	5860	6	G	A	A	A	585	45	FAM83B	2	2
HCRTR2	3062	broad.mit.edu	37	6	55147091	55147091	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55147091G>T	uc003pcl.2	+	c.1174G>T	c.(1174-1176)GAT>TAT	p.D392Y	HCRTR2_uc010jzv.2_Non-coding_Transcript	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2	392	Cytoplasmic (Potential).				feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)	2	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.35	18.718457	19.115709	7	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55147091	55147091	7285	6	G	T	T	T	533	41	HCRTR2	2	2
GFRAL	389400	broad.mit.edu	37	6	55198734	55198734	+	Missense_Mutation	SNP	A	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55198734A>G	uc003pcm.1	+	c.308A>G	c.(307-309)AAT>AGT	p.N103S		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	103	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.166667	37.486435	48.860025	18	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55198734	55198734	6619	6	A	G	G	G	52	4	GFRAL	4	4
COL12A1	1303	broad.mit.edu	37	6	75884799	75884799	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:75884799A>T	uc003phs.2	-	c.2665T>A	c.(2665-2667)TCT>ACT	p.S889T	COL12A1_uc003pht.2_Intron	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	889	Fibronectin type-III 5.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)	8														0.20339	51.840432	61.479061	24	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75884799	75884799	3807	6	A	T	T	T	130	10	COL12A1	3	3
TTK	7272	broad.mit.edu	37	6	80724274	80724274	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:80724274C>A	uc003pjc.2	+	c.1079C>A	c.(1078-1080)ACG>AAG	p.T360K	TTK_uc003pjb.3_Missense_Mutation_p.T360K	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase	360					mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|large_intestine(2)|pancreas(1)	9		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)						471				0.307692	57.68813	59.824189	20	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80724274	80724274	17275	6	C	A	A	A	247	19	TTK	1	1
TTK	7272	broad.mit.edu	37	6	80749412	80749412	+	Splice_Site_SNP	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:80749412G>C	uc003pjc.2	+	c.2131_splice	c.e19-1	p.I711_splice	TTK_uc003pjb.3_Splice_Site_SNP_p.I710_splice	NM_003318	NP_003309			TTK protein kinase						mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|large_intestine(2)|pancreas(1)	9		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)						471				0.138462	16.137908	24.344973	9	56	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	80749412	80749412	17275	6	G	C	C	C	429	33	TTK	5	3
MDN1	23195	broad.mit.edu	37	6	90402561	90402561	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:90402561G>A	uc003pnn.1	-	c.10188C>T	c.(10186-10188)GCC>GCT	p.A3396A		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	3396					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)	8		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)										0.567568	70.280544	70.42828	21	16	KEEP	---	---	---	---	capture		Silent	SNP	90402561	90402561	9804	6	G	A	A	A	496	39	MDN1	1	1
MGAM	8972	broad.mit.edu	37	7	141750533	141750533	+	Nonsense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141750533A>T	uc003vwy.2	+	c.2674A>T	c.(2674-2676)AAG>TAG	p.K892*		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	892	Lumenal (Potential).|Maltase.				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.347826	42.83586	43.798714	16	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	141750533	141750533	9931	7	A	T	T	T	65	5	MGAM	5	3
GIMAP6	474344	broad.mit.edu	37	7	150325196	150325196	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150325196G>T	uc003whn.2	-	c.490C>A	c.(490-492)CGG>AGG	p.R164R	GIMAP6_uc003whm.2_Silent_p.R84R	NM_024711	NP_078987	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	164							GTP binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.386935	230.268103	232.483182	77	122	KEEP	---	---	---	---	capture		Silent	SNP	150325196	150325196	6651	7	G	T	T	T	506	39	GIMAP6	1	1
TMEM195	392636	broad.mit.edu	37	7	15458244	15458244	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:15458244G>A	uc003stb.1	-	c.548C>T	c.(547-549)CCT>CTT	p.P183L		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	183					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0														0.8	43.508844	44.764355	12	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15458244	15458244	16652	7	G	A	A	A	455	35	TMEM195	2	2
