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
C10orf2	56652	broad.mit.edu	37	10	102753132	102753132	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102753132G>C	uc001ksf.2	+	c.1920G>C	c.(1918-1920)AAG>AAC	p.K640N	C10orf2_uc001ksg.2_3'UTR|C10orf2_uc001ksi.2_3'UTR|C10orf2_uc010qpv.1_Missense_Mutation_p.K186N|C10orf2_uc001ksh.2_Non-coding_Transcript	NM_021830	NP_068602	Q96RR1	PEO1_HUMAN	twinkle isoform A	640					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)										0.108696	19.12263	40.058798	15	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102753132	102753132	1634	10	G	C	C	C	425	33	C10orf2	3	3
POLL	27343	broad.mit.edu	37	10	103343395	103343395	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:103343395T>G	uc001ktg.1	-	c.935A>C	c.(934-936)AAA>ACA	p.K312T	DPCD_uc010qpz.1_Intron|POLL_uc001ktd.1_5'Flank|POLL_uc001kte.1_Missense_Mutation_p.K4T|POLL_uc001kth.1_Missense_Mutation_p.K37T|POLL_uc001kti.1_Missense_Mutation_p.K312T|POLL_uc001ktj.1_Missense_Mutation_p.K312T|POLL_uc001ktf.2_Missense_Mutation_p.K220T|POLL_uc001ktk.1_Missense_Mutation_p.K51T|POLL_uc010qqa.1_Missense_Mutation_p.K51T|POLL_uc010qqb.1_Non-coding_Transcript|POLL_uc001ktm.2_Missense_Mutation_p.K312T|POLL_uc001ktl.2_Missense_Mutation_p.K224T|POLL_uc010qqc.1_Missense_Mutation_p.K4T|POLL_uc010qqd.1_Missense_Mutation_p.K170Q	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	DNA-directed DNA polymerase lambda	312		Schiff-base intermediate with DNA.		K->A: Reduces dRP lyase activity by over 90%.	DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)										0.176471	5.009282	6.696139	3	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103343395	103343395	12633	10	T	G	G	G	832	64	POLL	4	4
SORCS1	114815	broad.mit.edu	37	10	108439018	108439018	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:108439018C>A	uc001kyl.2	-	c.1736G>T	c.(1735-1737)AGA>ATA	p.R579I	SORCS1_uc001kym.2_Missense_Mutation_p.R579I|SORCS1_uc009xxs.2_Missense_Mutation_p.R579I|SORCS1_uc001kyn.1_Missense_Mutation_p.R579I|SORCS1_uc001kyo.2_Missense_Mutation_p.R579I	NM_001013031	NP_001013049	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform b	579	Lumenal (Potential).|BNR 4.					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)	1		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)										0.092105	1.361883	14.103701	7	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108439018	108439018	15430	10	C	A	A	A	416	32	SORCS1	2	2
TCERG1L	256536	broad.mit.edu	37	10	132944790	132944790	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:132944790G>T	uc001lkp.2	-	c.1168C>A	c.(1168-1170)CGC>AGC	p.R390S	TCERG1L_uc009yax.1_Non-coding_Transcript	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	390										large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)						800				0.14	12.101921	18.350244	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132944790	132944790	16212	10	G	T	T	T	520	40	TCERG1L	1	1
CUBN	8029	broad.mit.edu	37	10	16911667	16911667	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:16911667T>A	uc001ioo.2	-	c.9422A>T	c.(9421-9423)AAA>ATA	p.K3141I	CUBN_uc009xjq.1_Non-coding_Transcript|CUBN_uc009xjr.1_Missense_Mutation_p.K497I	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3141	CUB 23.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)	18					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)					2704				0.094828	5.260603	24.362653	11	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16911667	16911667	4211	10	T	A	A	A	832	64	CUBN	3	3
OR13A1	79290	broad.mit.edu	37	10	45799860	45799860	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:45799860C>T	uc001jcc.1	-	c.11G>A	c.(10-12)TGG>TAG	p.W4*	OR13A1_uc001jcd.1_5'UTR	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	4	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.109091	7.131962	15.436329	6	49	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	45799860	45799860	11339	10	C	T	T	T	273	21	OR13A1	5	2
PCDH15	65217	broad.mit.edu	37	10	55582459	55582459	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55582459G>T	uc010qhy.1	-	c.5048C>A	c.(5047-5049)ACT>AAT	p.T1683N	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.T1673N|PCDH15_uc010qhw.1_Missense_Mutation_p.T1636N|PCDH15_uc010qhx.1_Missense_Mutation_p.T1607N|PCDH15_uc010qhz.1_Missense_Mutation_p.T1678N|PCDH15_uc010qia.1_Missense_Mutation_p.T1656N|PCDH15_uc001jju.1_Missense_Mutation_p.T1676N|PCDH15_uc010qib.1_Missense_Mutation_p.T1653N	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	1676	Cytoplasmic (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				0.048193	-9.87299	8.150935	4	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55582459	55582459	11931	10	G	T	T	T	468	36	PCDH15	2	2
PCDH15	65217	broad.mit.edu	37	10	55943337	55943338	+	Missense_Mutation	DNP	CC	TA	TA			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55943337_55943338CC>TA	uc010qhy.1	-	c.1471_1472GG>TA	c.(1471-1473)GGT>TAT	p.G491Y	PCDH15_uc010qhq.1_Missense_Mutation_p.G491Y|PCDH15_uc010qhr.1_Missense_Mutation_p.G486Y|PCDH15_uc010qhs.1_Missense_Mutation_p.G498Y|PCDH15_uc010qht.1_Missense_Mutation_p.G493Y|PCDH15_uc010qhu.1_Missense_Mutation_p.G486Y|PCDH15_uc001jjv.1_Missense_Mutation_p.G464Y|PCDH15_uc010qhv.1_Missense_Mutation_p.G486Y|PCDH15_uc010qhw.1_Missense_Mutation_p.G449Y|PCDH15_uc010qhx.1_Missense_Mutation_p.G486Y|PCDH15_uc010qhz.1_Missense_Mutation_p.G486Y|PCDH15_uc010qia.1_Missense_Mutation_p.G464Y|PCDH15_uc001jju.1_Missense_Mutation_p.G486Y|PCDH15_uc010qib.1_Missense_Mutation_p.G464Y|PCDH15_uc001jjw.2_Missense_Mutation_p.G486Y	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	486	Cadherin 4.|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)							p.G486C(NCIH2342-Tumor)	1612				0.102564	5.842758	18.120542	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	55943337	55943338	11931	10	CC	TA	TA	TA	234	18	PCDH15	2	2
CARD16	114769	broad.mit.edu	37	11	104915140	104915140	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:104915140C>G	uc001pip.1	-	c.253G>C	c.(253-255)GAG>CAG	p.E85Q	CASP1_uc010rve.1_Intron|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CARD16_uc001pio.1_Missense_Mutation_p.E85Q	NM_001017534	NP_001017534	Q5EG05	CAR16_HUMAN	caspase-1 dominant-negative inhibitor pseudo-ICE	85	CARD.				regulation of apoptosis	intracellular	cysteine-type endopeptidase inhibitor activity				0														0.031469	-49.15432	19.542527	9	277	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104915140	104915140	2766	11	C	G	G	G	416	32	CARD16	3	3
CARD16	114769	broad.mit.edu	37	11	104915311	104915311	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:104915311C>T	uc001pip.1	-	c.82G>A	c.(82-84)GAA>AAA	p.E28K	CASP1_uc010rve.1_Intron|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CARD16_uc001pio.1_Missense_Mutation_p.E28K	NM_001017534	NP_001017534	Q5EG05	CAR16_HUMAN	caspase-1 dominant-negative inhibitor pseudo-ICE	28	CARD.				regulation of apoptosis	intracellular	cysteine-type endopeptidase inhibitor activity				0														0.032967	-63.728715	22.940975	12	352	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104915311	104915311	2766	11	C	T	T	T	377	29	CARD16	2	2
GRIA4	2893	broad.mit.edu	37	11	105623720	105623720	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:105623720T>A	uc001pix.2	+	c.261T>A	c.(259-261)TAT>TAA	p.Y87*	GRIA4_uc001piu.1_Nonsense_Mutation_p.Y87*|GRIA4_uc001piw.2_Nonsense_Mutation_p.Y87*|GRIA4_uc001piv.2_Nonsense_Mutation_p.Y87*|GRIA4_uc009yxk.1_Nonsense_Mutation_p.Y87*	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	87	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)									0.1	12.47623	33.25374	13	117	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	105623720	105623720	7048	11	T	A	A	A	673	52	GRIA4	5	3
NLRX1	79671	broad.mit.edu	37	11	119054062	119054062	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:119054062C>A	uc001pvu.2	+	c.2842C>A	c.(2842-2844)CTT>ATT	p.L948I	NLRX1_uc001pvv.2_Intron|NLRX1_uc001pvw.2_Missense_Mutation_p.L948I|NLRX1_uc001pvx.2_Missense_Mutation_p.L948I|PDZD3_uc001pvy.2_5'Flank|PDZD3_uc001pvz.2_5'Flank|PDZD3_uc010rzd.1_5'Flank|PDZD3_uc001pwa.2_5'Flank|PDZD3_uc001pwb.2_5'Flank	NM_024618	NP_078894	Q86UT6	NLRX1_HUMAN	NLR family member X1 isoform 1	948	Required for the repression of MAVS- induced interferon signaling.				innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production	mitochondrial outer membrane	ATP binding			ovary(1)	1	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)										0.071429	-1.60882	6.341181	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119054062	119054062	10888	11	C	A	A	A	312	24	NLRX1	2	2
OR8B4	283162	broad.mit.edu	37	11	124294638	124294638	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124294638C>A	uc010sak.1	-	c.130G>T	c.(130-132)GGC>TGC	p.G44C		NM_001005196	NP_001005196	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B,	44	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)										0.086957	2.343768	18.219989	8	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124294638	124294638	11640	11	C	A	A	A	286	22	OR8B4	2	2
ROBO4	54538	broad.mit.edu	37	11	124765507	124765507	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124765507T>C	uc001qbg.2	-	c.882A>G	c.(880-882)GGA>GGG	p.G294G	ROBO4_uc010sas.1_Silent_p.G149G|ROBO4_uc001qbh.2_Silent_p.G184G|ROBO4_uc001qbi.2_5'Flank|ROBO4_uc010sat.1_5'Flank	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	294	Fibronectin type-III 1.				angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)										0.218182	30.185908	34.202264	12	43	KEEP	---	---	---	---	capture		Silent	SNP	124765507	124765507	13995	11	T	C	C	C	691	54	ROBO4	4	4
ARHGAP32	9743	broad.mit.edu	37	11	128839487	128839487	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128839487C>T	uc009zcp.2	-	c.5579G>A	c.(5578-5580)AGC>AAC	p.S1860N	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Missense_Mutation_p.S819N|ARHGAP32_uc001qez.2_Missense_Mutation_p.S1511N	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1860	Interaction with FYN.				cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5														0.190476	6.280202	8.172453	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128839487	128839487	893	11	C	T	T	T	364	28	ARHGAP32	2	2
ARHGAP32	9743	broad.mit.edu	37	11	128848784	128848784	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128848784T>A	uc009zcp.2	-	c.1961A>T	c.(1960-1962)AAG>ATG	p.K654M	ARHGAP32_uc009zcq.1_Missense_Mutation_p.K614M|ARHGAP32_uc009zco.2_De_novo_Start_OutOfFrame|ARHGAP32_uc001qez.2_Missense_Mutation_p.K305M	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	654					cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5														0.111111	4.907907	12.987898	6	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128848784	128848784	893	11	T	A	A	A	728	56	ARHGAP32	3	3
ANO3	63982	broad.mit.edu	37	11	26669265	26669265	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:26669265T>A	uc001mqt.3	+	c.2438T>A	c.(2437-2439)CTT>CAT	p.L813H	ANO3_uc010rdr.1_Missense_Mutation_p.L797H|ANO3_uc010rds.1_Missense_Mutation_p.L652H|ANO3_uc010rdt.1_Missense_Mutation_p.L667H	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	813	Helical; (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.183673	20.044584	24.646331	9	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26669265	26669265	706	11	T	A	A	A	728	56	ANO3	3	3
RAG2	5897	broad.mit.edu	37	11	36614774	36614774	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36614774C>T	uc001mwv.3	-	c.945G>A	c.(943-945)AAG>AAA	p.K315K	C11orf74_uc010rfd.1_5'Flank|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank|C11orf74_uc010rfe.1_5'Flank	NM_000536	NP_000527	P55895	RAG2_HUMAN	recombination activating gene 2	315					chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_lung(20;0.226)	all_hematologic(20;0.00756)												0.102941	13.052635	34.40778	14	122	KEEP	---	---	---	---	capture		Silent	SNP	36614774	36614774	13465	11	C	T	T	T	415	32	RAG2	2	2
LRRC4C	57689	broad.mit.edu	37	11	40137259	40137259	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40137259C>A	uc001mxa.1	-	c.584G>T	c.(583-585)GGT>GTT	p.G195V	LRRC4C_uc001mxc.1_Missense_Mutation_p.G191V|LRRC4C_uc001mxd.1_Missense_Mutation_p.G191V|LRRC4C_uc001mxb.1_Missense_Mutation_p.G191V	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	195	LRR 5.				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)												0.168317	34.156653	44.646156	17	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40137259	40137259	9383	11	C	A	A	A	234	18	LRRC4C	2	2
MADD	8567	broad.mit.edu	37	11	47345285	47345285	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47345285G>A	uc001ner.1	+	c.4441G>A	c.(4441-4443)GAG>AAG	p.E1481K	MADD_uc001neq.2_Missense_Mutation_p.E1422K|MADD_uc001nev.1_Missense_Mutation_p.E1379K|MADD_uc001nes.1_Missense_Mutation_p.E1399K|MADD_uc001net.1_Missense_Mutation_p.E1442K|MADD_uc009yln.1_Missense_Mutation_p.E1375K|MADD_uc001neu.1_Missense_Mutation_p.E1379K|MADD_uc001nex.2_Missense_Mutation_p.E1481K|MADD_uc001nez.2_Missense_Mutation_p.E1378K|MADD_uc001new.2_Missense_Mutation_p.E1421K|MADD_uc009ylo.2_Missense_Mutation_p.E395K	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	1481					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(3)|central_nervous_system(2)	10				Lung(87;0.182)						5				0.089552	1.901145	13.294687	6	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47345285	47345285	9529	11	G	A	A	A	481	37	MADD	1	1
OR4A16	81327	broad.mit.edu	37	11	55110813	55110813	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55110813C>T	uc010rie.1	+	c.137C>T	c.(136-138)ACT>ATT	p.T46I		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	46	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3														0.176471	24.165008	30.868186	12	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55110813	55110813	11447	11	C	T	T	T	260	20	OR4A16	2	2
OR4A15	81328	broad.mit.edu	37	11	55135507	55135507	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55135507G>A	uc010rif.1	+	c.148G>A	c.(148-150)GAG>AAG	p.E50K		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	50	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.129032	10.954945	19.265859	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55135507	55135507	11446	11	G	A	A	A	585	45	OR4A15	2	2
OR5T3	390154	broad.mit.edu	37	11	56019977	56019977	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56019977C>A	uc010rjd.1	+	c.302C>A	c.(301-303)GCT>GAT	p.A101D		NM_001004747	NP_001004747	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T,	101	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00448)													0.086957	1.697998	13.613953	6	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56019977	56019977	11593	11	C	A	A	A	364	28	OR5T3	2	2
OR5M3	219482	broad.mit.edu	37	11	56237921	56237921	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56237921C>A	uc010rjk.1	-	c.53G>T	c.(52-54)CGT>CTT	p.R18L		NM_001004742	NP_001004742	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.246575	49.421162	53.684063	18	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56237921	56237921	11585	11	C	A	A	A	247	19	OR5M3	1	1
OR5AP2	338675	broad.mit.edu	37	11	56409469	56409469	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56409469C>G	uc001njb.1	-	c.447G>C	c.(445-447)TTG>TTC	p.L149F		NM_001002925	NP_001002925	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|kidney(1)|central_nervous_system(1)	3														0.092593	6.867031	24.908345	10	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56409469	56409469	11554	11	C	G	G	G	324	25	OR5AP2	3	3
PLCB3	5331	broad.mit.edu	37	11	64029061	64029061	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64029061A>T	uc001nzb.2	+	c.1837A>T	c.(1837-1839)AAA>TAA	p.K613*	PLCB3_uc009ypg.1_Nonsense_Mutation_p.K613*|PLCB3_uc009yph.1_Nonsense_Mutation_p.K546*|PLCB3_uc009ypi.2_Nonsense_Mutation_p.K613*	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	613	PI-PLC Y-box.				intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2														0.21875	17.007928	19.340148	7	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	64029061	64029061	12455	11	A	T	T	T	65	5	PLCB3	5	3
APBB1	322	broad.mit.edu	37	11	6424580	6424580	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6424580C>T	uc001mdb.1	-	c.1009G>A	c.(1009-1011)GGG>AGG	p.G337R	APBB1_uc001mcz.1_5'Flank|APBB1_uc001mdd.3_Missense_Mutation_p.G117R|APBB1_uc001mda.2_5'UTR|APBB1_uc001mdc.1_Missense_Mutation_p.G337R|APBB1_uc010rab.1_5'Flank|APBB1_uc010rac.1_5'Flank|APBB1_uc010rad.1_5'Flank|APBB1_uc010rae.1_Missense_Mutation_p.G102R|APBB1_uc010raf.1_Missense_Mutation_p.G78R|APBB1_uc009yfa.2_Missense_Mutation_p.G78R|APBB1_uc009yey.2_Missense_Mutation_p.G78R|APBB1_uc010rag.1_Missense_Mutation_p.G78R|APBB1_uc009yfb.2_Missense_Mutation_p.G78R|APBB1_uc001mde.2_Missense_Mutation_p.G78R|APBB1_uc010rah.1_Missense_Mutation_p.G78R	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	337					apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription activator activity|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GBM(147;1810 2556 5672 39622)								0.169492	32.404576	44.650314	20	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6424580	6424580	769	11	C	T	T	T	286	22	APBB1	2	2
DEAF1	10522	broad.mit.edu	37	11	674761	674761	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:674761C>A	uc001lqq.1	-	c.1278G>T	c.(1276-1278)CTG>CTT	p.L426L	DEAF1_uc009ycf.1_Non-coding_Transcript	NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1	426	Pro-rich.				embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)										0.333333	30.032066	30.834974	11	22	KEEP	---	---	---	---	capture		Silent	SNP	674761	674761	4551	11	C	A	A	A	262	21	DEAF1	2	2
OR2D3	120775	broad.mit.edu	37	11	6943218	6943219	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6943218_6943219GG>TT	uc010rav.1	+	c.986_987GG>TT	c.(985-987)AGG>ATT	p.R329I		NM_001004684	NP_001004684	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D,	329	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)										0.074627	-0.345627	12.067328	5	62	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	6943218	6943219	11401	11	GG	TT	TT	TT	455	35	OR2D3	2	2
STAB2	55576	broad.mit.edu	37	12	104031840	104031840	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:104031840T>A	uc001tjw.2	+	c.756T>A	c.(754-756)TGT>TGA	p.C252*		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	252	Extracellular (Potential).|EGF-like 4.				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														0.115789	10.752845	24.587296	11	84	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	104031840	104031840	15756	12	T	A	A	A	738	57	STAB2	5	3
ASCL4	121549	broad.mit.edu	37	12	108169129	108169129	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:108169129C>A	uc001tmr.2	+	c.137C>A	c.(136-138)GCG>GAG	p.A46E		NM_203436	NP_982260	Q6XD76	ASCL4_HUMAN	achaete-scute complex-like 4	45					regulation of transcription from RNA polymerase II promoter|skin development|transcription, DNA-dependent	nucleus	DNA binding|RNA polymerase II transcription factor activity			central_nervous_system(1)	1						GBM(170;776 3695 11650)								0.333333	9.42284	9.643825	3	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108169129	108169129	1055	12	C	A	A	A	351	27	ASCL4	1	1
GOLGA3	2802	broad.mit.edu	37	12	133381309	133381309	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:133381309G>T	uc001ukz.1	-	c.1590C>A	c.(1588-1590)GAC>GAA	p.D530E	GOLGA3_uc001ula.1_Missense_Mutation_p.D530E|GOLGA3_uc001ulb.2_Missense_Mutation_p.D530E	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	530	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)										0.210526	18.900804	21.830767	8	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133381309	133381309	6823	12	G	T	T	T	620	48	GOLGA3	2	2