UBE3C	9690	broad.mit.edu	37	7	157023909	157023909	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:157023909G>A	uc010lqs.2	+	c.2369G>A	c.(2368-2370)GGG>GAG	p.G790E	UBE3C_uc003wni.3_Missense_Mutation_p.G153E	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	790	HECT.				protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			large_intestine(1)|ovary(1)	2		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)										0.463768	98.69789	98.775933	32	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157023909	157023909	17439	7	G	A	A	A	559	43	UBE3C	2	2
PION	54103	broad.mit.edu	37	7	77016752	77016752	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:77016752C>G	uc003ugf.2	-	c.381G>C	c.(379-381)TTG>TTC	p.L127F	PION_uc003ugg.1_5'UTR	NM_017439	NP_059135	A4D1B5	GSAP_HUMAN	pigeon homolog	127					beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1														0.145833	14.798862	20.582255	7	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77016752	77016752	12358	7	C	G	G	G	376	29	PION	3	3
PCLO	27445	broad.mit.edu	37	7	82585020	82585020	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82585020C>T	uc003uhx.2	-	c.5249G>A	c.(5248-5250)GGA>GAA	p.G1750E	PCLO_uc003uhv.2_Missense_Mutation_p.G1750E	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1681					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.285714	126.147762	132.744014	46	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82585020	82585020	12003	7	C	T	T	T	390	30	PCLO	2	2
CDK6	1021	broad.mit.edu	37	7	92300778	92300779	+	Missense_Mutation	DNP	CC	AG	AG			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92300778_92300779CC>AG	uc011khw.1	-	c.608_609GG>CT	c.(607-609)TGG>TCT	p.W203S	CDK6_uc010lez.2_Missense_Mutation_p.W203S	NM_001259	NP_001250	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	203	Protein kinase.				cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|protein phosphorylation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)							86				0.245902	37.395938	40.981706	15	46	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	92300778	92300779	3277	7	CC	AG	AG	AG	390	30	CDK6	2	2
COL1A2	1278	broad.mit.edu	37	7	94039086	94039086	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:94039086C>A	uc003ung.1	+	c.988C>A	c.(988-990)CCT>ACT	p.P330T	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	330					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging			central_nervous_system(3)|ovary(2)	5	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)									0.258065	53.150183	58.092955	24	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94039086	94039086	3816	7	C	A	A	A	390	30	COL1A2	2	2
STAG3	10734	broad.mit.edu	37	7	99786109	99786109	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99786109C>T	uc003utx.1	+	c.467C>T	c.(466-468)TCC>TTC	p.S156F	STAG3_uc010lgs.1_5'UTR|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3	156					chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(3)|skin(2)|lung(1)|kidney(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)									331				0.49827	451.982135	451.982282	144	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99786109	99786109	15762	7	C	T	T	T	390	30	STAG3	2	2
RNF19A	25897	broad.mit.edu	37	8	101276385	101276385	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:101276385C>T	uc003yjj.1	-	c.1345G>A	c.(1345-1347)GTA>ATA	p.V449I	RNF19A_uc003yjk.1_Missense_Mutation_p.V449I	NM_015435	NP_056250	Q9NV58	RN19A_HUMAN	ring finger protein 19	449					microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)											0.23913	27.006275	29.86188	11	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101276385	101276385	13948	8	C	T	T	T	247	19	RNF19A	1	1
ASAP1	50807	broad.mit.edu	37	8	131199494	131199494	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:131199494T>C	uc003yta.1	-	c.518A>G	c.(517-519)TAT>TGT	p.Y173C	ASAP1_uc011liw.1_Missense_Mutation_p.Y166C	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor	173					cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4														0.276596	39.357272	41.466929	13	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131199494	131199494	1028	8	T	C	C	C	637	49	ASAP1	4	4
FAM135B	51059	broad.mit.edu	37	8	139153548	139153548	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139153548A>T	uc003yuy.2	-	c.3683T>A	c.(3682-3684)CTC>CAC	p.L1228H	FAM135B_uc003yux.2_Missense_Mutation_p.L1129H|FAM135B_uc003yuz.2_Non-coding_Transcript	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1228										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.163636	13.10187	19.09041	9	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139153548	139153548	5646	8	A	T	T	T	143	11	FAM135B	3	3
FAM83H	286077	broad.mit.edu	37	8	144812633	144812633	+	Silent	SNP	C	A	A	rs118023699	by1000genomes	TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144812633C>A	uc003yzk.2	-	c.120G>T	c.(118-120)TCG>TCT	p.S40S	FAM83H_uc010mfk.1_5'Flank	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H	40					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(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)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)											0.145833	13.318272	19.08615	7	41	KEEP	---	---	---	---	capture		Silent	SNP	144812633	144812633	5866	8	C	A	A	A	288	23	FAM83H	1	1
RECQL4	9401	broad.mit.edu	37	8	145742150	145742150	+	Splice_Site_SNP	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145742150T>G	uc003zdj.2	-	c.355_splice	c.e5-1	p.A119_splice	LRRC14_uc003zdk.1_5'Flank|LRRC14_uc003zdl.1_5'Flank	NM_004260	NP_004251			RecQ protein-like 4						DNA duplex unwinding|DNA recombination|DNA repair	cytoplasm|nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding			skin(1)	1	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)							474				0.170213	12.775616	17.612351	8	39	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	145742150	145742150	13671	8	T	G	G	G	715	55	RECQL4	5	4
MYOM2	9172	broad.mit.edu	37	8	2017597	2017597	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:2017597G>T	uc003wpx.3	+	c.774G>T	c.(772-774)TCG>TCT	p.S258S	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	258					muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)	5		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)										0.243478	76.07766	82.950875	28	87	KEEP	---	---	---	---	capture		Silent	SNP	2017597	2017597	10487	8	G	T	T	T	496	39	MYOM2	1	1
NRG1	3084	broad.mit.edu	37	8	32621438	32621438	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:32621438G>T	uc003xiu.2	+	c.1456G>T	c.(1456-1458)GTG>TTG	p.V486L	NRG1_uc010lvo.2_3'UTR|NRG1_uc003xiw.2_Missense_Mutation_p.V478L|NRG1_uc003xit.2_3'UTR|NRG1_uc003xiv.2_Missense_Mutation_p.V481L|NRG1_uc010lvr.2_Missense_Mutation_p.V223L|NRG1_uc010lvs.2_Missense_Mutation_p.V223L|NRG1_uc010lvp.2_Missense_Mutation_p.V435L|NRG1_uc010lvq.2_Missense_Mutation_p.V418L|NRG1_uc011lbg.1_3'UTR|NRG1_uc011lbh.1_Missense_Mutation_p.V324L|NRG1_uc003xja.2_Missense_Mutation_p.V292L	NM_013956	NP_039250	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-beta1	481	Cytoplasmic (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)										0.362069	61.380684	62.342439	21	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32621438	32621438	11052	8	G	T	T	T	520	40	NRG1	1	1
UNC5D	137970	broad.mit.edu	37	8	35583900	35583900	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:35583900C>A	uc003xjr.1	+	c.1534C>A	c.(1534-1536)CAT>AAT	p.H512N	UNC5D_uc003xjs.1_Missense_Mutation_p.H507N|UNC5D_uc003xju.1_Missense_Mutation_p.H88N|UNC5D_uc003xjt.1_Missense_Mutation_p.H270N	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	512	Cytoplasmic (Potential).				apoptosis|axon guidance	integral to membrane	receptor activity			ovary(2)|pancreas(1)	3				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)										0.245902	39.795056	43.38091	15	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35583900	35583900	17553	8	C	A	A	A	273	21	UNC5D	2	2
IDO2	169355	broad.mit.edu	37	8	39840251	39840251	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:39840251C>A	uc010lwy.1	+	c.435C>A	c.(433-435)GAC>GAA	p.D145E	IDO2_uc003xno.1_Non-coding_Transcript|IDO2_uc010lwz.1_Intron	NM_194294	NP_919270	Q6ZQW0	I23O2_HUMAN	indoleamine-pyrrole 2,3 dioxygenase-like 1	132					oxidation-reduction process|tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2														0.454545	29.745982	29.785743	10	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39840251	39840251	7802	8	C	A	A	A	259	20	IDO2	2	2
PXDNL	137902	broad.mit.edu	37	8	52321964	52321964	+	Silent	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:52321964G>A	uc003xqu.3	-	c.2220C>T	c.(2218-2220)CCC>CCT	p.P740P	PXDNL_uc003xqt.3_Non-coding_Transcript	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	740					hydrogen peroxide catabolic process|oxidation-reduction process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)												0.555556	44.538221	44.614101	15	12	KEEP	---	---	---	---	capture		Silent	SNP	52321964	52321964	13306	8	G	A	A	A	600	47	PXDNL	2	2
IMPAD1	54928	broad.mit.edu	37	8	57876473	57876473	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:57876473C>A	uc003xte.3	-	c.959G>T	c.(958-960)GGT>GTT	p.G320V		NM_017813	NP_060283	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	320						Golgi apparatus|integral to membrane	inositol-1(or 4)-monophosphatase activity|metal ion binding			ovary(1)	1		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)												0.183673	17.746056	22.34797	9	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57876473	57876473	8026	8	C	A	A	A	234	18	IMPAD1	2	2