ERC1	23085	broad.mit.edu	37	12	1553905	1553905	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:1553905A>C	uc001qjb.2	+	c.3202A>C	c.(3202-3204)ACC>CCC	p.T1068P	ERC1_uc001qiz.2_Non-coding_Transcript|ERC1_uc001qjc.2_Missense_Mutation_p.T1040P|ERC1_uc001qja.2_Non-coding_Transcript|ERC1_uc001qjd.2_Non-coding_Transcript|ERC1_uc001qjf.2_Missense_Mutation_p.T1068P|ERC1_uc010sdv.1_3'UTR|ERC1_uc001qje.2_Non-coding_Transcript	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	1068	Potential.|FIP-RBD.				I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(1)	3	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)							378				0.1	5.110473	14.695552	6	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1553905	1553905	5403	12	A	C	C	C	130	10	ERC1	4	4
SLCO1B1	10599	broad.mit.edu	37	12	21350115	21350115	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21350115T>C	uc001req.3	+	c.963T>C	c.(961-963)AAT>AAC	p.N321N		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	321	Cytoplasmic (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)									0.181818	11.932323	15.069708	6	27	KEEP	---	---	---	---	capture		Silent	SNP	21350115	21350115	15220	12	T	C	C	C	660	51	SLCO1B1	4	4
ALG10B	144245	broad.mit.edu	37	12	38714474	38714474	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:38714474T>G	uc001rln.3	+	c.881T>G	c.(880-882)TTT>TGT	p.F294C	ALG10B_uc001rlo.3_Missense_Mutation_p.F264C|ALG10B_uc010skk.1_Missense_Mutation_p.F234C	NM_001013620	NP_001013642	Q5I7T1	AG10B_HUMAN	asparagine-linked glycosylation 10 homolog B	294	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|plasma membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)	2	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)												0.057377	-8.274082	16.80468	7	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38714474	38714474	515	12	T	G	G	G	832	64	ALG10B	4	4
KIF21A	55605	broad.mit.edu	37	12	39750632	39750632	+	Splice_Site_SNP	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:39750632A>G	uc001rly.2	-	c.1469_splice	c.e10+1	p.R490_splice	KIF21A_uc001rlx.2_Splice_Site_SNP_p.R490_splice|KIF21A_uc001rlz.2_Splice_Site_SNP_p.R490_splice|KIF21A_uc010skl.1_Splice_Site_SNP_p.R490_splice|KIF21A_uc001rma.1_Splice_Site_SNP_p.R498_splice	NM_017641	NP_060111			kinesin family member 21A						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|lung(1)|pancreas(1)	6		Lung NSC(34;0.179)|all_lung(34;0.213)												0.18	22.547469	27.359558	9	41	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	39750632	39750632	8599	12	A	G	G	G	182	14	KIF21A	5	4
CNTN1	1272	broad.mit.edu	37	12	41333204	41333204	+	Silent	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:41333204G>C	uc001rmm.1	+	c.1296G>C	c.(1294-1296)GTG>GTC	p.V432V	CNTN1_uc009zjy.1_Silent_p.V432V|CNTN1_uc001rmn.1_Silent_p.V421V|CNTN1_uc001rmo.2_Silent_p.V432V	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	432	Ig-like C2-type 5.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				ovary(3)|lung(2)|large_intestine(1)	6	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)							p.V432V(RL952-Tumor)	952				0.08	1.659162	10.656381	4	46	KEEP	---	---	---	---	capture		Silent	SNP	41333204	41333204	3778	12	G	C	C	C	574	45	CNTN1	3	3
PDZRN4	29951	broad.mit.edu	37	12	41903696	41903696	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:41903696C>A	uc010skn.1	+	c.587C>A	c.(586-588)ACA>AAA	p.T196K	PDZRN4_uc001rmq.3_Missense_Mutation_p.T137K|PDZRN4_uc009zjz.2_Missense_Mutation_p.T135K|PDZRN4_uc001rmr.2_Missense_Mutation_p.T22K	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	395							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	8	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)								467				0.205479	35.982641	41.855991	15	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41903696	41903696	12131	12	C	A	A	A	221	17	PDZRN4	2	2
ADAMTS20	80070	broad.mit.edu	37	12	43847848	43847848	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43847848C>A	uc010skx.1	-	c.1622G>T	c.(1621-1623)CGT>CTT	p.R541L		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	541	Disintegrin.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.070175	-1.840539	9.022632	4	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43847848	43847848	267	12	C	A	A	A	247	19	ADAMTS20	1	1
COL2A1	1280	broad.mit.edu	37	12	48375180	48375180	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:48375180C>T	uc001rqu.2	-	c.2410_splice	c.e37-1	p.G804_splice	COL2A1_uc009zkw.2_Splice_Site_SNP|COL2A1_uc001rqv.2_Splice_Site_SNP_p.G735_splice	NM_001844	NP_001835			collagen, type II, alpha 1 isoform 1 precursor						axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	extracellular matrix structural constituent conferring tensile strength|identical protein binding|platelet-derived growth factor binding			ovary(1)	1		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)									0.545455	20.050881	20.07064	6	5	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	48375180	48375180	3825	12	C	T	T	T	312	24	COL2A1	5	2
OR6C4	341418	broad.mit.edu	37	12	55945351	55945351	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55945351C>G	uc010spp.1	+	c.341C>G	c.(340-342)GCC>GGC	p.A114G		NM_001005494	NP_001005494	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C,	114	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.357616	162.95997	165.633387	54	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55945351	55945351	11603	12	C	G	G	G	338	26	OR6C4	3	3
NUP107	57122	broad.mit.edu	37	12	69096537	69096537	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:69096537A>T	uc001suf.2	+	c.702A>T	c.(700-702)TTA>TTT	p.L234F	NUP107_uc001sug.2_Missense_Mutation_p.L81F|NUP107_uc010stj.1_Missense_Mutation_p.L205F	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	234					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding				0	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)											0.25	21.785109	23.602609	8	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69096537	69096537	11158	12	A	T	T	T	193	15	NUP107	3	3
NAV3	89795	broad.mit.edu	37	12	78444689	78444689	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78444689G>T	uc001syp.2	+	c.2278G>T	c.(2278-2280)GGT>TGT	p.G760C	NAV3_uc001syo.2_Missense_Mutation_p.G760C|NAV3_uc010sub.1_Missense_Mutation_p.G260C	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	760						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.189189	13.602385	16.948917	7	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78444689	78444689	10581	12	G	T	T	T	559	43	NAV3	2	2
A2M	2	broad.mit.edu	37	12	9246133	9246133	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:9246133A>T	uc001qvk.1	-	c.2168T>A	c.(2167-2169)GTT>GAT	p.V723D	A2M_uc009zgk.1_Missense_Mutation_p.V573D	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	723	Bait region.|Inhibitory.				blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)	4					Bacitracin(DB00626)|Becaplermin(DB00102)									0.164179	18.674822	25.868297	11	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9246133	9246133	5	12	A	T	T	T	26	2	A2M	3	3
CLYBL	171425	broad.mit.edu	37	13	100518543	100518543	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:100518543G>C	uc001vok.2	+	c.684G>C	c.(682-684)AAG>AAC	p.K228N	CLYBL_uc010tix.1_Missense_Mutation_p.R229T|CLYBL_uc010tiy.1_Missense_Mutation_p.K194N	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor	228					cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.081081	2.687811	22.533043	9	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100518543	100518543	3711	13	G	C	C	C	425	33	CLYBL	3	3
PABPC3	5042	broad.mit.edu	37	13	25671839	25671839	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25671839C>T	uc001upy.2	+	c.1503C>T	c.(1501-1503)CGC>CGT	p.R501R		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	501					mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)										0.172414	7.761001	10.700837	5	24	KEEP	---	---	---	---	capture		Silent	SNP	25671839	25671839	11780	13	C	T	T	T	314	25	PABPC3	2	2
MTMR6	9107	broad.mit.edu	37	13	25840012	25840012	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25840012T>G	uc001uqf.3	-	c.536A>C	c.(535-537)AAG>ACG	p.K179T	MTMR6_uc001uqe.1_Missense_Mutation_p.K179T	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	179	Myotubularin phosphatase.					cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)										0.081967	0.450502	22.156933	10	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25840012	25840012	10340	13	T	G	G	G	728	56	MTMR6	4	4
OR4N2	390429	broad.mit.edu	37	14	20296219	20296219	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20296219C>T	uc010tkv.1	+	c.612C>T	c.(610-612)GGC>GGT	p.G204G		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.075758	-3.861393	20.414095	10	122	KEEP	---	---	---	---	capture		Silent	SNP	20296219	20296219	11487	14	C	T	T	T	327	26	OR4N2	2	2
IL25	64806	broad.mit.edu	37	14	23842337	23842337	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23842337C>T	uc001wjr.2	+	c.10C>T	c.(10-12)CGA>TGA	p.R4*	IL25_uc001wjq.2_Intron	NM_022789	NP_073626	Q9H293	IL25_HUMAN	interleukin 25 isoform 1 precursor	4					inflammatory response	extracellular space|membrane	cytokine activity|interleukin-17E receptor binding			ovary(1)	1	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)										0.136364	13.238781	21.683638	9	57	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	23842337	23842337	7979	14	C	T	T	T	347	27	IL25	5	1
MYH7	4625	broad.mit.edu	37	14	23884965	23884965	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23884965C>A	uc001wjx.2	-	c.5030G>T	c.(5029-5031)CGC>CTC	p.R1677L		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1677	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)	3	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)										0.075472	-0.937008	8.853748	4	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23884965	23884965	10434	14	C	A	A	A	351	27	MYH7	1	1
NID2	22795	broad.mit.edu	37	14	52505684	52505684	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:52505684T>C	uc001wzo.2	-	c.2038A>G	c.(2038-2040)ACA>GCA	p.T680A	NID2_uc010tqs.1_Missense_Mutation_p.T680A|NID2_uc010tqt.1_Missense_Mutation_p.T680A|NID2_uc001wzp.2_Missense_Mutation_p.T680A	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	680	Nidogen G2 beta-barrel.				bioluminescence|protein-chromophore linkage	basement membrane|membrane	calcium ion binding|collagen binding			breast(2)|pancreas(2)|ovary(1)|liver(1)	6	Breast(41;0.0639)|all_epithelial(31;0.123)													0.162162	13.029196	17.04196	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52505684	52505684	10816	14	T	C	C	C	741	57	NID2	4	4
KCNH5	27133	broad.mit.edu	37	14	63316464	63316464	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63316464T>C	uc001xfx.2	-	c.1476A>G	c.(1474-1476)CTA>CTG	p.L492L	KCNH5_uc001xfy.2_Silent_p.L492L|KCNH5_uc001xfz.1_Silent_p.L434L	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	492	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)										0.183486	48.136461	58.383387	20	89	KEEP	---	---	---	---	capture		Silent	SNP	63316464	63316464	8340	14	T	C	C	C	782	61	KCNH5	4	4
YLPM1	56252	broad.mit.edu	37	14	75276211	75276211	+	Silent	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75276211A>T	uc001xqj.3	+	c.4650A>T	c.(4648-4650)CCA>CCT	p.P1550P	YLPM1_uc001xql.3_Non-coding_Transcript|YLPM1_uc001xqm.1_Silent_p.P33P	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	1355					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)										0.16	7.487375	10.236593	4	21	KEEP	---	---	---	---	capture		Silent	SNP	75276211	75276211	18069	14	A	T	T	T	67	6	YLPM1	3	3
KCNK10	54207	broad.mit.edu	37	14	88652311	88652311	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:88652311C>A	uc001xwm.2	-	c.1200G>T	c.(1198-1200)GAG>GAT	p.E400D	KCNK10_uc001xwn.2_Missense_Mutation_p.E400D|KCNK10_uc001xwo.2_Missense_Mutation_p.E395D	NM_138318	NP_612191	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	395	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|pancreas(1)	3														0.209302	17.948061	21.315354	9	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88652311	88652311	8364	14	C	A	A	A	415	32	KCNK10	2	2
RYR3	6263	broad.mit.edu	37	15	34112970	34112970	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:34112970G>C	uc001zhi.2	+	c.10772G>C	c.(10771-10773)GGT>GCT	p.G3591A	RYR3_uc010bar.2_Missense_Mutation_p.G3586A	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3591					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.1875	7.915346	9.378312	3	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34112970	34112970	14250	15	G	C	C	C	572	44	RYR3	3	3
MAP1A	4130	broad.mit.edu	37	15	43821529	43821529	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43821529C>A	uc001zrt.2	+	c.7858C>A	c.(7858-7860)CGG>AGG	p.R2620R		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2620						cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(3)|breast(3)|pancreas(2)	8		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)									0.116279	6.75411	12.976155	5	38	KEEP	---	---	---	---	capture		Silent	SNP	43821529	43821529	9610	15	C	A	A	A	243	19	MAP1A	1	1
WDR76	79968	broad.mit.edu	37	15	44158515	44158515	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:44158515C>T	uc001zti.1	+	c.1806C>T	c.(1804-1806)CAC>CAT	p.H602H		NM_024908	NP_079184	Q9H967	WDR76_HUMAN	WD repeat domain 76	602	WD 7.										0		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)										0.105263	2.878831	8.762556	4	34	KEEP	---	---	---	---	capture		Silent	SNP	44158515	44158515	17899	15	C	T	T	T	233	18	WDR76	2	2
SPG11	80208	broad.mit.edu	37	15	44862813	44862813	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:44862813C>T	uc001ztx.2	-	c.6387G>A	c.(6385-6387)ACG>ACA	p.T2129T	SPG11_uc010bdw.2_Silent_p.T259T|SPG11_uc010ueh.1_Silent_p.T2016T|SPG11_uc010uei.1_Silent_p.T2129T	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	2129	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)	4		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)										0.1875	7.117435	8.578907	3	13	KEEP	---	---	---	---	capture		Silent	SNP	44862813	44862813	15553	15	C	T	T	T	236	19	SPG11	1	1
AP4E1	23431	broad.mit.edu	37	15	51223057	51223057	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51223057A>C	uc001zyx.1	+	c.758A>C	c.(757-759)CAA>CCA	p.Q253P	AP4E1_uc010ufi.1_Missense_Mutation_p.Q253P|AP4E1_uc010ufj.1_Non-coding_Transcript|AP4E1_uc010ufk.1_Non-coding_Transcript	NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1	253					intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)										0.092593	4.937601	13.952466	5	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51223057	51223057	762	15	A	C	C	C	65	5	AP4E1	4	4
GLDN	342035	broad.mit.edu	37	15	51693895	51693895	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51693895A>G	uc002aba.2	+	c.1133A>G	c.(1132-1134)AAC>AGC	p.N378S	GLDN_uc002abb.2_Missense_Mutation_p.N254S	NM_181789	NP_861454	Q6ZMI3	GLDN_HUMAN	gliomedin	378	Extracellular (Potential).|Olfactomedin-like.				cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)								OREG0023125	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.072727	-0.542106	9.785149	4	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51693895	51693895	6702	15	A	G	G	G	26	2	GLDN	4	4
GLDN	342035	broad.mit.edu	37	15	51696845	51696845	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51696845T>C	uc002aba.2	+	c.1550T>C	c.(1549-1551)CTT>CCT	p.L517P	GLDN_uc002abb.2_Missense_Mutation_p.L393P	NM_181789	NP_861454	Q6ZMI3	GLDN_HUMAN	gliomedin	517	Extracellular (Potential).|Olfactomedin-like.				cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)										0.103896	9.541986	21.565062	8	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51696845	51696845	6702	15	T	C	C	C	728	56	GLDN	4	4
WDR72	256764	broad.mit.edu	37	15	53889379	53889379	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:53889379G>T	uc002acj.2	-	c.3045C>A	c.(3043-3045)TCC>TCA	p.S1015S		NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	1015										lung(1)	1				all cancers(107;0.0511)										0.170213	45.864126	60.339091	24	117	KEEP	---	---	---	---	capture		Silent	SNP	53889379	53889379	17895	15	G	T	T	T	600	47	WDR72	2	2
TXNDC11	51061	broad.mit.edu	37	16	11829940	11829940	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:11829940G>T	uc010buu.1	-	c.404C>A	c.(403-405)CCT>CAT	p.P135H	TXNDC11_uc002dbg.1_Missense_Mutation_p.P135H	NM_015914	NP_056998	Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	135	Thioredoxin 1.				cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0														0.040462	-27.624849	11.761741	7	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11829940	11829940	17348	16	G	T	T	T	455	35	TXNDC11	2	2
SNX29	92017	broad.mit.edu	37	16	12371874	12371874	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:12371874A>G	uc002dby.3	+	c.608A>G	c.(607-609)TAC>TGC	p.Y203C		NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	203					cell communication		phosphatidylinositol binding			ovary(1)	1														0.056338	-4.954755	9.726945	4	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12371874	12371874	15398	16	A	G	G	G	182	14	SNX29	4	4
ABCC1	4363	broad.mit.edu	37	16	16110392	16110392	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:16110392G>A	uc010bvi.2	+	c.529G>A	c.(529-531)GTC>ATC	p.V177I	ABCC1_uc010bvj.2_Missense_Mutation_p.V177I|ABCC1_uc010bvk.2_Missense_Mutation_p.V177I|ABCC1_uc010bvl.2_Missense_Mutation_p.V177I|ABCC1_uc010bvm.2_Missense_Mutation_p.V177I|ABCC1_uc002del.3_Missense_Mutation_p.V61I|ABCC1_uc010bvn.2_Missense_Mutation_p.V40I	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	177	Helical; Name=5.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)									0.061069	-17.981847	34.693919	16	246	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16110392	16110392	50	16	G	A	A	A	520	40	ABCC1	1	1
GPR139	124274	broad.mit.edu	37	16	20043715	20043715	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20043715T>C	uc002dgu.1	-	c.404A>G	c.(403-405)AAG>AGG	p.K135R	GPR139_uc010vaw.1_Missense_Mutation_p.K42R	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	135	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)	2														0.090909	3.064019	16.060317	7	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20043715	20043715	6922	16	T	C	C	C	728	56	GPR139	4	4
GP2	2813	broad.mit.edu	37	16	20335217	20335217	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20335217C>A	uc002dgv.2	-	c.456G>T	c.(454-456)GTG>GTT	p.V152V	GP2_uc002dgw.2_Silent_p.V152V|GP2_uc002dgx.2_Intron|GP2_uc002dgy.2_Intron	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	152						anchored to membrane|extracellular region|plasma membrane				ovary(3)	3														0.088889	1.17135	8.849955	4	41	KEEP	---	---	---	---	capture		Silent	SNP	20335217	20335217	6856	16	C	A	A	A	314	25	GP2	2	2
OGFOD1	55239	broad.mit.edu	37	16	56485540	56485540	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56485540C>T	uc002ejb.2	+	c.16C>T	c.(16-18)CCA>TCA	p.P6S	OGFOD1_uc002ejc.2_Intron|NUDT21_uc002eja.2_5'Flank	NM_018233	NP_060703	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase	6					oxidation-reduction process		iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)									0.113208	4.818743	12.642571	6	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56485540	56485540	11246	16	C	T	T	T	338	26	OGFOD1	2	2
CCDC113	29070	broad.mit.edu	37	16	58296307	58296307	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:58296307G>C	uc002ene.2	+	c.646G>C	c.(646-648)GCC>CCC	p.A216P	CCDC113_uc010vid.1_Missense_Mutation_p.A162P	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1	216	Potential.					protein complex					0														0.145299	28.322072	42.651298	17	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58296307	58296307	2870	16	G	C	C	C	546	42	CCDC113	3	3
TSNAXIP1	55815	broad.mit.edu	37	16	67860156	67860156	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:67860156C>T	uc010vka.1	+	c.1246C>T	c.(1246-1248)CTG>TTG	p.L416L	TSNAXIP1_uc010cep.2_3'UTR|TSNAXIP1_uc010vjz.1_Silent_p.L239L|TSNAXIP1_uc002euf.3_Silent_p.L95L|TSNAXIP1_uc010vkb.1_Silent_p.L347L|TSNAXIP1_uc002eug.3_Silent_p.L70L|TSNAXIP1_uc002euh.3_Silent_p.L70L|TSNAXIP1_uc002eui.3_Silent_p.L70L|TSNAXIP1_uc002euj.2_Silent_p.L362L|TSNAXIP1_uc002euk.2_Silent_p.L95L	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	362					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)										0.263158	12.064169	13.030071	5	14	KEEP	---	---	---	---	capture		Silent	SNP	67860156	67860156	17183	16	C	T	T	T	363	28	TSNAXIP1	2	2
CNTNAP4	85445	broad.mit.edu	37	16	76572213	76572213	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:76572213C>G	uc002fex.1	+	c.3205C>G	c.(3205-3207)CTT>GTT	p.L1069V	CNTNAP4_uc002feu.1_Missense_Mutation_p.L1066V|CNTNAP4_uc002fev.1_Missense_Mutation_p.L930V|CNTNAP4_uc010chb.1_Missense_Mutation_p.L993V	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	1066	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2														0.085106	0.470776	8.672595	4	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76572213	76572213	3787	16	C	G	G	G	312	24	CNTNAP4	3	3
CDH13	1012	broad.mit.edu	37	16	83378607	83378607	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:83378607C>A	uc002fgx.2	+	c.777C>A	c.(775-777)CCC>CCA	p.P259P	CDH13_uc010vns.1_Silent_p.P306P|CDH13_uc010vnt.1_Silent_p.P5P|CDH13_uc010vnu.1_Silent_p.P220P	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	259	Cadherin 2.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)										0.098765	3.735464	16.786492	8	73	KEEP	---	---	---	---	capture		Silent	SNP	83378607	83378607	3228	16	C	A	A	A	262	21	CDH13	2	2
MYH1	4619	broad.mit.edu	37	17	10402375	10402375	+	Silent	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10402375T>A	uc002gmo.2	-	c.3900A>T	c.(3898-3900)ACA>ACT	p.T1300T		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1300	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.112069	12.478577	29.783478	13	103	KEEP	---	---	---	---	capture		Silent	SNP	10402375	10402375	10424	17	T	A	A	A	756	59	MYH1	3	3
TRPV2	51393	broad.mit.edu	37	17	16335351	16335351	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16335351C>T	uc002gpy.2	+	c.1726C>T	c.(1726-1728)CAG>TAG	p.Q576*	TRPV2_uc002gpz.2_Nonsense_Mutation_p.Q146*	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,	576					sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)										0.159091	11.140207	15.979409	7	37	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	16335351	16335351	17147	17	C	T	T	T	325	25	TRPV2	5	2
KRT26	353288	broad.mit.edu	37	17	38926577	38926577	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38926577A>T	uc002hvf.2	-	c.609T>A	c.(607-609)TGT>TGA	p.C203*		NM_181539	NP_853517	Q7Z3Y9	K1C26_HUMAN	keratin 26	203	Rod.|Coil 1B.					intermediate filament	structural molecule activity				0		Breast(137;0.00526)												0.172131	41.240138	53.601345	21	101	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	38926577	38926577	8778	17	A	T	T	T	180	14	KRT26	5	3
KRT28	162605	broad.mit.edu	37	17	38956072	38956072	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38956072T>C	uc002hvh.1	-	c.74A>G	c.(73-75)AAT>AGT	p.N25S		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	25	Gly-rich.|Head.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				Melanoma(19;789 869 15380 26882 39836)								0.066667	-3.482251	11.113752	5	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38956072	38956072	8780	17	T	C	C	C	676	52	KRT28	4	4
KRT15	3866	broad.mit.edu	37	17	39671752	39671752	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39671752G>C	uc002hwy.2	-	c.1219C>G	c.(1219-1221)CGC>GGC	p.R407G	KRT15_uc002hwz.2_Missense_Mutation_p.R309G|KRT15_uc002hxa.2_Missense_Mutation_p.R242G|KRT15_uc002hxb.1_Missense_Mutation_p.R242G	NM_002275	NP_002266	P19012	K1C15_HUMAN	keratin 15	407	Rod.|Coil 2.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000286)												0.194444	17.210709	20.340743	7	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39671752	39671752	8767	17	G	C	C	C	507	39	KRT15	3	3
AOC3	8639	broad.mit.edu	37	17	41003593	41003593	+	Missense_Mutation	SNP	G	T	T	rs402680	byFrequency	TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41003593G>T	uc002ibv.2	+	c.233G>T	c.(232-234)CGG>CTG	p.R78L		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	78	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)								0.074468	-0.842996	16.624373	7	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41003593	41003593	738	17	G	T	T	T	507	39	AOC3	1	1
ITGB3	3690	broad.mit.edu	37	17	45368339	45368339	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:45368339A>G	uc002ilj.2	+	c.1145A>G	c.(1144-1146)GAG>GGG	p.E382G	ITGB3_uc002ili.1_Missense_Mutation_p.E382G|ITGB3_uc010wkr.1_Non-coding_Transcript	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor	382	Extracellular (Potential).				activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)									0.038168	-19.00466	11.171115	5	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45368339	45368339	8199	17	A	G	G	G	143	11	ITGB3	4	4
KIF2B	84643	broad.mit.edu	37	17	51901229	51901229	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:51901229G>T	uc002iua.2	+	c.835G>T	c.(835-837)GTG>TTG	p.V279L		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	279	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.075	-1.00075	6.407175	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51901229	51901229	8609	17	G	T	T	T	572	44	KIF2B	2	2
BCAS3	54828	broad.mit.edu	37	17	59161875	59161875	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:59161875G>C	uc002iyv.3	+	c.2420G>C	c.(2419-2421)CGT>CCT	p.R807P	BCAS3_uc002iyu.3_Missense_Mutation_p.R792P|BCAS3_uc002iyw.3_Missense_Mutation_p.R788P|BCAS3_uc002iyy.3_Missense_Mutation_p.R563P|BCAS3_uc002iyz.3_Missense_Mutation_p.R361P|BCAS3_uc002iza.3_Missense_Mutation_p.R346P	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1	807						nucleus				ovary(2)|central_nervous_system(2)	4			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)											0.236842	24.359232	26.762141	9	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59161875	59161875	1373	17	G	C	C	C	520	40	BCAS3	3	3
TP53	7157	broad.mit.edu	37	17	7578413	7578413	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578413C>T	uc002gim.2	-	c.517G>A	c.(517-519)GTG>ATG	p.V173M	TP53_uc002gig.1_Missense_Mutation_p.V173M|TP53_uc002gih.2_Missense_Mutation_p.V173M|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.V41M|TP53_uc010cng.1_Missense_Mutation_p.V41M|TP53_uc002gii.1_Missense_Mutation_p.V41M|TP53_uc010cnh.1_Missense_Mutation_p.V173M|TP53_uc010cni.1_Missense_Mutation_p.V173M|TP53_uc002gij.2_Missense_Mutation_p.V173M|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.V80M|TP53_uc002gio.2_Missense_Mutation_p.V41M|TP53_uc010vug.1_Missense_Mutation_p.V134M	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	173	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		V -> M (in LFS; germline mutation and in sporadic cancers; somatic mutation).|V -> W (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|V -> E (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> A (in sporadic cancers; somatic mutation).|V -> L (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.V173L(48)|p.V173M(37)|p.0?(6)|p.V173fs*1(4)|p.V173fs*59(2)|p.V157_C176del20(1)|p.H168fs*69(1)|p.V173W(1)|p.E171fs*1(1)|p.V172_R174delVVR(1)|p.P151_V173del23(1)|p.V173fs*69(1)|p.E171_H179delEVVRRCPHH(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.S149fs*72(1)|p.V173fs*8(1)|p.V172_E180delVVRRCPHHE(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.V173M(MOLM16-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.269231	33.772883	36.243937	14	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7578413	7578413	16923	17	C	T	T	T	221	17	TP53	2	2
DNAH2	146754	broad.mit.edu	37	17	7667441	7667441	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7667441C>T	uc002giu.1	+	c.3186C>T	c.(3184-3186)AGC>AGT	p.S1062S		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1062	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.076923	-0.715359	8.789692	4	48	KEEP	---	---	---	---	capture		Silent	SNP	7667441	7667441	4785	17	C	T	T	T	337	26	DNAH2	2	2
DSG1	1828	broad.mit.edu	37	18	28935116	28935116	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28935116C>A	uc002kwp.2	+	c.2957C>A	c.(2956-2958)GCT>GAT	p.A986D	DSG1_uc010xbp.1_Missense_Mutation_p.A345D	NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	986	Cytoplasmic (Potential).|Gly/Ser-rich.				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			ovary(2)|central_nervous_system(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00559)											0.15	22.054318	33.820249	15	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28935116	28935116	4960	18	C	A	A	A	364	28	DSG1	2	2
WDR7	23335	broad.mit.edu	37	18	54605764	54605764	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:54605764G>T	uc002lgk.1	+	c.3832G>T	c.(3832-3834)GTA>TTA	p.V1278L	WDR7_uc002lgl.1_Missense_Mutation_p.V1245L	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	1278										ovary(2)	2				Lung(128;0.0238)|Colorectal(16;0.0296)										0.069767	-1.509563	6.7084	3	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54605764	54605764	17893	18	G	T	T	T	572	44	WDR7	2	2
TNFRSF11A	8792	broad.mit.edu	37	18	60036549	60036549	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:60036549G>T	uc002lin.2	+	c.1399G>T	c.(1399-1401)GGA>TGA	p.G467*	TNFRSF11A_uc010dpv.2_Intron	NM_003839	NP_003830	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily,	467	Cytoplasmic (Potential).				adaptive immune response|cell-cell signaling|circadian temperature homeostasis|monocyte chemotaxis|osteoclast differentiation|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|response to interleukin-1|response to lipopolysaccharide	external side of plasma membrane|integral to membrane	metal ion binding|tumor necrosis factor receptor activity				0		Colorectal(73;0.188)												0.076923	-1.878111	10.039245	5	60	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	60036549	60036549	16825	18	G	T	T	T	611	47	TNFRSF11A	5	2
ANKRD12	23253	broad.mit.edu	37	18	9256880	9256880	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:9256880C>T	uc002knv.2	+	c.3615C>T	c.(3613-3615)TCC>TCT	p.S1205S	ANKRD12_uc002knw.2_Silent_p.S1182S|ANKRD12_uc002knx.2_Silent_p.S1182S|ANKRD12_uc010dkx.1_Silent_p.S912S	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	1205						nucleus				ovary(2)|central_nervous_system(1)	3														0.217054	65.243052	74.75996	28	101	KEEP	---	---	---	---	capture		Silent	SNP	9256880	9256880	643	18	C	T	T	T	262	21	ANKRD12	2	2
RALBP1	10928	broad.mit.edu	37	18	9517288	9517288	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:9517288C>T	uc002kob.2	+	c.690C>T	c.(688-690)ATC>ATT	p.I230I	RALBP1_uc002koc.2_Silent_p.I230I	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1	230	Rho-GAP.				chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1										246				0.057143	-6.360999	8.055887	4	66	KEEP	---	---	---	---	capture		Silent	SNP	9517288	9517288	13472	18	C	T	T	T	408	32	RALBP1	2	2
KANK2	25959	broad.mit.edu	37	19	11286646	11286646	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11286646G>T	uc002mqm.2	-	c.1804C>A	c.(1804-1806)CTC>ATC	p.L602I	KANK2_uc010dxv.2_Missense_Mutation_p.L594I|KANK2_uc002mqo.3_Missense_Mutation_p.L594I|KANK2_uc002mqp.1_Missense_Mutation_p.L403I	NM_015493	NP_056308	Q63ZY3	KANK2_HUMAN	ankyrin repeat domain 25 isoform 1	594											0														0.115385	3.805228	7.594146	3	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11286646	11286646	8281	19	G	T	T	T	455	35	KANK2	2	2
CYP4F12	66002	broad.mit.edu	37	19	15784478	15784478	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15784478C>T	uc002nbl.2	+	c.139C>T	c.(139-141)CGG>TGG	p.R47W	CYP4F12_uc010xoo.1_Missense_Mutation_p.R47W|CYP4F12_uc010xop.1_Missense_Mutation_p.R47W	NM_023944	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F,	47					oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|central_nervous_system(2)	4	Acute lymphoblastic leukemia(2;0.0367)													0.075812	-4.782166	46.260232	21	256	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15784478	15784478	4352	19	C	T	T	T	295	23	CYP4F12	1	1
ZNF181	339318	broad.mit.edu	37	19	35231858	35231858	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35231858A>G	uc002nvu.3	+	c.572A>G	c.(571-573)AAC>AGC	p.N191S	ZNF181_uc010xsa.1_Missense_Mutation_p.N190S|ZNF181_uc010xsb.1_Missense_Mutation_p.N190S|ZNF181_uc010xsc.1_Missense_Mutation_p.N126S	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	191					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)											0.153846	17.389105	23.327335	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35231858	35231858	18340	19	A	G	G	G	26	2	ZNF181	4	4
NPHS1	4868	broad.mit.edu	37	19	36339163	36339163	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36339163T>C	uc002oby.2	-	c.1307A>G	c.(1306-1308)AAC>AGC	p.N436S		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	436	Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.1	2.896091	12.549514	6	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36339163	36339163	10986	19	T	C	C	C	780	60	NPHS1	4	4
SPTBN4	57731	broad.mit.edu	37	19	41062057	41062057	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:41062057G>A	uc002ony.2	+	c.5152G>A	c.(5152-5154)GAG>AAG	p.E1718K	SPTBN4_uc002onx.2_Missense_Mutation_p.E1718K|SPTBN4_uc002onz.2_Missense_Mutation_p.E1718K|SPTBN4_uc010egx.2_Missense_Mutation_p.E461K|SPTBN4_uc002ooa.2_Missense_Mutation_p.E394K	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	1718	Spectrin 14.				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)											0.3	8.221324	8.578574	3	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41062057	41062057	15635	19	G	A	A	A	533	41	SPTBN4	2	2
CYP2B6	1555	broad.mit.edu	37	19	41509908	41509908	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:41509908C>A	uc002opr.1	+	c.174C>A	c.(172-174)TTC>TTA	p.F58L	CYP2A7_uc002opo.2_Intron|CYP2B6_uc010xvu.1_Missense_Mutation_p.F18L	NM_000767	NP_000758	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B,	58					cellular ketone metabolic process|exogenous drug catabolic process|oxidation-reduction process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(20;0.00322)		Bupropion(DB01156)|Butalbital(DB00241)|Carbamazepine(DB00564)|Clopidogrel(DB00758)|Cyclophosphamide(DB00531)|Efavirenz(DB00625)|Ifosfamide(DB01181)|Memantine(DB01043)|Meperidine(DB00454)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicotine(DB00184)|Orphenadrine(DB01173)|Phenytoin(DB00252)|Propofol(DB00818)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Ticlopidine(DB00208)|Troleandomycin(DB01361)					56				0.117647	3.940311	11.259623	6	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41509908	41509908	4329	19	C	A	A	A	389	30	CYP2B6	2	2
CEACAM20	125931	broad.mit.edu	37	19	45029235	45029235	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45029235A>T	uc010ejn.1	-	c.95T>A	c.(94-96)CTC>CAC	p.L32H	CEACAM20_uc010ejo.1_Missense_Mutation_p.L32H|CEACAM20_uc010ejp.1_Missense_Mutation_p.L32H|CEACAM20_uc010ejq.1_Missense_Mutation_p.L32H	NM_001102597	NP_001096067	Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion	32	Extracellular (Potential).					integral to membrane				large_intestine(2)	2		Prostate(69;0.0352)												0.100917	12.127344	46.769758	22	196	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45029235	45029235	3324	19	A	T	T	T	143	11	CEACAM20	3	3
C5AR1	728	broad.mit.edu	37	19	47823817	47823817	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:47823817G>A	uc002pgj.1	+	c.783G>A	c.(781-783)ACG>ACA	p.T261T		NM_001736	NP_001727	P21730	C5AR_HUMAN	complement component 5 receptor 1	261	Helical; Name=6; (Potential).				activation of MAPK activity|activation of phospholipase C activity|cellular defense response|elevation of cytosolic calcium ion concentration|immune response|sensory perception of chemical stimulus	integral to plasma membrane	C5a anaphylatoxin receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)										0.136364	5.905403	11.579252	6	38	KEEP	---	---	---	---	capture		Silent	SNP	47823817	47823817	2379	19	G	A	A	A	496	39	C5AR1	1	1
ZNF808	388558	broad.mit.edu	37	19	53058234	53058234	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53058234G>A	uc010epq.1	+	c.2065G>A	c.(2065-2067)GTG>ATG	p.V689M	ZNF808_uc002pzq.2_Non-coding_Transcript|ZNF808_uc010epr.1_5'Flank	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	689	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)										0.040752	-47.365094	25.036458	13	306	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53058234	53058234	18771	19	G	A	A	A	520	40	ZNF808	1	1
ZNF582	147948	broad.mit.edu	37	19	56895314	56895314	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56895314C>T	uc002qmy.2	-	c.1565G>A	c.(1564-1566)AGT>AAT	p.S522N	ZNF582_uc002qmz.1_Missense_Mutation_p.S491N	NM_144690	NP_653291	Q96NG8	ZN582_HUMAN	zinc finger protein 582	491					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|large_intestine(1)	4		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		Ovarian(183;1887 2032 4349 30507 51343)								0.157025	34.991192	48.536767	19	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56895314	56895314	18609	19	C	T	T	T	260	20	ZNF582	2	2
PEG3	5178	broad.mit.edu	37	19	57328638	57328638	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57328638T>C	uc002qnu.2	-	c.1172A>G	c.(1171-1173)AAG>AGG	p.K391R	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.K362R|PEG3_uc002qnv.2_Missense_Mutation_p.K391R|PEG3_uc002qnw.2_Missense_Mutation_p.K267R|PEG3_uc002qnx.2_Missense_Mutation_p.K265R|PEG3_uc010etr.2_Missense_Mutation_p.K391R	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	391					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)										0.049383	-17.205225	17.691758	8	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57328638	57328638	12141	19	T	C	C	C	728	56	PEG3	4	4
MUC16	94025	broad.mit.edu	37	19	9071130	9071130	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9071130G>T	uc002mkp.2	-	c.16316C>A	c.(16315-16317)TCT>TAT	p.S5439Y		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5441	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.114478	32.824001	76.358191	34	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9071130	9071130	10367	19	G	T	T	T	429	33	MUC16	2	2
COL11A1	1301	broad.mit.edu	37	1	103487271	103487272	+	Missense_Mutation	DNP	CC	AT	AT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:103487271_103487272CC>AT	uc001dum.2	-	c.1335_1336GG>AT	c.(1333-1338)GTGGTT>GTATTT	p.V446F	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dul.2_Missense_Mutation_p.V434F|COL11A1_uc001dun.2_Missense_Mutation_p.V395F|COL11A1_uc009weh.2_Missense_Mutation_p.V318F	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	434	Triple-helical region (interrupted).				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)										0.233333	16.407673	18.362404	7	23	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	103487271	103487272	3805	1	CC	AT	AT	AT	234	18	COL11A1	2	2