CHD7	55636	broad.mit.edu	37	8	61778121	61778121	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:61778121G>T	uc003xue.2	+	c.8623G>T	c.(8623-8625)GGT>TGT	p.G2875C		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2875					central nervous system development|chromatin assembly or disassembly|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	chromatin|nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|lung(1)|breast(1)|pancreas(1)	8		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)											0.621622	75.131997	75.611887	23	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61778121	61778121	3464	8	G	T	T	T	611	47	CHD7	2	2
C8orf45	157777	broad.mit.edu	37	8	67813464	67813464	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:67813464G>T	uc003xwz.3	+	c.1650G>T	c.(1648-1650)TTG>TTT	p.L550F	C8orf45_uc011lev.1_Missense_Mutation_p.L550F|C8orf45_uc011lew.1_Missense_Mutation_p.L481F|C8orf45_uc011lex.1_Missense_Mutation_p.L308F|C8orf45_uc003xwy.3_Missense_Mutation_p.L550F	NM_173518	NP_775789	Q4G0Z9	CH045_HUMAN	minichromosome maintenance complex	550					DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)											0.126984	10.566127	19.10985	8	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67813464	67813464	2540	8	G	T	T	T	581	45	C8orf45	2	2
TRAM1	23471	broad.mit.edu	37	8	71510383	71510383	+	Missense_Mutation	SNP	C	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:71510383C>G	uc003xyo.1	-	c.295G>C	c.(295-297)GAG>CAG	p.E99Q	TRAM1_uc011lfc.1_Missense_Mutation_p.E68Q	NM_014294	NP_055109	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	99	Cytoplasmic (Potential).				cotranslational protein targeting to membrane|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity			ovary(1)	1			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			Ovarian(85;984 1334 5116 12432 40638)								0.115385	10.038143	17.590902	6	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71510383	71510383	16995	8	C	G	G	G	416	32	TRAM1	3	3
LACTB2	51110	broad.mit.edu	37	8	71553275	71553275	+	Silent	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:71553275T>G	uc011lfd.1	-	c.603A>C	c.(601-603)CCA>CCC	p.P201P	LACTB2_uc003xyp.2_Silent_p.P201P	NM_016027	NP_057111	Q53H82	LACB2_HUMAN	lactamase, beta 2	201							hydrolase activity|metal ion binding			ovary(1)	1	Breast(64;0.0716)		Epithelial(68;0.00319)|all cancers(69;0.0175)|OV - Ovarian serous cystadenocarcinoma(28;0.0628)|BRCA - Breast invasive adenocarcinoma(89;0.166)											0.552632	70.378962	70.470715	21	17	KEEP	---	---	---	---	capture		Silent	SNP	71553275	71553275	8921	8	T	G	G	G	704	55	LACTB2	4	4
KCNB2	9312	broad.mit.edu	37	8	73849991	73849991	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:73849991A>T	uc003xzb.2	+	c.2401A>T	c.(2401-2403)AGG>TGG	p.R801W		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	801	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4	Breast(64;0.137)		Epithelial(68;0.105)											0.637931	109.789545	110.773694	37	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73849991	73849991	8318	8	A	T	T	T	140	11	KCNB2	3	3
CA13	377677	broad.mit.edu	37	8	86163066	86163066	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:86163066C>T	uc003ydg.2	+	c.135C>T	c.(133-135)CTC>CTT	p.L45L	CA13_uc003ydf.1_Non-coding_Transcript	NM_198584	NP_940986	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	45					one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0														0.350877	173.131987	176.44923	60	111	KEEP	---	---	---	---	capture		Silent	SNP	86163066	86163066	2630	8	C	T	T	T	379	30	CA13	2	2
GRIN3A	116443	broad.mit.edu	37	9	104449372	104449372	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:104449372G>C	uc004bbp.1	-	c.810C>G	c.(808-810)TGC>TGG	p.C270W	GRIN3A_uc004bbq.1_Missense_Mutation_p.C270W	NM_133445	NP_597702	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic,	270	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|central_nervous_system(1)|pancreas(1)	6		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)					27				0.489796	80.163284	80.168453	24	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104449372	104449372	7062	9	G	C	C	C	542	42	GRIN3A	3	3