AKNAD1	254268	broad.mit.edu	37	1	109385769	109385769	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109385769A>G	uc001dwa.2	-	c.1366T>C	c.(1366-1368)TTT>CTT	p.F456L	AKNAD1_uc010ovb.1_Missense_Mutation_p.F163L|AKNAD1_uc001dwb.2_Non-coding_Transcript	NM_152763	NP_689976	Q5T1N1	AKND1_HUMAN	hypothetical protein LOC254268	456	Potential.									ovary(3)	3														0.119403	30.742395	59.62689	24	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109385769	109385769	467	1	A	G	G	G	39	3	AKNAD1	4	4
SYPL2	284612	broad.mit.edu	37	1	110018304	110018304	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110018304C>G	uc001dxp.2	+	c.231C>G	c.(229-231)ATC>ATG	p.I77M	SYPL2_uc001dxo.2_Missense_Mutation_p.I77M|SYPL2_uc010ovk.1_Missense_Mutation_p.I77M|SYPL2_uc001dxq.2_5'Flank	NM_001040709	NP_001035799	Q5VXT5	SYPL2_HUMAN	mitsugumin 29	77	Vesicular (Potential).|MARVEL.					integral to membrane|synaptic vesicle	transporter activity			ovary(1)	1		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)										0.09375	6.208123	16.817158	6	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110018304	110018304	15984	1	C	G	G	G	395	31	SYPL2	3	3
FLG	2312	broad.mit.edu	37	1	152276508	152276508	+	Silent	SNP	T	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152276508T>G	uc001ezu.1	-	c.10854A>C	c.(10852-10854)GCA>GCC	p.A3618A		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3618	Filaggrin 22.|Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.035191	-55.483497	24.593012	12	329	KEEP	---	---	---	---	capture		Silent	SNP	152276508	152276508	6160	1	T	G	G	G	808	63	FLG	4	4
BCAN	63827	broad.mit.edu	37	1	156622659	156622659	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156622659T>C	uc001fpp.2	+	c.1917T>C	c.(1915-1917)GGT>GGC	p.G639G	BCAN_uc001fpo.2_Silent_p.G639G	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	639					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.122222	8.898307	21.681741	11	79	KEEP	---	---	---	---	capture		Silent	SNP	156622659	156622659	1366	1	T	C	C	C	756	59	BCAN	4	4
HDGF	3068	broad.mit.edu	37	1	156714082	156714082	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156714082C>A	uc010phr.1	-	c.431G>T	c.(430-432)GGT>GTT	p.G144V	HDGF_uc009wsd.2_Missense_Mutation_p.G89V|HDGF_uc001fpy.3_Missense_Mutation_p.G121V|HDGF_uc001fpz.3_Missense_Mutation_p.G114V|HDGF_uc009wse.2_Missense_Mutation_p.G137V|HDGF_uc009wsf.2_Missense_Mutation_p.G89V|HDGF_uc009wsg.2_Missense_Mutation_p.G121V	NM_001126050	NP_001119522	P51858	HDGF_HUMAN	hepatoma-derived growth factor isoform b	121	Glu-rich.				cell proliferation|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	DNA binding|growth factor activity|heparin binding|nucleotide binding			lung(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)										0.244253	200.501163	221.246985	85	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156714082	156714082	7301	1	C	A	A	A	234	18	HDGF	2	2
PEAR1	375033	broad.mit.edu	37	1	156874545	156874545	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156874545C>T	uc001fqj.1	+	c.107C>T	c.(106-108)ACT>ATT	p.T36I	PEAR1_uc009wsl.1_5'Flank|PEAR1_uc001fqk.1_5'Flank	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	36	EMI.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)													0.156863	28.038375	39.495685	16	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156874545	156874545	12133	1	C	T	T	T	260	20	PEAR1	2	2
FCRL1	115350	broad.mit.edu	37	1	157773775	157773775	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157773775G>A	uc001frg.2	-	c.179C>T	c.(178-180)GCC>GTC	p.A60V	FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Missense_Mutation_p.A60V|FCRL1_uc001fri.2_Missense_Mutation_p.A60V|FCRL1_uc001frj.2_Non-coding_Transcript	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor	60	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)								0.20202	39.635703	47.741801	20	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157773775	157773775	6031	1	G	A	A	A	546	42	FCRL1	2	2
SPTA1	6708	broad.mit.edu	37	1	158585142	158585143	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158585142_158585143CC>AA	uc001fst.1	-	c.6651_6652GG>TT	c.(6649-6654)GTGGAC>GTTTAC	p.D2218Y		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2218	Spectrin 21.				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)													0.108359	27.965131	77.037405	35	288	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	158585142	158585143	15630	1	CC	AA	AA	AA	390	30	SPTA1	2	2
SPTA1	6708	broad.mit.edu	37	1	158648262	158648262	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158648262C>A	uc001fst.1	-	c.741G>T	c.(739-741)GAG>GAT	p.E247D		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	247	Spectrin 3.				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)													0.070707	-4.544838	14.266218	7	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158648262	158648262	15630	1	C	A	A	A	363	28	SPTA1	2	2
IFI16	3428	broad.mit.edu	37	1	159002342	159002342	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:159002342A>T	uc001ftg.2	+	c.1190A>T	c.(1189-1191)AAT>ATT	p.N397I	IFI16_uc010pis.1_Missense_Mutation_p.N341I|IFI16_uc001fth.2_5'UTR|IFI16_uc010pit.1_5'UTR	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	397					cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nucleolus|nucleoplasm	double-stranded DNA binding|transcription repressor activity			ovary(1)	1	all_hematologic(112;0.0429)													0.143939	28.539522	44.654314	19	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159002342	159002342	7812	1	A	T	T	T	52	4	IFI16	3	3
LMX1A	4009	broad.mit.edu	37	1	165218775	165218775	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:165218775G>T	uc001gcy.1	-	c.366C>A	c.(364-366)TGC>TGA	p.C122*	LMX1A_uc001gcz.1_Nonsense_Mutation_p.C122*	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	122	LIM zinc-binding 2.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4	all_hematologic(923;0.248)													0.263158	36.397109	39.290438	15	42	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	165218775	165218775	9190	1	G	T	T	T	438	34	LMX1A	5	2
TNR	7143	broad.mit.edu	37	1	175360456	175360456	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:175360456C>A	uc001gkp.1	-	c.1475G>T	c.(1474-1476)CGC>CTC	p.R492L	TNR_uc009wwu.1_Missense_Mutation_p.R492L	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	492	Fibronectin type-III 2.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)													0.325	36.975628	38.055225	13	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175360456	175360456	16879	1	C	A	A	A	351	27	TNR	1	1
CEP350	9857	broad.mit.edu	37	1	179983551	179983551	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179983551A>G	uc001gnt.2	+	c.1963A>G	c.(1963-1965)AGG>GGG	p.R655G	CEP350_uc009wxl.2_Missense_Mutation_p.R654G|CEP350_uc001gnu.2_Missense_Mutation_p.R489G	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	655						centrosome|nucleus|spindle				ovary(4)	4														0.288889	40.458327	42.255059	13	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179983551	179983551	3387	1	A	G	G	G	192	15	CEP350	4	4
CACNA1E	777	broad.mit.edu	37	1	181701820	181701820	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181701820C>T	uc001gow.2	+	c.2598C>T	c.(2596-2598)GCC>GCT	p.A866A	CACNA1E_uc009wxs.2_Silent_p.A754A|CACNA1E_uc001gox.1_Silent_p.A92A|CACNA1E_uc009wxt.2_Silent_p.A92A	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	866	Cytoplasmic (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														0.166667	6.115119	8.010118	3	15	KEEP	---	---	---	---	capture		Silent	SNP	181701820	181701820	2658	1	C	T	T	T	275	22	CACNA1E	2	2
RGL1	23179	broad.mit.edu	37	1	183885736	183885736	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:183885736G>T	uc001gqm.2	+	c.2010G>T	c.(2008-2010)TCG>TCT	p.S670S	RGL1_uc010pog.1_Silent_p.S633S|RGL1_uc010poh.1_Silent_p.S633S|RGL1_uc001gqo.2_Silent_p.S635S|RGL1_uc010poi.1_Silent_p.S606S	NM_015149	NP_055964	Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation	635					cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			ovary(3)|breast(3)|lung(1)	7										871				0.24031	75.602341	83.513989	31	98	KEEP	---	---	---	---	capture		Silent	SNP	183885736	183885736	13749	1	G	T	T	T	470	37	RGL1	1	1
KCNT2	343450	broad.mit.edu	37	1	196227513	196227513	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196227513G>A	uc001gtd.1	-	c.3022C>T	c.(3022-3024)CCC>TCC	p.P1008S	KCNT2_uc009wyt.1_Non-coding_Transcript|KCNT2_uc001gte.1_Missense_Mutation_p.P941S|KCNT2_uc001gtf.1_Missense_Mutation_p.P984S|KCNT2_uc001gtg.1_Non-coding_Transcript|KCNT2_uc001gth.1_Missense_Mutation_p.P512S	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1008	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|catalytic activity|voltage-gated potassium channel activity			ovary(4)|breast(1)	5														0.210526	27.367822	31.787049	12	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196227513	196227513	8397	1	G	A	A	A	533	41	KCNT2	2	2
LHX9	56956	broad.mit.edu	37	1	197887011	197887011	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197887011A>T	uc001guk.1	+	c.58A>T	c.(58-60)ATG>TTG	p.M20L	LHX9_uc009wzc.1_Non-coding_Transcript|LHX9_uc001gui.1_Missense_Mutation_p.M11L|LHX9_uc001guj.1_Missense_Mutation_p.M26L	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1	20					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(1)	1														0.068376	-3.379222	19.149397	8	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197887011	197887011	9103	1	A	T	T	T	104	8	LHX9	3	3
PRELP	5549	broad.mit.edu	37	1	203452736	203452736	+	Missense_Mutation	SNP	G	A	A	rs56086342		TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:203452736G>A	uc001gzs.2	+	c.424G>A	c.(424-426)GAC>AAC	p.D142N	PRELP_uc001gzt.2_Missense_Mutation_p.D142N	NM_002725	NP_002716	P51888	PRELP_HUMAN	proline arginine-rich end leucine-rich repeat	142	LRR 3.				skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(1)|central_nervous_system(1)|pancreas(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.109)											0.204545	60.819871	71.555189	27	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	203452736	203452736	12916	1	G	A	A	A	429	33	PRELP	2	2
USH2A	7399	broad.mit.edu	37	1	216373437	216373437	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216373437G>A	uc001hku.1	-	c.3343C>T	c.(3343-3345)CTG>TTG	p.L1115L	USH2A_uc001hkv.2_Silent_p.L1115L	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1115	Extracellular (Potential).|Fibronectin type-III 1.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.071429	-1.143175	9.453082	4	52	KEEP	---	---	---	---	capture		Silent	SNP	216373437	216373437	17598	1	G	A	A	A	451	35	USH2A	2	2
OBSCN	84033	broad.mit.edu	37	1	228444509	228444509	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228444509C>T	uc009xez.1	+	c.4467C>T	c.(4465-4467)CGC>CGT	p.R1489R	OBSCN_uc001hsn.2_Silent_p.R1489R	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1489	Ig-like 15.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.15	9.162984	13.829508	6	34	KEEP	---	---	---	---	capture		Silent	SNP	228444509	228444509	11217	1	C	T	T	T	314	25	OBSCN	2	2
NUP133	55746	broad.mit.edu	37	1	229631292	229631292	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229631292T>A	uc001htn.2	-	c.996A>T	c.(994-996)GAA>GAT	p.E332D		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	332					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|ovary(1)	5	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)								578				0.214286	14.634373	16.74512	6	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229631292	229631292	11159	1	T	A	A	A	725	56	NUP133	3	3
URB2	9816	broad.mit.edu	37	1	229773769	229773769	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229773769G>T	uc001hts.1	+	c.3409G>T	c.(3409-3411)GCC>TCC	p.A1137S	URB2_uc009xfd.1_Missense_Mutation_p.A1137S	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	1137						nucleolus				central_nervous_system(2)|ovary(1)	3									p.A1137P(AN3CA-Tumor)	340				0.166667	4.937669	6.81559	3	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229773769	229773769	17587	1	G	T	T	T	546	42	URB2	2	2
EDARADD	128178	broad.mit.edu	37	1	236645924	236645924	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236645924G>C	uc001hxu.1	+	c.623G>C	c.(622-624)CGT>CCT	p.R208P	EDARADD_uc001hxv.1_Missense_Mutation_p.R198P	NM_145861	NP_665860	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain isoform A	208					cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)											0.161765	23.989282	31.381629	11	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	236645924	236645924	5093	1	G	C	C	C	520	40	EDARADD	3	3
ZNF670	93474	broad.mit.edu	37	1	247200850	247200850	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247200850C>T	uc001icd.1	-	c.1071G>A	c.(1069-1071)AGG>AGA	p.R357R	ZNF695_uc001ica.2_Intron|ZNF695_uc001icb.1_Intron	NM_033213	NP_149990	Q9BS34	ZN670_HUMAN	zinc finger protein 670	357	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)											0.404494	107.879774	108.590182	36	53	KEEP	---	---	---	---	capture		Silent	SNP	247200850	247200850	18672	1	C	T	T	T	389	30	ZNF670	2	2
OR2L13	284521	broad.mit.edu	37	1	248262962	248262962	+	Silent	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248262962A>T	uc001ids.2	+	c.285A>T	c.(283-285)GGA>GGT	p.G95G		NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	95	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(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;0.0132)							85				0.190769	130.214327	159.228756	62	263	KEEP	---	---	---	---	capture		Silent	SNP	248262962	248262962	11412	1	A	T	T	T	145	12	OR2L13	3	3
OR2T34	127068	broad.mit.edu	37	1	248737278	248737278	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248737278A>G	uc001iep.1	-	c.781T>C	c.(781-783)TTC>CTC	p.F261L		NM_001001821	NP_001001821	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T,	261	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	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)											0.27	74.478945	79.253434	27	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248737278	248737278	11431	1	A	G	G	G	39	3	OR2T34	4	4
PGBD2	267002	broad.mit.edu	37	1	249211295	249211295	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:249211295A>G	uc001ifh.2	+	c.512A>G	c.(511-513)AAT>AGT	p.N171S	PGBD2_uc001ifg.2_Intron|PGBD2_uc009xhd.2_Missense_Mutation_p.N168S	NM_170725	NP_733843	Q6P3X8	PGBD2_HUMAN	hypothetical protein LOC267002 isoform a	171										ovary(1)	1	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)											0.353261	208.522051	212.014577	65	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	249211295	249211295	12204	1	A	G	G	G	52	4	PGBD2	4	4
CNKSR1	10256	broad.mit.edu	37	1	26507069	26507069	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26507069A>T	uc001bln.3	+	c.178A>T	c.(178-180)ATC>TTC	p.I60F	CNKSR1_uc010oex.1_Non-coding_Transcript|CNKSR1_uc001blm.3_Missense_Mutation_p.I60F|CNKSR1_uc009vsd.2_5'UTR|CNKSR1_uc009vse.2_5'UTR|CNKSR1_uc001blo.2_5'UTR	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras	60	SAM.				Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			kidney(1)	1		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		NSCLC(180;1396 2109 28270 30756 34275)								0.092593	3.335366	12.35374	5	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26507069	26507069	3744	1	A	T	T	T	104	8	CNKSR1	3	3
RLF	6018	broad.mit.edu	37	1	40703619	40703619	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:40703619C>T	uc001cfc.3	+	c.3245C>T	c.(3244-3246)TCA>TTA	p.S1082L	RLF_uc001cfd.3_Missense_Mutation_p.S773L	NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	1082					chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|protein binding|transcription activator activity|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)											0.173077	18.041096	23.291045	9	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40703619	40703619	13866	1	C	T	T	T	377	29	RLF	2	2
TMCO2	127391	broad.mit.edu	37	1	40713903	40713903	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:40713903G>T	uc001cfe.2	+	c.237_splice	c.e1+1	p.Q79_splice		NM_001008740	NP_001008740			transmembrane and coiled-coil domains 2							integral to membrane				ovary(1)	1	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)											0.071429	-0.306865	7.639196	3	39	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	40713903	40713903	16526	1	G	T	T	T	572	44	TMCO2	5	2
POMGNT1	55624	broad.mit.edu	37	1	46657877	46657877	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46657877A>G	uc001cpe.2	-	c.1432T>C	c.(1432-1434)TGG>CGG	p.W478R	POMGNT1_uc010olx.1_Missense_Mutation_p.W456R|POMGNT1_uc010oly.1_Non-coding_Transcript|POMGNT1_uc010olz.1_Missense_Mutation_p.W335R|POMGNT1_uc001cpg.2_Missense_Mutation_p.W478R|POMGNT1_uc001cpf.2_Missense_Mutation_p.W145R|POMGNT1_uc001cph.1_Missense_Mutation_p.W56R|POMGNT1_uc001cpi.1_Missense_Mutation_p.W145R	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose	478	Lumenal (Potential).				protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.153846	21.361183	30.288877	12	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46657877	46657877	12672	1	A	G	G	G	78	6	POMGNT1	4	4
DMRTB1	63948	broad.mit.edu	37	1	53927166	53927166	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53927166C>A	uc001cvq.1	+	c.598C>A	c.(598-600)CCG>ACG	p.P200T		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	200	Pro-rich.				regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.12	6.615056	13.702537	6	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53927166	53927166	4770	1	C	A	A	A	286	22	DMRTB1	2	2
C8A	731	broad.mit.edu	37	1	57351650	57351650	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:57351650G>A	uc001cyo.2	+	c.906G>A	c.(904-906)AAG>AAA	p.K302K		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	302	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)	2														0.142857	28.252223	41.158236	15	90	KEEP	---	---	---	---	capture		Silent	SNP	57351650	57351650	2525	1	G	A	A	A	425	33	C8A	2	2
HOOK1	51361	broad.mit.edu	37	1	60324150	60324150	+	Silent	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:60324150A>G	uc009wad.2	+	c.1293A>G	c.(1291-1293)CGA>CGG	p.R431R	HOOK1_uc001czo.2_Silent_p.R431R|HOOK1_uc001czp.2_Non-coding_Transcript|HOOK1_uc010oor.1_Silent_p.R389R	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	431	Potential.|Sufficient for interaction with microtubules.				early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)													0.125	3.808031	7.105991	3	21	KEEP	---	---	---	---	capture		Silent	SNP	60324150	60324150	7574	1	A	G	G	G	145	12	HOOK1	4	4
RAVER2	55225	broad.mit.edu	37	1	65243492	65243492	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:65243492T>C	uc001dbs.1	+	c.503T>C	c.(502-504)ATT>ACT	p.I168T	RAVER2_uc001dbt.1_Missense_Mutation_p.I47T|RAVER2_uc010opb.1_Missense_Mutation_p.I47T	NM_018211	NP_060681	Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	168	RRM 2.					cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)	1														0.082596	8.64848	68.723236	28	311	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65243492	65243492	13556	1	T	C	C	C	676	52	RAVER2	4	4
HHLA3	11147	broad.mit.edu	37	1	70820791	70820791	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70820791G>T	uc001dfc.2	+	c.157G>T	c.(157-159)GTA>TTA	p.V53L	ANKRD13C_uc001dex.3_5'Flank|ANKRD13C_uc009wbk.2_5'Flank|ANKRD13C_uc001dey.3_5'Flank|HHLA3_uc010oqp.1_Splice_Site_SNP|HHLA3_uc001dfa.2_Missense_Mutation_p.V53L|HHLA3_uc001dfb.2_Splice_Site_SNP_p.A52_splice	NM_001031693	NP_001026863	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3 isoform 1	53							protein binding				0														0.192308	11.861302	14.158777	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70820791	70820791	7381	1	G	T	T	T	520	40	HHLA3	1	1