CDK5RAP2	55755	broad.mit.edu	37	9	123206000	123206000	+	Missense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:123206000C>A	uc004bkf.2	-	c.3046G>T	c.(3046-3048)GCC>TCC	p.A1016S	CDK5RAP2_uc010mvi.2_Intron|CDK5RAP2_uc004bke.2_Missense_Mutation_p.A301S|CDK5RAP2_uc004bkg.2_Missense_Mutation_p.A1016S|CDK5RAP2_uc011lxw.1_Missense_Mutation_p.A281S|CDK5RAP2_uc011lxx.1_Non-coding_Transcript|CDK5RAP2_uc011lxy.1_Non-coding_Transcript|CDK5RAP2_uc011lxz.1_Missense_Mutation_p.A281S|CDK5RAP2_uc011lya.1_Missense_Mutation_p.A281S|CDK5RAP2_uc004bkh.1_Missense_Mutation_p.A786S|CDK5RAP2_uc004bki.2_Missense_Mutation_p.A783S	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1016	Interaction with MAPRE1.				brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|promoter binding			ovary(2)|lung(1)|skin(1)	4														0.571429	73.702243	73.888801	24	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123206000	123206000	3275	9	C	A	A	A	364	28	CDK5RAP2	2	2
OR1J2	26740	broad.mit.edu	37	9	125273352	125273352	+	Missense_Mutation	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125273352C>T	uc004bmj.1	+	c.272C>T	c.(271-273)TCG>TTG	p.S91L	OR1J2_uc011lyv.1_Missense_Mutation_p.S91L	NM_054107	NP_473448	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J,	91	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|breast(1)|skin(1)	3														0.644737	162.498017	163.903524	49	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125273352	125273352	11366	9	C	T	T	T	403	31	OR1J2	1	1
NUP214	8021	broad.mit.edu	37	9	134003738	134003738	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134003738G>T	uc004cag.2	+	c.261G>T	c.(259-261)TTG>TTT	p.L87F	NUP214_uc004cah.2_Missense_Mutation_p.L87F|NUP214_uc004caf.1_Missense_Mutation_p.L87F	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	87					carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		Pancreas(4;24 48 25510 30394 32571)				1058				0.637931	121.588781	122.560136	37	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134003738	134003738	11167	9	G	T	T	T	594	46	NUP214	2	2
SETX	23064	broad.mit.edu	37	9	135206681	135206681	+	Missense_Mutation	SNP	T	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135206681T>C	uc004cbk.2	-	c.993A>G	c.(991-993)ATA>ATG	p.I331M	SETX_uc004cbj.2_5'Flank|SETX_uc010mzt.2_5'Flank	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	331					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA binding|DNA helicase activity			ovary(2)	2		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)										0.526316	101.05216	101.080919	30	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135206681	135206681	14630	9	T	C	C	C	732	57	SETX	4	4
NOTCH1	4851	broad.mit.edu	37	9	139395153	139395153	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139395153C>A	uc004chz.2	-	c.5785G>T	c.(5785-5787)GAG>TAG	p.E1929*		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	1929	Cytoplasmic (Potential).|ANK 1.				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of gene-specific transcription|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(781)|lung(11)|central_nervous_system(10)|breast(4)|upper_aerodigestive_tract(1)|large_intestine(1)|oesophagus(1)|pancreas(1)	810	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)						1552				0.506667	117.536759	117.539555	38	37	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	139395153	139395153	10950	9	C	A	A	A	403	31	NOTCH1	5	1
ADAMTSL1	92949	broad.mit.edu	37	9	18777725	18777726	+	Silent	DNP	CC	AT	AT			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:18777725_18777726CC>AT	uc003zne.3	+	c.3498_3499CC>AT	c.(3496-3501)ATCCTG>ATATTG	p.1166_1167IL>IL		NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	1166_1167	Ig-like C2-type 2.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|lung(1)	4				GBM - Glioblastoma multiforme(50;1.29e-17)										0.352941	14.250254	14.571887	6	11	KEEP	---	---	---	---	capture		Silent	DNP	18777725	18777726	275	9	CC	AT	AT	AT	382	30	ADAMTSL1	2	2
DENND4C	55667	broad.mit.edu	37	9	19369895	19369895	+	Missense_Mutation	SNP	A	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19369895A>C	uc003znq.2	+	c.4730A>C	c.(4729-4731)GAA>GCA	p.E1577A	DENND4C_uc011lnc.1_Missense_Mutation_p.E907A|DENND4C_uc011lnd.1_Missense_Mutation_p.E865A|DENND4C_uc003znr.2_Missense_Mutation_p.E865A|DENND4C_uc003zns.2_Missense_Mutation_p.E759A	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1577						integral to membrane				ovary(1)	1														0.307692	24.591643	25.448014	8	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19369895	19369895	4614	9	A	C	C	C	117	9	DENND4C	4	4