C1orf173	127254	broad.mit.edu	37	1	75038451	75038451	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75038451G>T	uc001dgg.2	-	c.2943C>A	c.(2941-2943)GCC>GCA	p.A981A		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	981	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.071429	-4.73079	19.124252	9	117	KEEP	---	---	---	---	capture		Silent	SNP	75038451	75038451	2081	1	G	T	T	T	600	47	C1orf173	2	2
C1orf173	127254	broad.mit.edu	37	1	75055724	75055724	+	Silent	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75055724A>T	uc001dgg.2	-	c.1767T>A	c.(1765-1767)CCT>CCA	p.P589P	C1orf173_uc001dgi.3_Silent_p.P383P	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	589	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.194444	15.602888	18.739488	7	29	KEEP	---	---	---	---	capture		Silent	SNP	75055724	75055724	2081	1	A	T	T	T	28	3	C1orf173	3	3
C1orf173	127254	broad.mit.edu	37	1	75065524	75065524	+	Silent	SNP	C	G	G	rs74093443	byFrequency;by1000genomes	TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75065524C>G	uc001dgg.2	-	c.1581G>C	c.(1579-1581)CCG>CCC	p.P527P	C1orf173_uc001dgi.3_Silent_p.P321P	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	527	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.083333	2.928919	26.212857	11	121	KEEP	---	---	---	---	capture		Silent	SNP	75065524	75065524	2081	1	C	G	G	G	340	27	C1orf173	3	3
CLCA2	9635	broad.mit.edu	37	1	86913416	86913416	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86913416G>T	uc001dlr.3	+	c.1939G>T	c.(1939-1941)GAG>TAG	p.E647*		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	647	Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)	2		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)								0.061538	-4.956466	8.087553	4	61	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	86913416	86913416	3594	1	G	T	T	T	429	33	CLCA2	5	2
ANKRD5	63926	broad.mit.edu	37	20	10019172	10019172	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:10019172G>A	uc002wno.2	+	c.223G>A	c.(223-225)GAT>AAT	p.D75N	ANKRD5_uc002wnp.2_Missense_Mutation_p.D75N|ANKRD5_uc010gbz.2_5'UTR	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	75	ANK 1.						calcium ion binding			ovary(1)|breast(1)	2														0.107843	10.145702	25.705081	11	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10019172	10019172	684	20	G	A	A	A	585	45	ANKRD5	2	2
SLC24A3	57419	broad.mit.edu	37	20	19665877	19665877	+	Missense_Mutation	SNP	G	A	A	rs75574349	by1000genomes	TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:19665877G>A	uc002wrl.2	+	c.1196G>A	c.(1195-1197)CGG>CAG	p.R399Q		NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24	399	Cytoplasmic (Potential).					integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1														0.060241	-5.973018	10.787227	5	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19665877	19665877	14964	20	G	A	A	A	507	39	SLC24A3	1	1
NANP	140838	broad.mit.edu	37	20	25596690	25596690	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:25596690T>C	uc002wuy.2	-	c.618A>G	c.(616-618)ACA>ACG	p.T206T		NM_152667	NP_689880	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase	206					N-acetylneuraminate biosynthetic process		N-acylneuraminate-9-phosphatase activity|phosphoglycolate phosphatase activity				0														0.119048	6.146892	12.130509	5	37	KEEP	---	---	---	---	capture		Silent	SNP	25596690	25596690	10550	20	T	C	C	C	704	55	NANP	4	4
C20orf185	359710	broad.mit.edu	37	20	31656612	31656612	+	Missense_Mutation	SNP	C	G	G	rs113939875		TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31656612C>G	uc002wym.1	+	c.982C>G	c.(982-984)CTG>GTG	p.L328V		NM_182658	NP_872599	P59826	LPLC3_HUMAN	antimicrobial peptide RYA3 precursor	328					innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4														0.081633	-2.965993	14.509236	8	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31656612	31656612	2175	20	C	G	G	G	311	24	C20orf185	3	3
NCOA6	23054	broad.mit.edu	37	20	33345447	33345447	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33345447C>A	uc002xav.2	-	c.1104G>T	c.(1102-1104)ACG>ACT	p.T368T	NCOA6_uc002xaw.2_Silent_p.T368T|NCOA6_uc010gew.1_Silent_p.T325T	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	368	TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding|transcription activator activity			ovary(3)|breast(3)|central_nervous_system(1)	7														0.145455	13.572765	20.215457	8	47	KEEP	---	---	---	---	capture		Silent	SNP	33345447	33345447	10632	20	C	A	A	A	340	27	NCOA6	1	1
PHF20	51230	broad.mit.edu	37	20	34459638	34459638	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34459638A>T	uc002xek.1	+	c.1169A>T	c.(1168-1170)GAT>GTT	p.D390V	PHF20_uc002xei.1_Missense_Mutation_p.D390V|PHF20_uc010gfo.1_Missense_Mutation_p.D390V|PHF20_uc002xej.1_Missense_Mutation_p.D274V	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	390					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)													0.203947	69.184706	81.518326	31	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34459638	34459638	12254	20	A	T	T	T	156	12	PHF20	3	3
RBL1	5933	broad.mit.edu	37	20	35693826	35693826	+	Splice_Site_SNP	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:35693826C>G	uc002xgi.2	-	c.896_splice	c.e7+1	p.S299_splice	RBL1_uc010zvt.1_Splice_Site_SNP|RBL1_uc002xgj.1_Splice_Site_SNP_p.S299_splice|RBL1_uc010gfv.1_Splice_Site_SNP	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|ovary(2)	7		Myeloproliferative disorder(115;0.00878)								419				0.15	19.237674	26.28112	9	51	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	35693826	35693826	13570	20	C	G	G	G	234	18	RBL1	5	3
TOX2	84969	broad.mit.edu	37	20	42694513	42694514	+	Missense_Mutation	DNP	CC	GG	GG			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42694513_42694514CC>GG	uc010ggo.2	+	c.1122_1123CC>GG	c.(1120-1125)GCCCGG>GCGGGG	p.R375G	TOX2_uc002xle.3_Missense_Mutation_p.R333G|TOX2_uc010ggp.2_Missense_Mutation_p.R333G|TOX2_uc002xlf.3_Missense_Mutation_p.R357G|TOX2_uc002xlg.2_Intron|TOX2_uc010zwk.1_Missense_Mutation_p.R253G	NM_001098797	NP_001092267	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	357					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)											0.366667	32.778715	33.22227	11	19	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	42694513	42694514	16920	20	CC	GG	GG	GG	275	22	TOX2	3	3
SEMG2	6407	broad.mit.edu	37	20	43851066	43851066	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43851066A>G	uc010ggz.2	+	c.793A>G	c.(793-795)AAG>GAG	p.K265E	SEMG2_uc002xnk.2_Missense_Mutation_p.K265E|SEMG2_uc002xnl.2_Missense_Mutation_p.K265E	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	265	Repeat-rich region.|4 X 60 AA tandem repeats, type I.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity				0		Myeloproliferative disorder(115;0.0122)												0.19685	57.997792	68.87673	25	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43851066	43851066	14531	20	A	G	G	G	65	5	SEMG2	4	4
PCIF1	63935	broad.mit.edu	37	20	44567887	44567888	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:44567887_44567888GG>TT	uc002xqs.2	+	c.158_159GG>TT	c.(157-159)TGG>TTT	p.W53F		NM_022104	NP_071387	Q9H4Z3	PCIF1_HUMAN	phosphorylated CTD interacting factor 1	53	WW.					nucleus					0														0.214286	7.116959	8.172603	3	11	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	44567887	44567888	12000	20	GG	TT	TT	TT	611	47	PCIF1	2	2
ATP9A	10079	broad.mit.edu	37	20	50230268	50230268	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:50230268G>A	uc002xwg.1	-	c.2519C>T	c.(2518-2520)GCC>GTC	p.A840V	ATP9A_uc010gih.1_Missense_Mutation_p.A704V|ATP9A_uc002xwf.1_Missense_Mutation_p.A12V	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	840	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4														0.1	3.768581	16.534856	8	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50230268	50230268	1217	20	G	A	A	A	546	42	ATP9A	2	2
NRIP1	8204	broad.mit.edu	37	21	16340473	16340473	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:16340473T>A	uc002yjx.2	-	c.41A>T	c.(40-42)GAT>GTT	p.D14V		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	14					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)										0.157895	11.445383	15.669962	6	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16340473	16340473	11057	21	T	A	A	A	650	50	NRIP1	3	3
C21orf29	54084	broad.mit.edu	37	21	45987842	45987842	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45987842C>G	uc002zfe.1	-	c.130G>C	c.(130-132)GCC>CCC	p.A44P	C21orf29_uc010gpv.1_5'UTR	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor	44					cell adhesion	extracellular region	structural molecule activity				0														0.121951	8.049959	13.785014	5	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45987842	45987842	2204	21	C	G	G	G	351	27	C21orf29	3	3
SMC1B	27127	broad.mit.edu	37	22	45750875	45750875	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:45750875T>C	uc003bgc.2	-	c.3082A>G	c.(3082-3084)AAG>GAG	p.K1028E	SMC1B_uc003bgd.2_Missense_Mutation_p.K1028E	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	1028	Potential.				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)										0.09434	4.433956	13.195001	5	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45750875	45750875	15280	22	T	C	C	C	832	64	SMC1B	4	4
PAX8	7849	broad.mit.edu	37	2	114002157	114002157	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:114002157G>C	uc010yxt.1	-	c.236C>G	c.(235-237)TCC>TGC	p.S79C	PAX8_uc010yxu.1_Missense_Mutation_p.S79C|PAX8_uc010yxv.1_Missense_Mutation_p.S79C|PAX8_uc002tjm.2_Missense_Mutation_p.S79C|PAX8_uc002tjn.2_Missense_Mutation_p.S79C|PAX8_uc010fku.1_Missense_Mutation_p.S79C|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A	79	Paired.				mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric nephron tubule formation|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of gene-specific transcription|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity|transcription activator activity			ovary(1)	1						Ovarian(188;7 2067 9084 29802 29892)				171				0.095541	12.868875	38.580298	15	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114002157	114002157	11905	2	G	C	C	C	533	41	PAX8	3	3
R3HDM1	23518	broad.mit.edu	37	2	136481642	136481642	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:136481642G>A	uc002tuo.2	+	c.3080G>A	c.(3079-3081)CGT>CAT	p.R1027H	R3HDM1_uc010fni.2_Missense_Mutation_p.R1026H|R3HDM1_uc002tup.2_Missense_Mutation_p.R972H|R3HDM1_uc010zbh.1_Missense_Mutation_p.R775H	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	1027							nucleic acid binding				0				BRCA - Breast invasive adenocarcinoma(221;0.127)										0.114286	8.680364	18.921257	8	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136481642	136481642	13346	2	G	A	A	A	520	40	R3HDM1	1	1
LRP1B	53353	broad.mit.edu	37	2	141027875	141027875	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141027875C>A	uc002tvj.1	-	c.13183G>T	c.(13183-13185)GAT>TAT	p.D4395Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4395	Extracellular (Potential).|EGF-like 14.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	p.D4395Y(1)		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)			0.353846	65.805223	67.02958	23	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141027875	141027875	9328	2	C	A	A	A	377	29	LRP1B	2	2
TPO	7173	broad.mit.edu	37	2	1457533	1457533	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1457533G>A	uc002qww.2	+	c.550G>A	c.(550-552)GGC>AGC	p.G184S	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.G184S|TPO_uc002qwr.2_Missense_Mutation_p.G184S|TPO_uc002qwx.2_Missense_Mutation_p.G184S|TPO_uc010yio.1_Missense_Mutation_p.G184S|TPO_uc010yip.1_Missense_Mutation_p.G184S	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	184	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(6)|pancreas(6)|skin(3)|lung(1)|kidney(1)	17	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)					723				0.2	10.190862	11.863025	4	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1457533	1457533	16954	2	G	A	A	A	507	39	TPO	1	1
KIF5C	3800	broad.mit.edu	37	2	149806425	149806425	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:149806425G>A	uc010zbu.1	+	c.787G>A	c.(787-789)GGA>AGA	p.G263R	KIF5C_uc002tws.1_Non-coding_Transcript	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C	263	Kinesin-motor.|Microtubule-binding.				microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)										0.185185	12.459951	14.967733	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149806425	149806425	8618	2	G	A	A	A	611	47	KIF5C	2	2
SLC4A10	57282	broad.mit.edu	37	2	162833373	162833373	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:162833373T>C	uc002ubx.3	+	c.3331T>C	c.(3331-3333)TTT>CTT	p.F1111L	SLC4A10_uc002uby.3_Missense_Mutation_p.F1081L|SLC4A10_uc010zcs.1_Missense_Mutation_p.F1092L	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	1111	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5														0.3	18.842373	19.556978	6	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	162833373	162833373	15148	2	T	C	C	C	728	56	SLC4A10	4	4
SCN2A	6326	broad.mit.edu	37	2	166201109	166201109	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166201109G>T	uc002udc.2	+	c.2607G>T	c.(2605-2607)ATG>ATT	p.M869I	SCN2A_uc002udd.2_Missense_Mutation_p.M869I|SCN2A_uc002ude.2_Missense_Mutation_p.M869I	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	869	II.				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)									0.197531	36.6517	43.554186	16	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166201109	166201109	14398	2	G	T	T	T	598	46	SCN2A	2	2
SCN1A	6323	broad.mit.edu	37	2	166897784	166897784	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166897784G>T	uc010zcz.1	-	c.2339C>A	c.(2338-2340)CCA>CAA	p.P780Q	SCN1A_uc002udo.3_Missense_Mutation_p.P660Q|SCN1A_uc010fpk.2_Missense_Mutation_p.P632Q	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	791	II.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|large_intestine(1)	7					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)									0.102564	3.769493	9.909136	4	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166897784	166897784	14396	2	G	T	T	T	611	47	SCN1A	2	2
SCN7A	6332	broad.mit.edu	37	2	167262949	167262949	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:167262949A>T	uc002udu.1	-	c.4190T>A	c.(4189-4191)TTT>TAT	p.F1397Y		NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	1397	Helical; Name=S5 of repeat IV; (By similarity).				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1														0.087591	-0.205522	23.395073	12	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167262949	167262949	14405	2	A	T	T	T	13	1	SCN7A	3	3
LRP2	4036	broad.mit.edu	37	2	170042168	170042168	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170042168C>A	uc002ues.2	-	c.9690G>T	c.(9688-9690)GTG>GTT	p.V3230V		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3230	Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.129032	17.988404	30.406433	12	81	KEEP	---	---	---	---	capture		Silent	SNP	170042168	170042168	9329	2	C	A	A	A	262	21	LRP2	2	2
TLK1	9874	broad.mit.edu	37	2	171906414	171906414	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:171906414C>A	uc002ugo.2	-	c.953G>T	c.(952-954)CGA>CTA	p.R318L	TLK1_uc002ugn.2_Missense_Mutation_p.R297L|TLK1_uc002ugp.2_Missense_Mutation_p.R249L|TLK1_uc002ugq.2_Non-coding_Transcript|TLK1_uc010zdn.1_Missense_Mutation_p.R201L|TLK1_uc002ugr.1_Missense_Mutation_p.R80L	NM_001136554	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 2	297					cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|protein phosphorylation|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1										247				0.15493	21.788801	29.857908	11	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171906414	171906414	16473	2	C	A	A	A	403	31	TLK1	1	1
HOXD1	3231	broad.mit.edu	37	2	177054663	177054663	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:177054663C>G	uc002ukv.3	+	c.780C>G	c.(778-780)ATC>ATG	p.I260M	HOXD1_uc010fqy.2_3'UTR|HOXD1_uc010zez.1_Missense_Mutation_p.I260M	NM_024501	NP_078777	Q9GZZ0	HXD1_HUMAN	homeobox D1	260	Homeobox.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)										0.137778	56.237988	84.739826	31	194	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177054663	177054663	7610	2	C	G	G	G	395	31	HOXD1	3	3
TTN	7273	broad.mit.edu	37	2	179439236	179439236	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179439236T>C	uc010zfg.1	-	c.63919A>G	c.(63919-63921)ACT>GCT	p.T21307A	TTN_uc010zfh.1_Missense_Mutation_p.T15002A|TTN_uc010zfi.1_Missense_Mutation_p.T14935A|TTN_uc010zfj.1_Missense_Mutation_p.T14810A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1117										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				0.103896	18.407246	42.442457	16	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179439236	179439236	17290	2	T	C	C	C	754	58	TTN	4	4
TTN	7273	broad.mit.edu	37	2	179465807	179465807	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179465807G>A	uc010zfg.1	-	c.48120C>T	c.(48118-48120)GGC>GGT	p.G16040G	TTN_uc010zfh.1_Silent_p.G9735G|TTN_uc010zfi.1_Silent_p.G9668G|TTN_uc010zfj.1_Silent_p.G9543G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5111										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				0.131313	17.678442	30.700676	13	86	KEEP	---	---	---	---	capture		Silent	SNP	179465807	179465807	17290	2	G	A	A	A	431	34	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179538410	179538411	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179538410_179538411GG>TT	uc010zfg.1	-	c.30832_30833CC>AA	c.(30832-30834)CCT>AAT	p.P10278N	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P6939N|TTN_uc010fre.1_Missense_Mutation_p.P786N|TTN_uc010zfk.1_5'Flank|TTN_uc002una.1_Non-coding_Transcript|TTN_uc010frf.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	549										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				0.142857	12.790461	18.814077	7	42	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	179538410	179538411	17290	2	GG	TT	TT	TT	455	35	TTN	2	2
KCNS3	3790	broad.mit.edu	37	2	18113551	18113551	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:18113551G>A	uc002rcv.2	+	c.1276G>A	c.(1276-1278)GAG>AAG	p.E426K	KCNS3_uc002rcw.2_Missense_Mutation_p.E426K	NM_002252	NP_002243	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel	426	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium channel regulator activity			ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)													0.141975	34.711672	54.74624	23	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18113551	18113551	8395	2	G	A	A	A	585	45	KCNS3	2	2
SATB2	23314	broad.mit.edu	37	2	200137209	200137209	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:200137209C>A	uc002uuy.1	-	c.1927G>T	c.(1927-1929)GAA>TAA	p.E643*	SATB2_uc010fsq.1_Nonsense_Mutation_p.E525*|SATB2_uc002uuz.1_Nonsense_Mutation_p.E643*|SATB2_uc002uva.1_Nonsense_Mutation_p.E643*	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	643	Homeobox.					cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						Colon(30;262 767 11040 24421 36230)								0.10989	6.095058	19.802222	10	81	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	200137209	200137209	14335	2	C	A	A	A	390	30	SATB2	5	2
FN1	2335	broad.mit.edu	37	2	216271930	216271930	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:216271930A>T	uc002vfa.2	-	c.2633T>A	c.(2632-2634)ATC>AAC	p.I878N	FN1_uc002vfb.2_Missense_Mutation_p.I878N|FN1_uc002vfc.2_Missense_Mutation_p.I878N|FN1_uc002vfd.2_Missense_Mutation_p.I878N|FN1_uc002vfe.2_Missense_Mutation_p.I878N|FN1_uc002vff.2_Missense_Mutation_p.I878N|FN1_uc002vfg.2_Missense_Mutation_p.I878N|FN1_uc002vfh.2_Missense_Mutation_p.I878N|FN1_uc002vfi.2_Missense_Mutation_p.I878N|FN1_uc002vfj.2_Missense_Mutation_p.I878N	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	878	Fibronectin type-III 3.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1374				0.131783	26.388112	43.381232	17	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216271930	216271930	6204	2	A	T	T	T	156	12	FN1	3	3