UBAP1	51271	broad.mit.edu	37	9	34249927	34249927	+	Missense_Mutation	SNP	G	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:34249927G>A	uc011loj.1	+	c.1426G>A	c.(1426-1428)GCC>ACC	p.A476T	UBAP1_uc010mka.1_Missense_Mutation_p.A448T|UBAP1_uc003ztx.2_Missense_Mutation_p.A412T|UBAP1_uc003zty.2_Missense_Mutation_p.A412T|UBAP1_uc011loi.1_Missense_Mutation_p.A448T|KIF24_uc010mkb.2_Intron|UBAP1_uc003ztz.2_Missense_Mutation_p.A412T	NM_016525	NP_057609	Q9NZ09	UBAP1_HUMAN	ubiquitin associated protein 1	412	UBA 1.					cytoplasm					0			LUSC - Lung squamous cell carcinoma(29;0.00272)			NSCLC(109;1074 1634 14978 20375 39620)								0.169231	21.382892	28.116511	11	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34249927	34249927	17393	9	G	A	A	A	442	34	UBAP1	2	2
FAM120A	23196	broad.mit.edu	37	9	96324522	96324522	+	Missense_Mutation	SNP	T	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:96324522T>G	uc004atw.2	+	c.2981T>G	c.(2980-2982)ATT>AGT	p.I994S	FAM120A_uc004aty.2_Missense_Mutation_p.I775S|FAM120A_uc004atz.2_Missense_Mutation_p.I642S|FAM120A_uc010mrg.2_Missense_Mutation_p.I261S|FAM120A_uc004aua.1_5'Flank	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	oxidative stress-associated Src activator	994	RNA binding.					cytoplasm|plasma membrane	RNA binding				0														0.588235	35.953277	36.068897	10	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96324522	96324522	5612	9	T	G	G	G	676	52	FAM120A	4	4
NXF2B	728343	broad.mit.edu	37	X	101581408	101581408	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:101581408G>C	uc004eiv.3	+	c.1861G>C	c.(1861-1863)GCC>CCC	p.A621P	NXF2B_uc004eiu.3_Missense_Mutation_p.A621P|NXF2B_uc004eiw.3_3'UTR|NXF2_uc004eix.3_Missense_Mutation_p.A621P	NM_001099686	NP_001093156	Q9GZY0	NXF2_HUMAN	nuclear RNA export factor 2B	621	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														0.707317	100.188287	101.765734	29	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101581408	101581408	11189	23	G	C	C	C	546	42	NXF2B	3	3
GUCY2F	2986	broad.mit.edu	37	X	108718455	108718455	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:108718455G>T	uc004eod.3	-	c.711C>A	c.(709-711)CAC>CAA	p.H237Q	GUCY2F_uc011msq.1_Non-coding_Transcript	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	237	Extracellular (Potential).				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8										308		OREG0019905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.775	101.729675	104.503865	31	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108718455	108718455	7178	23	G	T	T	T	568	44	GUCY2F	2	2
CT47A6	728062	broad.mit.edu	37	X	120094450	120094450	+	Silent	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:120094450G>T	uc004eth.2	-	c.633C>A	c.(631-633)CCC>CCA	p.P211P	CT47A1_uc004eti.2_Intron	NM_001080141	NP_001073610	Q5JQC4	CT47A_HUMAN	cancer/testis antigen family 47, member A6	211											0														0.845679	450.732164	469.277185	137	25	KEEP	---	---	---	---	capture		Silent	SNP	120094450	120094450	4142	23	G	T	T	T	496	39	CT47A6	1	1
ACTRT1	139741	broad.mit.edu	37	X	127185207	127185207	+	Missense_Mutation	SNP	G	C	C			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:127185207G>C	uc004eum.2	-	c.979C>G	c.(979-981)CCC>GCC	p.P327A		NM_138289	NP_612146	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	327						cytoplasm|cytoskeleton				ovary(2)|central_nervous_system(2)	4														0.338235	71.804579	73.377871	23	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127185207	127185207	219	23	G	C	C	C	533	41	ACTRT1	3	3
SLC25A14	9016	broad.mit.edu	37	X	129479160	129479160	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:129479160A>T	uc004evr.1	+	c.71A>T	c.(70-72)CAG>CTG	p.Q24L	SLC25A14_uc011mut.1_5'UTR|SLC25A14_uc011muu.1_Missense_Mutation_p.Q27L|SLC25A14_uc010nrg.2_Missense_Mutation_p.Q24L|SLC25A14_uc004evn.1_Missense_Mutation_p.Q27L|SLC25A14_uc004evo.1_5'UTR|SLC25A14_uc004evp.1_Missense_Mutation_p.Q27L|SLC25A14_uc004evq.1_Missense_Mutation_p.Q24L	NM_022810	NP_073721	O95258	UCP5_HUMAN	solute carrier family 25, member 14 isoform	27					aerobic respiration|mitochondrial transport	integral to plasma membrane|mitochondrial inner membrane	binding			ovary(1)	1														0.297297	64.938879	67.64709	22	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129479160	129479160	14973	23	A	T	T	T	91	7	SLC25A14	3	3
DDX26B	203522	broad.mit.edu	37	X	134713798	134713798	+	Silent	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:134713798A>T	uc004eyw.3	+	c.2094A>T	c.(2092-2094)CCA>CCT	p.P698P	DDX26B_uc004eyx.3_Silent_p.P299P	NM_182540	NP_872346	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	698											0	Acute lymphoblastic leukemia(192;6.56e-05)													0.863636	139.582034	145.217251	38	6	KEEP	---	---	---	---	capture		Silent	SNP	134713798	134713798	4524	23	A	T	T	T	93	8	DDX26B	3	3