DNER	92737	broad.mit.edu	37	2	230223358	230223358	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:230223358C>A	uc002vpv.2	-	c.2112G>T	c.(2110-2112)AAG>AAT	p.K704N		NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing	704	Cytoplasmic (Potential).				central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			ovary(1)	1		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)										0.185185	19.91552	24.936194	10	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	230223358	230223358	4850	2	C	A	A	A	415	32	DNER	2	2
CAB39	51719	broad.mit.edu	37	2	231682502	231682502	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231682502T>G	uc002vqx.2	+	c.727T>G	c.(727-729)TTC>GTC	p.F243V	CAB39_uc010fxr.2_Missense_Mutation_p.F243V|CAB39_uc010fxq.2_Missense_Mutation_p.F243V|CAB39_uc002vqy.2_5'UTR	NM_016289	NP_057373	Q9Y376	CAB39_HUMAN	calcium binding protein 39	243					cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	kinase binding			central_nervous_system(1)	1		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)										0.088889	1.063519	8.752491	4	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231682502	231682502	2641	2	T	G	G	G	728	56	CAB39	4	4
DNAJB3	414061	broad.mit.edu	37	2	234652498	234652498	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234652498G>A	uc002vuz.2	-	c.65C>T	c.(64-66)GCG>GTG	p.A22V	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Intron|UGT1A3_uc002vuy.2_Intron	NM_001001394	NP_001001394	Q8WWF6	DNJB3_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 3	22	J.				protein folding		heat shock protein binding|unfolded protein binding				0														0.145161	11.724781	19.16317	9	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234652498	234652498	4804	2	G	A	A	A	494	38	DNAJB3	1	1
PASK	23178	broad.mit.edu	37	2	242046118	242046118	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242046118C>G	uc010fzl.1	-	c.3856G>C	c.(3856-3858)GCG>CCG	p.A1286P	PASK_uc010zol.1_Missense_Mutation_p.A1093P|PASK_uc002wao.1_Missense_Mutation_p.A1279P|PASK_uc010zom.1_Missense_Mutation_p.A1244P|PASK_uc010zon.1_Missense_Mutation_p.A1060P	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1279					protein phosphorylation|regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)						754				0.15873	19.417111	26.404212	10	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242046118	242046118	11889	2	C	G	G	G	325	25	PASK	3	3
TTC27	55622	broad.mit.edu	37	2	32961852	32961852	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32961852T>G	uc002rom.2	+	c.1421T>G	c.(1420-1422)ATT>AGT	p.I474S	TTC27_uc010ymx.1_Missense_Mutation_p.I424S|TTC27_uc002ron.2_Non-coding_Transcript	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	474	TPR 2.						protein binding			central_nervous_system(1)	1														0.304348	20.416981	21.20214	7	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32961852	32961852	17249	2	T	G	G	G	676	52	TTC27	4	4
MSH6	2956	broad.mit.edu	37	2	48030811	48030811	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48030811C>T	uc002rwd.3	+	c.3425C>T	c.(3424-3426)ACG>ATG	p.T1142M	MSH6_uc010fbj.2_Missense_Mutation_p.T840M|MSH6_uc010yoi.1_Missense_Mutation_p.T1012M|MSH6_uc010yoj.1_Missense_Mutation_p.T840M	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	1142					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|endometrium(28)|central_nervous_system(27)|stomach(21)|haematopoietic_and_lymphoid_tissue(9)|skin(6)|urinary_tract(5)|lung(5)|ovary(3)|breast(2)|thyroid(1)	160		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)							517				0.141361	44.526712	68.201558	27	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48030811	48030811	10267	2	C	T	T	T	247	19	MSH6	1	1
FSHR	2492	broad.mit.edu	37	2	49190205	49190205	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:49190205C>A	uc002rww.2	-	c.1755G>T	c.(1753-1755)ATG>ATT	p.M585I	FSHR_uc002rwx.2_Missense_Mutation_p.M523I|FSHR_uc010fbn.2_Missense_Mutation_p.M559I	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	585	Helical; Name=6; (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)	4		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									0.224719	48.45433	54.651006	20	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49190205	49190205	6324	2	C	A	A	A	273	21	FSHR	2	2
NRXN1	9378	broad.mit.edu	37	2	50765733	50765733	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:50765733G>T	uc010fbq.2	-	c.1921C>A	c.(1921-1923)CCT>ACT	p.P641T	NRXN1_uc002rxb.3_Missense_Mutation_p.P273T|NRXN1_uc002rxe.3_Missense_Mutation_p.P601T|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	205	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.24	38.829501	43.449014	18	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50765733	50765733	11070	2	G	T	T	T	533	41	NRXN1	2	2
CCDC88A	55704	broad.mit.edu	37	2	55546086	55546086	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:55546086C>G	uc002ryv.2	-	c.3214G>C	c.(3214-3216)GAG>CAG	p.E1072Q	CCDC88A_uc010yoz.1_Missense_Mutation_p.E1073Q|CCDC88A_uc010ypa.1_Missense_Mutation_p.E1072Q|CCDC88A_uc002ryu.2_Missense_Mutation_p.E355Q|CCDC88A_uc002rys.2_Missense_Mutation_p.E58Q|CCDC88A_uc002ryw.2_Missense_Mutation_p.E356Q|CCDC88A_uc010fby.1_5'UTR	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	1073	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)	2														0.111111	6.940609	13.669474	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55546086	55546086	2988	2	C	G	G	G	377	29	CCDC88A	3	3
PELI1	57162	broad.mit.edu	37	2	64323337	64323337	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:64323337T>C	uc002scs.3	-	c.612A>G	c.(610-612)GGA>GGG	p.G204G	PELI1_uc002sct.3_Silent_p.G204G|PELI1_uc002scr.3_Silent_p.G25G	NM_020651	NP_065702	Q96FA3	PELI1_HUMAN	pellino protein	204					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol				ovary(1)	1														0.379121	228.055297	230.37937	69	113	KEEP	---	---	---	---	capture		Silent	SNP	64323337	64323337	12142	2	T	C	C	C	795	62	PELI1	4	4
C2orf78	388960	broad.mit.edu	37	2	74040815	74040815	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74040815C>G	uc002sjr.1	+	c.309C>G	c.(307-309)AGC>AGG	p.S103R		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	103	Ser-rich.									ovary(2)	2														0.137931	21.480626	32.47792	12	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74040815	74040815	2285	2	C	G	G	G	324	25	C2orf78	3	3
LRRTM1	347730	broad.mit.edu	37	2	80529899	80529899	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:80529899T>A	uc002sok.1	-	c.1046A>T	c.(1045-1047)CAG>CTG	p.Q349L	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_Non-coding_Transcript	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	349	LRRCT.|Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)	3														0.210526	9.895949	11.363944	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80529899	80529899	9415	2	T	A	A	A	715	55	LRRTM1	3	3
GGCX	2677	broad.mit.edu	37	2	85781383	85781383	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85781383C>T	uc002sps.2	-	c.772G>A	c.(772-774)GGT>AGT	p.G258S	GGCX_uc010yss.1_Missense_Mutation_p.G97S|GGCX_uc010yst.1_Missense_Mutation_p.G201S	NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1	258	Lumenal (Potential).				blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)									0.065217	-4.597013	13.43701	6	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85781383	85781383	6624	2	C	T	T	T	286	22	GGCX	2	2
ZNF514	84874	broad.mit.edu	37	2	95815962	95815962	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:95815962A>G	uc002sud.1	-	c.487T>C	c.(487-489)TCC>CCC	p.S163P	ZNF514_uc002sue.1_Missense_Mutation_p.S90P	NM_032788	NP_116177	Q96K75	ZN514_HUMAN	zinc finger protein 514	90					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.119403	24.941747	43.959244	16	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95815962	95815962	18553	2	A	G	G	G	117	9	ZNF514	4	4
DRD3	1814	broad.mit.edu	37	3	113849973	113849973	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113849973A>G	uc003ebd.2	-	c.998T>C	c.(997-999)ATT>ACT	p.I333T	DRD3_uc010hqn.1_Missense_Mutation_p.I333T|DRD3_uc003ebb.1_Missense_Mutation_p.I300T|DRD3_uc003ebc.1_Missense_Mutation_p.I333T	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	333	Helical; Name=6.				activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|dopamine metabolic process|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|regulation of dopamine uptake|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)									0.142857	11.230781	16.385023	6	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113849973	113849973	4942	3	A	G	G	G	52	4	DRD3	4	4
KIAA1257	57501	broad.mit.edu	37	3	128711899	128711899	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:128711899G>C	uc003elj.3	-	c.249C>G	c.(247-249)TTC>TTG	p.F83L	KIAA1257_uc003elg.1_Missense_Mutation_p.F83L|KIAA1257_uc003eli.3_5'Flank	NM_020741	NP_065792	Q9ULG3	K1257_HUMAN	hypothetical protein LOC57501	83											0														0.127119	25.037766	40.956744	15	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128711899	128711899	8527	3	G	C	C	C	529	41	KIAA1257	3	3
BFSP2	8419	broad.mit.edu	37	3	133119134	133119134	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:133119134G>T	uc003epn.1	+	c.207G>T	c.(205-207)TTG>TTT	p.L69F		NM_003571	NP_003562	Q13515	BFSP2_HUMAN	phakinin	69	Head.				response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0														0.235294	7.777259	8.886487	4	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133119134	133119134	1440	3	G	T	T	T	607	47	BFSP2	2	2
STAG1	10274	broad.mit.edu	37	3	136068096	136068096	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:136068096C>G	uc003era.1	-	c.3175G>C	c.(3175-3177)GAT>CAT	p.D1059H	STAG1_uc003erb.1_Missense_Mutation_p.D1059H	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1059					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2														0.236842	23.454689	25.860897	9	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136068096	136068096	15760	3	C	G	G	G	377	29	STAG1	3	3
CEP70	80321	broad.mit.edu	37	3	138219396	138219396	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:138219396G>A	uc003esl.2	-	c.1382C>T	c.(1381-1383)CCA>CTA	p.P461L	CEP70_uc011bmk.1_Missense_Mutation_p.P441L|CEP70_uc011bml.1_Missense_Mutation_p.P443L|CEP70_uc011bmm.1_Missense_Mutation_p.P309L|CEP70_uc003esm.2_Missense_Mutation_p.P461L	NM_024491	NP_077817	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70 kDa	461					G2/M transition of mitotic cell cycle	cytosol|microtubule organizing center	protein binding				0														0.144186	57.517814	83.689472	31	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138219396	138219396	3392	3	G	A	A	A	611	47	CEP70	2	2
EHHADH	1962	broad.mit.edu	37	3	184910322	184910322	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:184910322G>A	uc003fpf.2	-	c.1864C>T	c.(1864-1866)CGC>TGC	p.R622C	EHHADH_uc011brs.1_Missense_Mutation_p.R526C	NM_001966	NP_001957	Q08426	ECHP_HUMAN	enoyl-Coenzyme A, hydratase/3-hydroxyacyl	622						peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)									0.095745	2.905909	18.322364	9	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	184910322	184910322	5171	3	G	A	A	A	520	40	EHHADH	1	1
ATP13A4	84239	broad.mit.edu	37	3	193176932	193176932	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:193176932G>A	uc003ftd.2	-	c.1612C>T	c.(1612-1614)CTT>TTT	p.L538F	ATP13A4_uc003fte.1_Missense_Mutation_p.L538F|ATP13A4_uc011bsr.1_Missense_Mutation_p.L9F|ATP13A4_uc010hzi.2_Non-coding_Transcript|ATP13A4_uc003ftf.3_Missense_Mutation_p.L244F	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	538	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)										0.127451	21.804922	35.605838	13	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	193176932	193176932	1145	3	G	A	A	A	455	35	ATP13A4	2	2
NEK10	152110	broad.mit.edu	37	3	27297818	27297818	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:27297818T>C	uc003cdt.1	-	c.2059A>G	c.(2059-2061)ACC>GCC	p.T687A	NEK10_uc003cds.1_Missense_Mutation_p.T84A	NM_199347	NP_955379	Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10 isoform 3	687	Protein kinase.				protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	11										332				0.368421	17.810088	18.102788	7	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27297818	27297818	10721	3	T	C	C	C	767	59	NEK10	4	4
TRANK1	9881	broad.mit.edu	37	3	36898690	36898690	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36898690T>A	uc003cgj.2	-	c.741A>T	c.(739-741)GAA>GAT	p.E247D		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	797					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2														0.210744	110.605165	129.330203	51	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36898690	36898690	16998	3	T	A	A	A	829	64	TRANK1	3	3
OR5H1	26341	broad.mit.edu	37	3	97852218	97852218	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97852218T>A	uc011bgt.1	+	c.677T>A	c.(676-678)TTA>TAA	p.L226*		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	226	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2														0.183099	25.840141	32.528589	13	58	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	97852218	97852218	11569	3	T	A	A	A	793	61	OR5H1	5	3
TET2	54790	broad.mit.edu	37	4	106155397	106155397	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:106155397G>T	uc011cez.1	+	c.361G>T	c.(361-363)GAA>TAA	p.E121*	TET2_uc003hxk.2_Nonsense_Mutation_p.E100*|TET2_uc003hxj.2_Non-coding_Transcript|TET2_uc010ilp.1_Nonsense_Mutation_p.E100*|TET2_uc003hxi.1_Nonsense_Mutation_p.E100*	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a	100					cell cycle|myeloid cell differentiation|oxidation-reduction process		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(668)|pancreas(1)	669		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)						111				0.2	51.497602	61.968715	25	100	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	106155397	106155397	16297	4	G	T	T	T	585	45	TET2	5	2
FAM198B	51313	broad.mit.edu	37	4	159052016	159052016	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:159052016A>T	uc003ipq.3	-	c.1298T>A	c.(1297-1299)TTG>TAG	p.L433*	FAM198B_uc003ipp.3_Nonsense_Mutation_p.L425*|FAM198B_uc003ipr.3_Nonsense_Mutation_p.L425*	NM_001031700	NP_001026870	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 1	425	Extracellular (Potential).					Golgi membrane|integral to membrane					0														0.22	27.096794	30.708309	11	39	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	159052016	159052016	5743	4	A	T	T	T	65	5	FAM198B	5	3
MTNR1A	4543	broad.mit.edu	37	4	187455200	187455200	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187455200C>A	uc003izd.1	-	c.696G>T	c.(694-696)CAG>CAT	p.Q232H		NM_005958	NP_005949	P48039	MTR1A_HUMAN	melatonin receptor 1A	232	Cytoplasmic (Potential).				circadian rhythm|G-protein signaling, coupled to cyclic nucleotide second messenger|mating behavior	integral to plasma membrane	melatonin receptor activity			ovary(1)	1		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Melatonin(DB01065)|Ramelteon(DB00980)									0.076087	-1.251936	15.693459	7	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187455200	187455200	10344	4	C	A	A	A	311	24	MTNR1A	2	2
FAT1	2195	broad.mit.edu	37	4	187510357	187510357	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187510357A>G	uc003izf.2	-	c.13156T>C	c.(13156-13158)TCA>CCA	p.S4386P	FAT1_uc010isn.2_Missense_Mutation_p.S33P|FAT1_uc003ize.2_Missense_Mutation_p.S277P	NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	4386	Cytoplasmic (Potential).				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						Colon(197;1040 2055 4143 4984 49344)								0.141892	38.778045	57.077434	21	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187510357	187510357	5925	4	A	G	G	G	156	12	FAT1	4	4
POLN	353497	broad.mit.edu	37	4	2230953	2230953	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2230953T>C	uc003ger.2	-	c.6A>G	c.(4-6)GAA>GAG	p.E2E	POLN_uc011bvi.1_Silent_p.E2E|HAUS3_uc011bvj.1_Intron|HAUS3_uc003ges.1_3'UTR|HAUS3_uc003get.1_3'UTR	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu	2					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)											0.146341	11.028681	15.954143	6	35	KEEP	---	---	---	---	capture		Silent	SNP	2230953	2230953	12635	4	T	C	C	C	829	64	POLN	4	4
GBA3	57733	broad.mit.edu	37	4	22749300	22749300	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:22749300C>G	uc003gqp.3	+	c.668C>G	c.(667-669)TCA>TGA	p.S223*	GBA3_uc010iep.2_Intron|GBA3_uc011bxo.1_Nonsense_Mutation_p.S224*	NM_020973	NP_066024	Q9H227	GBA3_HUMAN	cytosolic beta-glucosidase isoform a	223					glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity				0														0.146199	51.490883	72.03984	25	146	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22749300	22749300	6534	4	C	G	G	G	377	29	GBA3	5	3
GABRG1	2565	broad.mit.edu	37	4	46066479	46066479	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46066479A>T	uc003gxb.2	-	c.604T>A	c.(604-606)TGT>AGT	p.C202S		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	202	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)										0.162791	14.896644	19.544437	7	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46066479	46066479	6422	4	A	T	T	T	91	7	GABRG1	3	3
GABRA4	2557	broad.mit.edu	37	4	46973176	46973176	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46973176C>A	uc003gxg.2	-	c.798G>T	c.(796-798)CCG>CCT	p.P266P		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	266	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|breast(1)	3					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	Ovarian(6;283 369 8234 12290 33402)								0.102564	2.770144	8.915558	4	35	KEEP	---	---	---	---	capture		Silent	SNP	46973176	46973176	6414	4	C	A	A	A	236	19	GABRA4	1	1
PDGFRA	5156	broad.mit.edu	37	4	55127551	55127551	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55127551A>C	uc003han.3	+	c.339A>C	c.(337-339)GAA>GAC	p.E113D	PDGFRA_uc003haa.2_Intron|PDGFRA_uc003hal.2_Missense_Mutation_p.E113D|PDGFRA_uc010igq.1_Intron|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	113	Ig-like C2-type 1.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.165829	52.137302	73.240252	33	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55127551	55127551	12082	4	A	C	C	C	37	3	PDGFRA	4	4
LPHN3	23284	broad.mit.edu	37	4	62800583	62800583	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:62800583T>C	uc010ihh.2	+	c.1934T>C	c.(1933-1935)CTC>CCC	p.L645P	LPHN3_uc003hcq.3_Missense_Mutation_p.L645P|LPHN3_uc003hct.2_Missense_Mutation_p.L38P|LPHN3_uc003hcs.1_Missense_Mutation_p.L461P	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	632	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.275	30.206468	32.031266	11	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62800583	62800583	9290	4	T	C	C	C	702	54	LPHN3	4	4
AFAP1	60312	broad.mit.edu	37	4	7870433	7870433	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:7870433C>T	uc011bwk.1	-	c.141G>A	c.(139-141)AAG>AAA	p.K47K	AFAP1_uc003gkg.1_Silent_p.K47K	NM_001134647	NP_001128119	Q8N556	AFAP1_HUMAN	actin filament associated protein 1 isoform a	47						actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0														0.157895	5.411747	7.533159	3	16	KEEP	---	---	---	---	capture		Silent	SNP	7870433	7870433	354	4	C	T	T	T	311	24	AFAP1	2	2