GPR112	139378	broad.mit.edu	37	X	135487998	135487998	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135487998G>T	uc004ezu.1	+	c.8802G>T	c.(8800-8802)ATG>ATT	p.M2934I	GPR112_uc010nsb.1_Missense_Mutation_p.M2729I	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2934	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)								p.M2934I(NCIH1651-Tumor)	487				0.731959	227.55166	232.288371	71	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135487998	135487998	6903	23	G	T	T	T	585	45	GPR112	2	2
LDOC1	23641	broad.mit.edu	37	X	140270799	140270799	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140270799G>T	uc004fbj.2	-	c.408C>A	c.(406-408)GAC>GAA	p.D136E		NM_012317	NP_036449	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	136	Asp/Glu-rich (highly acidic).				negative regulation of cell proliferation	nucleus	protein binding				0	Acute lymphoblastic leukemia(192;7.65e-05)													0.242424	22.708532	24.68768	8	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140270799	140270799	9033	23	G	T	T	T	516	40	LDOC1	1	1
GAB3	139716	broad.mit.edu	37	X	153927568	153927568	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153927568C>A	uc004fmk.1	-	c.1345_splice	c.e6+1	p.S449_splice	GAB3_uc004fmj.1_Splice_Site_SNP_p.S448_splice|GAB3_uc010nve.1_Splice_Site_SNP_p.S449_splice|GAB3_uc004fml.1_Splice_Site_SNP_p.S68_splice	NM_001081573	NP_001075042			Gab3 protein isoform 1											ovary(1)	1	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.422414	159.079999	159.683031	49	67	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	153927568	153927568	6401	23	C	A	A	A	221	17	GAB3	5	2
MBTPS2	51360	broad.mit.edu	37	X	21900704	21900704	+	Silent	SNP	C	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:21900704C>T	uc004dae.2	+	c.1491C>T	c.(1489-1491)ATC>ATT	p.I497I	MBTPS2_uc010nfr.2_Silent_p.I90I	NM_015884	NP_056968	O43462	MBTP2_HUMAN	membrane-bound transcription factor peptidase,	497	Helical; (Potential).				cholesterol metabolic process|proteolysis	Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity			ovary(1)	1														0.207317	39.757944	46.247152	17	65	KEEP	---	---	---	---	capture		Silent	SNP	21900704	21900704	9751	23	C	T	T	T	408	32	MBTPS2	2	2
MAGEB16	139604	broad.mit.edu	37	X	35820657	35820657	+	Missense_Mutation	SNP	A	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:35820657A>T	uc010ngt.1	+	c.344A>T	c.(343-345)CAG>CTG	p.Q115L		NM_001099921	NP_001093391	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	115	MAGE.									lung(3)|ovary(2)|breast(1)	6										43				0.6	21.552925	21.640768	6	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35820657	35820657	9555	23	A	T	T	T	91	7	MAGEB16	3	3
CXorf59	286464	broad.mit.edu	37	X	36122632	36122632	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:36122632G>T	uc004ddk.1	+	c.869G>T	c.(868-870)CGT>CTT	p.R290L		NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464	290						integral to membrane				central_nervous_system(1)	1														0.514286	62.653028	62.659329	18	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36122632	36122632	4279	23	G	T	T	T	520	40	CXorf59	1	1
KDM6A	7403	broad.mit.edu	37	X	44949010	44949010	+	Missense_Mutation	SNP	G	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:44949010G>T	uc011mkz.1	+	c.3727G>T	c.(3727-3729)GGT>TGT	p.G1243C	KDM6A_uc004dge.3_Missense_Mutation_p.G1191C|KDM6A_uc011mla.1_Missense_Mutation_p.G1146C|KDM6A_uc011mlb.1_Missense_Mutation_p.G1198C|KDM6A_uc011mlc.1_Missense_Mutation_p.G895C|KDM6A_uc011mld.1_Missense_Mutation_p.G830C	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide	1191	JmjC.				histone H3-K4 methylation|oxidation-reduction process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84						Colon(129;1273 1667 15230 27352 52914)				372				0.5625	27.475386	27.529596	9	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44949010	44949010	8443	23	G	T	T	T	559	43	KDM6A	2	2
OR52A4	390053	broad.mit.edu	37	11	5142720	5142721	+	Frame_Shift_Ins	INS	-	A	A			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5142720_5142721insA	uc001lzz.1	-	c.88_89insT	c.(88-90)TGGfs	p.W30fs	OR52A4_uc001maa.2_Non-coding_Transcript	NM_001005222	NP_001005222	A6NMU1	O52A4_HUMAN	olfactory receptor, family 52, subfamily A,	30	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)										0.54			36	31		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	5142720	5142721	11519	11	-	A	A	A	273	21	OR52A4	5	5