GRID2	2895	broad.mit.edu	37	4	94411878	94411878	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:94411878G>T	uc011cdt.1	+	c.1947G>T	c.(1945-1947)ACG>ACT	p.T649T	GRID2_uc011cdu.1_Silent_p.T554T	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	649	Helical; (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|large_intestine(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)									0.062069	-8.737421	20.254457	9	136	KEEP	---	---	---	---	capture		Silent	SNP	94411878	94411878	7050	4	G	T	T	T	496	39	GRID2	1	1
APC	324	broad.mit.edu	37	5	112176102	112176102	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112176102C>T	uc010jby.2	+	c.4811C>T	c.(4810-4812)CCT>CTT	p.P1604L	APC_uc011cvt.1_Missense_Mutation_p.P1586L|APC_uc003kpz.3_Missense_Mutation_p.P1604L|APC_uc003kpy.3_Missense_Mutation_p.P1604L|APC_uc010jbz.2_Missense_Mutation_p.P1321L|APC_uc010jca.2_Missense_Mutation_p.P904L	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1604	Ser-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of protein catabolic process|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.K1192fs*3(1)|p.?(1)		large_intestine(2012)|stomach(123)|soft_tissue(55)|small_intestine(34)|pancreas(25)|breast(23)|urinary_tract(20)|lung(18)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|upper_aerodigestive_tract(6)|adrenal_gland(6)|NS(5)|bone(5)|skin(4)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2396		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		12		629	TSP Lung(16;0.13)			0.169014	76.582421	98.662736	36	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112176102	112176102	773	5	C	T	T	T	312	24	APC	2	2
SLC27A6	28965	broad.mit.edu	37	5	128362981	128362981	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128362981G>T	uc003kuy.2	+	c.1411G>T	c.(1411-1413)GAC>TAC	p.D471Y	SLC27A6_uc003kuz.2_Missense_Mutation_p.D471Y	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	471					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)										0.144928	14.700291	23.075178	10	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128362981	128362981	15027	5	G	T	T	T	533	41	SLC27A6	2	2
DNAH5	1767	broad.mit.edu	37	5	13794128	13794128	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:13794128T>C	uc003jfd.2	-	c.7927A>G	c.(7927-7929)ACA>GCA	p.T2643A		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2643	AAA 3 (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)													0.074074	-0.141403	9.918226	4	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13794128	13794128	4787	5	T	C	C	C	780	60	DNAH5	4	4
ARAP3	64411	broad.mit.edu	37	5	141059221	141059221	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:141059221G>T	uc003llm.2	-	c.589C>A	c.(589-591)CAC>AAC	p.H197N	ARAP3_uc003lln.2_Missense_Mutation_p.H119N|ARAP3_uc003llo.1_Missense_Mutation_p.H197N	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	197					cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7														0.185185	10.758437	13.267864	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141059221	141059221	851	5	G	T	T	T	598	46	ARAP3	2	2
SPARC	6678	broad.mit.edu	37	5	151043764	151043764	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:151043764C>G	uc003luh.2	-	c.767G>C	c.(766-768)CGT>CCT	p.R256P	GM2A_uc011dcs.1_Intron|SPARC_uc003lug.2_Missense_Mutation_p.R90P|SPARC_uc003lui.2_Missense_Mutation_p.R256P	NM_003118	NP_003109	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich	256					ossification|platelet activation|platelet degranulation|signal transduction	basement membrane|extracellular space|platelet alpha granule lumen	calcium ion binding|collagen binding			central_nervous_system(1)	1		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)	Becaplermin(DB00102)									0.28125	25.770611	27.141127	9	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151043764	151043764	15503	5	C	G	G	G	247	19	SPARC	3	3
HAVCR1	26762	broad.mit.edu	37	5	156476071	156476071	+	Silent	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156476071T>A	uc010jij.1	-	c.759A>T	c.(757-759)TCA>TCT	p.S253S	HAVCR1_uc011ddl.1_Silent_p.S84S|HAVCR1_uc003lwi.2_Silent_p.S253S	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	248	Extracellular (Potential).				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.130841	17.877682	32.063483	14	93	KEEP	---	---	---	---	capture		Silent	SNP	156476071	156476071	7255	5	T	A	A	A	756	59	HAVCR1	3	3
CLINT1	9685	broad.mit.edu	37	5	157232889	157232889	+	Silent	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:157232889A>T	uc011ddv.1	-	c.927T>A	c.(925-927)CCT>CCA	p.P309P	CLINT1_uc003lxi.1_Silent_p.P291P|CLINT1_uc003lxj.1_Silent_p.P309P	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4	309					endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Colon(22;427 587 2170 6147 14291)								0.302326	29.956407	31.45858	13	30	KEEP	---	---	---	---	capture		Silent	SNP	157232889	157232889	3669	5	A	T	T	T	132	11	CLINT1	3	3
CDH6	1004	broad.mit.edu	37	5	31323411	31323411	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31323411C>G	uc003jhe.1	+	c.2369C>G	c.(2368-2370)TCC>TGC	p.S790C		NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	790	Cytoplasmic (Potential).				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														0.168539	33.674122	42.929172	15	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31323411	31323411	3243	5	C	G	G	G	390	30	CDH6	3	3
NNT	23530	broad.mit.edu	37	5	43613236	43613236	+	Silent	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:43613236C>G	uc003joe.2	+	c.378C>G	c.(376-378)GTC>GTG	p.V126V	NNT_uc003jof.2_Silent_p.V126V	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	126	Mitochondrial matrix.				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)									0.191176	29.532605	35.595742	13	55	KEEP	---	---	---	---	capture		Silent	SNP	43613236	43613236	10913	5	C	G	G	G	366	29	NNT	3	3
CMYA5	202333	broad.mit.edu	37	5	79029704	79029705	+	Missense_Mutation	DNP	GA	AT	AT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:79029704_79029705GA>AT	uc003kgc.2	+	c.5116_5117GA>AT	c.(5116-5118)GAG>ATG	p.E1706M		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1706						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)										0.13	17.606797	30.929987	13	87	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	79029704	79029705	3728	5	GA	AT	AT	AT	533	41	CMYA5	2	2
GPR98	84059	broad.mit.edu	37	5	90002055	90002055	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90002055C>G	uc003kju.2	+	c.8574C>G	c.(8572-8574)ATC>ATG	p.I2858M	GPR98_uc003kjt.2_Missense_Mutation_p.I564M|GPR98_uc003kjv.2_Missense_Mutation_p.I458M	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2858	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.192982	28.890977	33.906525	11	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90002055	90002055	6997	5	C	G	G	G	369	29	GPR98	3	3
GRIK2	2898	broad.mit.edu	37	6	102069929	102069929	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:102069929C>G	uc003pqp.3	+	c.221C>G	c.(220-222)ACT>AGT	p.T74S	GRIK2_uc003pqn.2_Missense_Mutation_p.T74S|GRIK2_uc003pqo.3_Missense_Mutation_p.T74S|GRIK2_uc010kcw.2_Missense_Mutation_p.T74S	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	74	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|breast(1)|pancreas(1)	4		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)									0.202703	39.183568	45.25686	15	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102069929	102069929	7053	6	C	G	G	G	260	20	GRIK2	3	3
PRDM1	639	broad.mit.edu	37	6	106555120	106555120	+	Missense_Mutation	SNP	A	T	T	rs76571405	byFrequency;by1000genomes	TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:106555120A>T	uc003prd.2	+	c.2237A>T	c.(2236-2238)GAG>GTG	p.E746V	PRDM1_uc003pre.2_Missense_Mutation_p.E612V	NM_001198	NP_001189	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain isoform	746					negative regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)										0.049587	-13.752947	12.304212	6	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106555120	106555120	12892	6	A	T	T	T	143	11	PRDM1	3	3
SOBP	55084	broad.mit.edu	37	6	107954957	107954957	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:107954957G>A	uc003prx.2	+	c.909G>A	c.(907-909)CCG>CCA	p.P303P		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	303							metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)										0.081967	0.734543	11.577986	5	56	KEEP	---	---	---	---	capture		Silent	SNP	107954957	107954957	15412	6	G	A	A	A	483	38	SOBP	1	1
KIAA1919	91749	broad.mit.edu	37	6	111585053	111585053	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:111585053A>G	uc003puv.3	+	c.217A>G	c.(217-219)ACC>GCC	p.T73A		NM_153369	NP_699200	Q5TF39	NAGT1_HUMAN	sodium-dependent glucose transporter 1	73	Helical; (Potential).				carbohydrate transport|sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(3)	3		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)										0.09375	1.709986	7.011635	3	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111585053	111585053	8573	6	A	G	G	G	78	6	KIAA1919	4	4
LAMA4	3910	broad.mit.edu	37	6	112463320	112463320	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:112463320C>T	uc003pvu.2	-	c.2667_splice	c.e20+1	p.N889_splice	LAMA4_uc003pvv.2_Splice_Site_SNP_p.N882_splice|LAMA4_uc003pvt.2_Splice_Site_SNP_p.N882_splice	NM_001105206	NP_001098676			laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)										0.235294	39.776452	44.126434	16	52	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	112463320	112463320	8931	6	C	T	T	T	247	19	LAMA4	5	1
LAMA2	3908	broad.mit.edu	37	6	129802476	129802476	+	Silent	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:129802476A>G	uc003qbn.2	+	c.7641A>G	c.(7639-7641)GGA>GGG	p.G2547G	LAMA2_uc003qbo.2_Silent_p.G2543G	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2547	Laminin G-like 3.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)										0.122807	19.375573	35.252533	14	100	KEEP	---	---	---	---	capture		Silent	SNP	129802476	129802476	8929	6	A	G	G	G	106	9	LAMA2	4	4
GRM1	2911	broad.mit.edu	37	6	146720539	146720539	+	Silent	SNP	G	A	A	rs114187147	by1000genomes	TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146720539G>A	uc010khw.1	+	c.2364G>A	c.(2362-2364)GCG>GCA	p.A788A	GRM1_uc010khv.1_Silent_p.A788A|GRM1_uc003qll.2_Silent_p.A788A|GRM1_uc011edz.1_Silent_p.A788A|GRM1_uc011eea.1_Silent_p.A788A	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	788	Helical; Name=6; (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.083333	0.235161	21.341338	10	110	KEEP	---	---	---	---	capture		Silent	SNP	146720539	146720539	7075	6	G	A	A	A	509	40	GRM1	1	1
ULBP3	79465	broad.mit.edu	37	6	150386651	150386651	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:150386651C>G	uc003qns.3	-	c.511G>C	c.(511-513)GAG>CAG	p.E171Q	ULBP3_uc011eej.1_Missense_Mutation_p.E46Q|ULBP3_uc011eek.1_Missense_Mutation_p.E122Q	NM_024518	NP_078794	Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3 precursor	171	MHC class I alpha-2 like.				antigen processing and presentation|immune response|natural killer cell activation	anchored to membrane|MHC class I protein complex	MHC class I receptor activity				0		Ovarian(120;0.12)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.45e-12)										0.137931	15.659501	23.012702	8	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150386651	150386651	17532	6	C	G	G	G	416	32	ULBP3	3	3
NOX3	50508	broad.mit.edu	37	6	155776924	155776924	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:155776924C>T	uc003qqm.2	-	c.11G>A	c.(10-12)TGC>TAC	p.C4Y		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	4	Cytoplasmic (Potential).				oxidation-reduction process		electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)										0.128205	4.843312	10.106109	5	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155776924	155776924	10961	6	C	T	T	T	325	25	NOX3	2	2
ACAT2	39	broad.mit.edu	37	6	160199778	160199778	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160199778G>C	uc011efw.1	+	c.1198G>C	c.(1198-1200)GAG>CAG	p.E400Q	ACAT2_uc010kjy.2_Missense_Mutation_p.E371Q|TCP1_uc003qsr.2_3'UTR|TCP1_uc003qss.2_3'UTR|TCP1_uc010kjz.2_3'UTR|TCP1_uc003qst.2_3'UTR	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2	371					lipid metabolic process	mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)										0.078947	2.008779	15.750769	6	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160199778	160199778	123	6	G	C	C	C	533	41	ACAT2	3	3
QKI	9444	broad.mit.edu	37	6	163956145	163956145	+	Silent	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:163956145A>G	uc003qui.2	+	c.534A>G	c.(532-534)TTA>TTG	p.L178L	QKI_uc003que.2_Silent_p.L178L|QKI_uc003quf.2_Silent_p.L178L|QKI_uc003qug.2_Silent_p.L178L|QKI_uc003quh.2_Silent_p.L178L|QKI_uc003quj.2_Silent_p.L178L	NM_006775	NP_006766	Q96PU8	QKI_HUMAN	quaking homolog, KH domain RNA binding isoform	178					mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)										0.242857	46.844752	51.061023	17	53	KEEP	---	---	---	---	capture		Silent	SNP	163956145	163956145	13331	6	A	G	G	G	206	16	QKI	4	4
SLC17A3	10786	broad.mit.edu	37	6	25861921	25861921	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:25861921G>C	uc003nfk.3	-	c.556C>G	c.(556-558)CAG>GAG	p.Q186E	SLC17A3_uc003nfi.3_Missense_Mutation_p.Q108E|SLC17A3_uc011djz.1_Missense_Mutation_p.Q186E|SLC17A3_uc011dka.1_Missense_Mutation_p.Q108E	NM_001098486	NP_001091956	O00476	NPT4_HUMAN	solute carrier family 17 (sodium phosphate),	108					glucose-6-phosphate transport|urate metabolic process	apical plasma membrane|brush border membrane|endoplasmic reticulum membrane|integral to plasma membrane|perinuclear region of cytoplasm	drug transmembrane transporter activity|efflux transmembrane transporter activity|organic anion transmembrane transporter activity|sodium:phosphate symporter activity|toxin transporter activity|urate transmembrane transporter activity|voltage-gated anion channel activity				0														0.225352	43.960812	48.881946	16	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25861921	25861921	14914	6	G	C	C	C	585	45	SLC17A3	3	3
ZNF184	7738	broad.mit.edu	37	6	27419946	27419946	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:27419946G>A	uc003njj.2	-	c.1392C>T	c.(1390-1392)CAC>CAT	p.H464H	ZNF184_uc010jqv.2_Silent_p.H464H|ZNF184_uc003nji.2_Silent_p.H464H	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	464	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.098361	4.453788	14.255447	6	55	KEEP	---	---	---	---	capture		Silent	SNP	27419946	27419946	18342	6	G	A	A	A	568	44	ZNF184	2	2
OR12D2	26529	broad.mit.edu	37	6	29365302	29365302	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29365302A>C	uc003nmf.3	+	c.826A>C	c.(826-828)ATG>CTG	p.M276L		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	276	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.032086	-31.401124	13.34345	6	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29365302	29365302	11337	6	A	C	C	C	104	8	OR12D2	4	4
TREM1	54210	broad.mit.edu	37	6	41250157	41250157	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41250157G>T	uc003oqf.1	-	c.382C>A	c.(382-384)CGC>AGC	p.R128S	TREM1_uc003oqg.1_Missense_Mutation_p.R128S	NM_018643	NP_061113	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	128	Extracellular (Potential).|Ig-like V-type.				blood coagulation|humoral immune response|intracellular signal transduction|leukocyte migration	extracellular region|integral to membrane|plasma membrane	receptor activity			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)				Glutathione(DB00143)									0.118644	8.584249	17.01082	7	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41250157	41250157	17014	6	G	T	T	T	481	37	TREM1	1	1
CRISP1	167	broad.mit.edu	37	6	49814333	49814333	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49814333C>A	uc003ozw.2	-	c.335G>T	c.(334-336)TGG>TTG	p.W112L	CRISP1_uc003ozx.2_Missense_Mutation_p.W112L	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1	112					fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)													0.111111	10.683914	24.141946	10	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49814333	49814333	4018	6	C	A	A	A	273	21	CRISP1	2	2
TFAP2D	83741	broad.mit.edu	37	6	50683242	50683242	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:50683242C>A	uc003paf.2	+	c.453C>A	c.(451-453)GGC>GGA	p.G151G	TFAP2D_uc011dwt.1_Non-coding_Transcript	NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1	151					regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)													0.189542	58.205033	71.986879	29	124	KEEP	---	---	---	---	capture		Silent	SNP	50683242	50683242	16318	6	C	A	A	A	353	28	TFAP2D	2	2
EFHC1	114327	broad.mit.edu	37	6	52303263	52303263	+	Silent	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:52303263A>T	uc003pap.3	+	c.447A>T	c.(445-447)ATA>ATT	p.I149I	EFHC1_uc011dwv.1_Silent_p.I58I|EFHC1_uc011dww.1_Silent_p.I130I	NM_018100	NP_060570	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	149	DM10 1.					axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)	2	Lung NSC(77;0.109)													0.181818	14.155588	18.372247	8	36	KEEP	---	---	---	---	capture		Silent	SNP	52303263	52303263	5134	6	A	T	T	T	163	13	EFHC1	3	3
PHF3	23469	broad.mit.edu	37	6	64422420	64422420	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:64422420A>G	uc003pep.1	+	c.4936A>G	c.(4936-4938)ATC>GTC	p.I1646V	PHF3_uc003pen.2_Missense_Mutation_p.I1558V|PHF3_uc011dxs.1_Missense_Mutation_p.I915V	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1646					multicellular organismal development	nucleus	zinc ion binding			ovary(2)|lung(1)|skin(1)	4	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GBM(135;136 1820 29512 34071 46235)				350				0.357143	49.0162	49.769951	15	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64422420	64422420	12259	6	A	G	G	G	208	16	PHF3	4	4
COL12A1	1303	broad.mit.edu	37	6	75829168	75829168	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:75829168C>G	uc003phs.2	-	c.7108G>C	c.(7108-7110)GAT>CAT	p.D2370H	COL12A1_uc003pht.2_Missense_Mutation_p.D1206H	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2370	VWFA 4.				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														0.132353	15.831085	24.75485	9	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75829168	75829168	3807	6	C	G	G	G	403	31	COL12A1	3	3
C6orf167	253714	broad.mit.edu	37	6	97676987	97676987	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:97676987C>A	uc003ppb.2	-	c.1822G>T	c.(1822-1824)GTG>TTG	p.V608L	C6orf167_uc011eaf.1_Missense_Mutation_p.V568L	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714	608					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)										0.202703	34.584094	40.658003	15	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97676987	97676987	2447	6	C	A	A	A	234	18	C6orf167	2	2
RELN	5649	broad.mit.edu	37	7	103180650	103180650	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103180650G>T	uc003vca.2	-	c.6924C>A	c.(6922-6924)ATC>ATA	p.I2308I	RELN_uc010liz.2_Silent_p.I2308I	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2308					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.083333	1.372965	9.832143	4	44	KEEP	---	---	---	---	capture		Silent	SNP	103180650	103180650	13689	7	G	T	T	T	473	37	RELN	1	1
DOCK4	9732	broad.mit.edu	37	7	111409724	111409724	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:111409724T>A	uc003vfy.2	-	c.3797A>T	c.(3796-3798)TAT>TTT	p.Y1266F	DOCK4_uc011kml.1_Missense_Mutation_p.Y102F|DOCK4_uc011kmm.1_Missense_Mutation_p.Y128F|DOCK4_uc003vfw.2_Missense_Mutation_p.Y671F|DOCK4_uc003vfx.2_Missense_Mutation_p.Y1221F	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1221	DHR-2.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(1;0.0441)												0.230769	22.27788	24.852312	9	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111409724	111409724	4873	7	T	A	A	A	637	49	DOCK4	3	3