KEAP1	9817	broad.mit.edu	37	19	10597426	10597426	+	Frame_Shift_Del	DEL	C	-	-			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10597426_10597426delC	uc002moq.1	-	c.1777_1777delG	c.(1777-1779)GAGfs	p.E593fs	KEAP1_uc002mop.1_Frame_Shift_Del_p.E252fs|KEAP1_uc002mor.1_Frame_Shift_Del_p.E593fs	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	593	Kelch 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			breast(2)|ovary(1)|pancreas(1)	4			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)											0.69			66	29		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	10597426	10597426	8447	19	C	-	-	-	403	31	KEAP1	5	5
SPTBN4	57731	broad.mit.edu	37	19	41073667	41073668	+	Frame_Shift_Ins	INS	-	T	T			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:41073667_41073668insT	uc002ony.2	+	c.6435_6436insT	c.(6433-6438)GCGCCCfs	p.A2145fs	SPTBN4_uc002onz.2_Frame_Shift_Ins_p.A2145fs|SPTBN4_uc010egx.2_Frame_Shift_Ins_p.A888fs	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	2145_2146					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)											0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	41073667	41073668	15635	19	-	T	T	T	483	38	SPTBN4	5	5
USP4	7375	broad.mit.edu	37	3	49321528	49321528	+	Frame_Shift_Del	DEL	T	-	-			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49321528_49321528delT	uc003cwq.2	-	c.2432_2432delA	c.(2431-2433)AAGfs	p.K811fs	USP4_uc003cwo.2_Frame_Shift_Del_p.K523fs|USP4_uc003cwp.2_Frame_Shift_Del_p.K541fs|USP4_uc003cwr.2_Frame_Shift_Del_p.K764fs	NM_003363	NP_003354	Q13107	UBP4_HUMAN	ubiquitin specific protease 4 isoform a	811					negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)	3		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)										0.60			38	25		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	49321528	49321528	17635	3	T	-	-	-	728	56	USP4	5	5
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	Frame_Shift_Del	DEL	AGAGCTCC	-	-			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:74300557_74300564delAGAGCTCC	uc003ubj.3	-	c.243_250delGGAGCTCT	c.(241-252)CTGGAGCTCTTCfs	p.L81fs	STAG3L2_uc011kfj.1_Non-coding_Transcript	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like	81_84	SCD.					nucleus					0														0.44			4	5		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	74300557	74300564	15764	7	AGAGCTCC	-	-	-	39	3	STAG3L2	5	5
EFR3A	23167	broad.mit.edu	37	8	132968101	132968102	+	Frame_Shift_Ins	INS	-	G	G			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:132968101_132968102insG	uc003yte.2	+	c.725_726insG	c.(724-726)CTGfs	p.L242fs		NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A	242						plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)											0.43			53	69		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	132968101	132968102	5146	8	-	G	G	G	715	55	EFR3A	5	5
LYPD2	137797	broad.mit.edu	37	8	143831874	143831874	+	Frame_Shift_Del	DEL	C	-	-			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:143831874_143831874delC	uc003ywz.2	-	c.205_205delG	c.(205-207)GTGfs	p.V69fs		NM_205545	NP_991108	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2 precursor	69	UPAR/Ly6.					anchored to membrane|plasma membrane					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)													0.45			5	6		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	143831874	143831874	9487	8	C	-	-	-	234	18	LYPD2	5	5
GTF2E2	2961	broad.mit.edu	37	8	30464658	30464658	+	Frame_Shift_Del	DEL	C	-	-			TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30464658_30464658delC	uc003xig.2	-	c.559_559delG	c.(559-561)GACfs	p.D187fs		NM_002095	NP_002086	P29084	T2EB_HUMAN	general transcription factor IIE, polypeptide 2,	187					regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIE complex	DNA binding|protein binding|RNA polymerase II transcription factor activity				0				KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)										0.34			22	42		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	30464658	30464658	7137	8	C	-	-	-	390	30	GTF2E2	5	5
DAB2IP	153090	broad.mit.edu	37	9	124522620	124522631	+	In_Frame_Del	DEL	GGGCTGTGTGCA	-	-	rs112361531		TCGA-35-5375-01	TCGA-35-5375-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:124522620_124522631delGGGCTGTGTGCA	uc004bln.2	+	c.988_999delGGGCTGTGTGCA	c.(988-999)GGGCTGTGTGCAdel	p.GLCA330del	DAB2IP_uc004blo.2_In_Frame_Del_p.GLCA234del	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	358_361					activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of Ras protein signal transduction|positive regulation of apoptosis|positive regulation of gene-specific transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2														0.33			4	8		---	---	---	---	capture_indel		In_Frame_Del	DEL	124522620	124522631	4385	9	GGGCTGTGTGCA	-	-	-	559	43	DAB2IP	5	5