PPP1R3A	5506	broad.mit.edu	37	7	113518398	113518398	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:113518398A>G	uc010ljy.1	-	c.2749T>C	c.(2749-2751)TCC>CCC	p.S917P		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	917					glycogen metabolic process	integral to membrane				ovary(9)|pancreas(7)|skin(2)|breast(2)|lung(1)	21										235				0.056	-8.457963	17.428743	7	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113518398	113518398	12806	7	A	G	G	G	117	9	PPP1R3A	4	4
KCND2	3751	broad.mit.edu	37	7	119915005	119915005	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:119915005C>A	uc003vjj.1	+	c.319C>A	c.(319-321)CCT>ACT	p.P107T		NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related	107	Cytoplasmic (Potential).				regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)	4	all_neural(327;0.117)													0.097015	4.987183	26.803433	13	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119915005	119915005	8324	7	C	A	A	A	390	30	KCND2	2	2
HYAL4	23553	broad.mit.edu	37	7	123516914	123516914	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123516914A>G	uc003vlc.2	+	c.1151A>G	c.(1150-1152)AAT>AGT	p.N384S	HYAL4_uc011knz.1_3'UTR	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	384	Extracellular (Potential).				fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity				0														0.2	19.678944	23.025735	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123516914	123516914	7766	7	A	G	G	G	52	4	HYAL4	4	4
SPAM1	6677	broad.mit.edu	37	7	123594355	123594355	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123594355A>G	uc003vle.2	+	c.731A>G	c.(730-732)AAA>AGA	p.K244R	SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vld.2_Missense_Mutation_p.K244R|SPAM1_uc003vlf.3_Missense_Mutation_p.K244R|SPAM1_uc010lku.2_Missense_Mutation_p.K244R	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	244					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.051282	-6.961693	9.659244	4	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123594355	123594355	15489	7	A	G	G	G	13	1	SPAM1	4	4
GARS	2617	broad.mit.edu	37	7	30643155	30643155	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:30643155A>C	uc003tbm.2	+	c.702A>C	c.(700-702)GAA>GAC	p.E234D		NM_002047	NP_002038	P41250	SYG_HUMAN	glycyl-tRNA synthetase	234					cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)									0.097561	4.268475	10.917126	4	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30643155	30643155	6506	7	A	C	C	C	11	1	GARS	4	4
CCDC129	223075	broad.mit.edu	37	7	31691641	31691641	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31691641C>A	uc011kae.1	+	c.2878C>A	c.(2878-2880)CAA>AAA	p.Q960K	CCDC129_uc011kad.1_Missense_Mutation_p.Q944K|CCDC129_uc003tcj.1_Missense_Mutation_p.Q934K|CCDC129_uc003tci.1_Missense_Mutation_p.Q785K|CCDC129_uc003tck.1_Missense_Mutation_p.Q842K	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	934	Potential.										0														0.222222	19.281443	21.836365	8	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31691641	31691641	2884	7	C	A	A	A	325	25	CCDC129	2	2
NPSR1	387129	broad.mit.edu	37	7	34867013	34867013	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:34867013A>G	uc003teh.1	+	c.479A>G	c.(478-480)GAA>GGA	p.E160G	AAA1_uc010kwq.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teg.1_Missense_Mutation_p.E160G|NPSR1_uc010kwt.1_Missense_Mutation_p.E7G|NPSR1_uc010kwu.1_5'UTR|NPSR1_uc010kwv.1_Missense_Mutation_p.E94G|NPSR1_uc003tei.1_Missense_Mutation_p.E160G|NPSR1_uc010kww.1_Missense_Mutation_p.E149G|NPSR1_uc011kar.1_Missense_Mutation_p.E94G|AAA1_uc010kwy.2_Intron|AAA1_uc003tek.3_Intron	NM_207173	NP_997056	Q6W5P4	NPSR1_HUMAN	G protein-coupled receptor for asthma	160	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			pancreas(1)|skin(1)	2					Halothane(DB01159)									0.076923	-2.485751	12.124733	6	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34867013	34867013	11005	7	A	G	G	G	117	9	NPSR1	4	4
ELMO1	9844	broad.mit.edu	37	7	36934500	36934500	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:36934500G>T	uc003tfk.1	-	c.1560C>A	c.(1558-1560)TCC>TCA	p.S520S	ELMO1_uc003tfi.1_Silent_p.S40S|ELMO1_uc003tfj.1_Silent_p.S40S|ELMO1_uc011kbb.1_Non-coding_Transcript|ELMO1_uc011kbc.1_Silent_p.S424S|ELMO1_uc010kxg.1_Silent_p.S520S	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	520					actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)	3														0.303571	48.5944	50.500156	17	39	KEEP	---	---	---	---	capture		Silent	SNP	36934500	36934500	5257	7	G	T	T	T	496	39	ELMO1	1	1
TXNDC3	51314	broad.mit.edu	37	7	37927918	37927918	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:37927918C>A	uc003tfn.2	+	c.1287C>A	c.(1285-1287)AAC>AAA	p.N429K		NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3	429	NDK 2.				cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						Ovarian(108;903 1537 27096 29907 47400)								0.06015	-11.213905	15.725664	8	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37927918	37927918	17354	7	C	A	A	A	233	18	TXNDC3	2	2
POM121L12	285877	broad.mit.edu	37	7	53103754	53103754	+	Silent	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:53103754A>T	uc003tpz.2	+	c.390A>T	c.(388-390)CCA>CCT	p.P130P		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	130											0														0.115385	3.409977	7.195693	3	23	KEEP	---	---	---	---	capture		Silent	SNP	53103754	53103754	12669	7	A	T	T	T	80	7	POM121L12	3	3
RFC2	5982	broad.mit.edu	37	7	73661077	73661077	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73661077T>C	uc003uaj.2	-	c.349A>G	c.(349-351)AGG>GGG	p.R117G	RFC2_uc011kfa.1_Non-coding_Transcript|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Missense_Mutation_p.R16G	NM_181471	NP_852136	P35250	RFC2_HUMAN	replication factor C 2 isoform 1	117					cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2														0.2	17.108609	20.035819	7	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73661077	73661077	13716	7	T	C	C	C	700	54	RFC2	4	4
CACNA2D1	781	broad.mit.edu	37	7	81643766	81643766	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81643766T>C	uc003uhr.1	-	c.1173A>G	c.(1171-1173)CAA>CAG	p.Q391Q		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	391	Extracellular (Potential).|VWFA.					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)									0.206897	16.534495	18.842481	6	23	KEEP	---	---	---	---	capture		Silent	SNP	81643766	81643766	2664	7	T	C	C	C	777	60	CACNA2D1	4	4
COL1A2	1278	broad.mit.edu	37	7	94041394	94041394	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:94041394C>A	uc003ung.1	+	c.1365C>A	c.(1363-1365)TCC>TCA	p.S455S	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	455					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)									0.090909	1.99885	7.566541	3	30	KEEP	---	---	---	---	capture		Silent	SNP	94041394	94041394	3816	7	C	A	A	A	275	22	COL1A2	2	2
ASB4	51666	broad.mit.edu	37	7	95157271	95157271	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:95157271C>T	uc011kij.1	+	c.634C>T	c.(634-636)CTG>TTG	p.L212L	ASB4_uc003unx.2_Silent_p.L212L	NM_016116	NP_057200	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box-containing protein 4	212	ANK 5.				intracellular signal transduction					central_nervous_system(1)	1	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)									OREG0018172	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.218182	30.872494	34.89658	12	43	KEEP	---	---	---	---	capture		Silent	SNP	95157271	95157271	1043	7	C	T	T	T	311	24	ASB4	2	2
RIMS2	9699	broad.mit.edu	37	8	105105708	105105708	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:105105708G>C	uc003yls.2	+	c.2731G>C	c.(2731-2733)GGA>CGA	p.G911R	RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Missense_Mutation_p.G984R|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	366					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)							728				0.255474	88.708325	96.187791	35	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105105708	105105708	13845	8	G	C	C	C	443	35	RIMS2	3	3
PKHD1L1	93035	broad.mit.edu	37	8	110394800	110394800	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110394800C>T	uc003yne.2	+	c.417C>T	c.(415-417)AAC>AAT	p.N139N		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	139	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.153153	31.111227	43.878411	17	94	KEEP	---	---	---	---	capture		Silent	SNP	110394800	110394800	12397	8	C	T	T	T	246	19	PKHD1L1	1	1
CSMD3	114788	broad.mit.edu	37	8	113504781	113504781	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113504781G>A	uc003ynu.2	-	c.5215C>T	c.(5215-5217)CTC>TTC	p.L1739F	CSMD3_uc003yns.2_Missense_Mutation_p.L1011F|CSMD3_uc003ynt.2_Missense_Mutation_p.L1699F|CSMD3_uc011lhx.1_Missense_Mutation_p.L1635F	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1739	Extracellular (Potential).|Sushi 9.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.230769	58.546406	65.454956	24	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113504781	113504781	4087	8	G	A	A	A	468	36	CSMD3	2	2
CSMD3	114788	broad.mit.edu	37	8	113569006	113569006	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113569006A>G	uc003ynu.2	-	c.4220T>C	c.(4219-4221)CTG>CCG	p.L1407P	CSMD3_uc003yns.2_Missense_Mutation_p.L679P|CSMD3_uc003ynt.2_Missense_Mutation_p.L1367P|CSMD3_uc011lhx.1_Missense_Mutation_p.L1303P	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1407	Extracellular (Potential).|Sushi 7.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.103448	2.903542	11.995094	6	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113569006	113569006	4087	8	A	G	G	G	91	7	CSMD3	4	4
COL14A1	7373	broad.mit.edu	37	8	121259925	121259925	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:121259925C>T	uc003yox.2	+	c.2553C>T	c.(2551-2553)CCC>CCT	p.P851P	COL14A1_uc003yoy.2_Silent_p.P529P	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	851	Fibronectin type-III 7.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)							1131				0.052083	-9.554269	10.763573	5	91	KEEP	---	---	---	---	capture		Silent	SNP	121259925	121259925	3809	8	C	T	T	T	275	22	COL14A1	2	2
FAM135B	51059	broad.mit.edu	37	8	139153549	139153550	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139153549_139153550GG>TT	uc003yuy.2	-	c.3681_3682CC>AA	c.(3679-3684)GTCCTC>GTAATC	p.L1228I	FAM135B_uc003yux.2_Missense_Mutation_p.L1129I|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)											0.153226	34.142328	48.407986	19	105	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	139153549	139153550	5646	8	GG	TT	TT	TT	455	35	FAM135B	2	2
LY6D	8581	broad.mit.edu	37	8	143867036	143867036	+	Silent	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:143867036G>T	uc003yxf.1	-	c.120C>A	c.(118-120)GCC>GCA	p.A40A		NM_003695	NP_003686	Q14210	LY6D_HUMAN	lymphocyte antigen 6 complex, locus D precursor	40	UPAR/Ly6.				cell adhesion	anchored to membrane|membrane fraction|plasma membrane	protein binding				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)													0.304348	18.615898	19.401973	7	16	KEEP	---	---	---	---	capture		Silent	SNP	143867036	143867036	9467	8	G	T	T	T	600	47	LY6D	2	2
ADAMDEC1	27299	broad.mit.edu	37	8	24250787	24250788	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:24250787_24250788CC>AA	uc003xdz.2	+	c.220_221CC>AA	c.(220-222)CCT>AAT	p.P74N	ADAMDEC1_uc010lub.2_De_novo_Start_OutOfFrame|ADAMDEC1_uc011lab.1_De_novo_Start_OutOfFrame	NM_014479	NP_055294	O15204	ADEC1_HUMAN	ADAM-like, decysin 1 isoform 1	74					integrin-mediated signaling pathway|negative regulation of cell adhesion|proteolysis	extracellular region|integral to membrane	integrin binding|metalloendopeptidase activity|zinc ion binding				0		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		Ovarian(147;687 1849 3699 25981 31337)								0.172414	10.957027	13.896863	5	24	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	24250787	24250788	255	8	CC	AA	AA	AA	234	18	ADAMDEC1	2	2
KIF13B	23303	broad.mit.edu	37	8	28998003	28998003	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:28998003G>A	uc003xhh.3	-	c.2466C>T	c.(2464-2466)ATC>ATT	p.I822I		NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	822					microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)										0.132353	11.810564	20.77933	9	59	KEEP	---	---	---	---	capture		Silent	SNP	28998003	28998003	8586	8	G	A	A	A	577	45	KIF13B	2	2
ADAM9	8754	broad.mit.edu	37	8	38884267	38884267	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:38884267T>A	uc003xmr.2	+	c.1068T>A	c.(1066-1068)AAT>AAA	p.N356K	ADAM9_uc011lcf.1_Non-coding_Transcript|ADAM9_uc011lcg.1_Non-coding_Transcript|ADAM9_uc010lwr.2_Non-coding_Transcript	NM_003816	NP_003807	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9 isoform 1	356	Extracellular (Potential).|Peptidase M12B.				activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|integrin-mediated signaling pathway|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway|visual perception	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)											0.117117	16.296948	32.298955	13	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38884267	38884267	254	8	T	A	A	A	647	50	ADAM9	3	3
ADAM2	2515	broad.mit.edu	37	8	39678647	39678647	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:39678647G>A	uc003xnj.2	-	c.387C>T	c.(385-387)CCC>CCT	p.P129P	ADAM2_uc003xnk.2_Silent_p.P129P|ADAM2_uc011lck.1_Silent_p.P129P|ADAM2_uc003xnl.2_Silent_p.P129P	NM_001464	NP_001455	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2 proprotein	129					cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)										0.061224	-3.217757	6.633264	3	46	KEEP	---	---	---	---	capture		Silent	SNP	39678647	39678647	242	8	G	A	A	A	548	43	ADAM2	2	2
SNAI2	6591	broad.mit.edu	37	8	49832983	49832983	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:49832983G>C	uc003xqp.2	-	c.97C>G	c.(97-99)CTC>GTC	p.L33V		NM_003068	NP_003059	O43623	SNAI2_HUMAN	snail 2	33					canonical Wnt receptor signaling pathway|ectoderm and mesoderm interaction|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)												0.145833	29.082957	40.662266	14	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49832983	49832983	15327	8	G	C	C	C	429	33	SNAI2	3	3
YTHDF3	253943	broad.mit.edu	37	8	64098705	64098705	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:64098705G>C	uc003xuy.2	+	c.136_splice	c.e4-1	p.S46_splice	YTHDF3_uc010lys.2_Splice_Site_SNP|YTHDF3_uc003xuz.2_Splice_Site_SNP|YTHDF3_uc003xva.2_Splice_Site_SNP|YTHDF3_uc011len.1_Splice_Site_SNP	NM_152758	NP_689971			YTH domain family, member 3												0	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)											0.09375	1.399392	6.710135	3	29	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	64098705	64098705	18083	8	G	C	C	C	429	33	YTHDF3	5	3
ZFHX4	79776	broad.mit.edu	37	8	77690536	77690536	+	Silent	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77690536G>C	uc003yav.2	+	c.3108G>C	c.(3106-3108)CTG>CTC	p.L1036L	ZFHX4_uc003yau.1_Silent_p.L1062L|ZFHX4_uc003yaw.1_Silent_p.L1036L	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1036	C2H2-type 7.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.055556	-13.781001	12.421487	7	119	KEEP	---	---	---	---	capture		Silent	SNP	77690536	77690536	18223	8	G	C	C	C	600	47	ZFHX4	3	3
ZFHX4	79776	broad.mit.edu	37	8	77767647	77767647	+	Silent	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77767647C>A	uc003yav.2	+	c.8355C>A	c.(8353-8355)TCC>TCA	p.S2785S	ZFHX4_uc003yau.1_Silent_p.S2830S|ZFHX4_uc003yaw.1_Silent_p.S2785S	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2785					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.223881	38.143224	42.800857	15	52	KEEP	---	---	---	---	capture		Silent	SNP	77767647	77767647	18223	8	C	A	A	A	288	23	ZFHX4	1	1
RUNX1T1	862	broad.mit.edu	37	8	92982976	92982976	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:92982976C>A	uc011lgi.1	-	c.1482G>T	c.(1480-1482)AGG>AGT	p.R494S	RUNX1T1_uc003yfc.1_Missense_Mutation_p.R456S|RUNX1T1_uc003yfd.2_Missense_Mutation_p.R483S|RUNX1T1_uc003yfe.1_Missense_Mutation_p.R446S|RUNX1T1_uc010mao.2_Missense_Mutation_p.R456S|RUNX1T1_uc010man.1_Missense_Mutation_p.R108S|RUNX1T1_uc003yfb.1_Missense_Mutation_p.R446S	NM_175636	NP_783554	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	483					generation of precursor metabolites and energy|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|central_nervous_system(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(11;0.0141)							213				0.344828	24.83137	25.452431	10	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92982976	92982976	14227	8	C	A	A	A	285	22	RUNX1T1	2	2
BAAT	570	broad.mit.edu	37	9	104133326	104133326	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:104133326C>T	uc010mtd.2	-	c.361G>A	c.(361-363)GCT>ACT	p.A121T	BAAT_uc004bbd.3_Missense_Mutation_p.A121T	NM_001127610	NP_001121082	Q14032	BAAT_HUMAN	bile acid Coenzyme A: amino acid	121					acyl-CoA metabolic process|bile acid and bile salt transport|bile acid biosynthetic process|digestion|fatty acid metabolic process|glycine metabolic process	cytosol|peroxisomal matrix	carboxylesterase activity|glycine N-choloyltransferase activity|N-acyltransferase activity|palmitoyl-CoA hydrolase activity			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)									0.135922	19.180737	32.40817	14	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104133326	104133326	1301	9	C	T	T	T	325	25	BAAT	2	2
DBC1	1620	broad.mit.edu	37	9	122004416	122004416	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:122004416G>A	uc004bkc.2	-	c.488C>T	c.(487-489)GCT>GTT	p.A163V	DBC1_uc004bkd.2_Missense_Mutation_p.A163V	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	163	MACPF.				cell cycle arrest|cell death	cytoplasm	protein binding			ovary(2)|central_nervous_system(2)|large_intestine(1)	5														0.090909	0.078152	9.326325	5	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122004416	122004416	4418	9	G	A	A	A	442	34	DBC1	2	2
SEC16A	9919	broad.mit.edu	37	9	139353685	139353685	+	Silent	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139353685T>C	uc004chx.2	-	c.5310A>G	c.(5308-5310)CCA>CCG	p.P1770P	SEC16A_uc004chu.2_5'Flank|SEC16A_uc004chv.3_Silent_p.P1160P|SEC16A_uc004chw.2_Silent_p.P1770P|SEC16A_uc010nbn.2_Silent_p.P1770P	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	1592					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)										0.172414	8.665739	11.59969	5	24	KEEP	---	---	---	---	capture		Silent	SNP	139353685	139353685	14472	9	T	C	C	C	652	51	SEC16A	4	4
FREM1	158326	broad.mit.edu	37	9	14737453	14737453	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:14737453G>T	uc003zlm.2	-	c.6481C>A	c.(6481-6483)CAA>AAA	p.Q2161K	FREM1_uc010mic.2_Non-coding_Transcript|FREM1_uc003zlk.2_Non-coding_Transcript|FREM1_uc003zll.2_Missense_Mutation_p.Q697K	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	2161	C-type lectin.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)										0.147059	8.952294	13.02101	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14737453	14737453	6291	9	G	T	T	T	598	46	FREM1	2	2
SLC24A2	25769	broad.mit.edu	37	9	19521004	19521004	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19521004C>G	uc003zoa.1	-	c.1624G>C	c.(1624-1626)GCT>CCT	p.A542P	SLC24A2_uc003zob.1_Missense_Mutation_p.A525P	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	542	Alpha-2.|Helical; (Potential).				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)										0.238095	28.029159	30.660258	10	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19521004	19521004	14963	9	C	G	G	G	325	25	SLC24A2	3	3
PIGO	84720	broad.mit.edu	37	9	35094351	35094351	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35094351G>A	uc003zwd.2	-	c.517C>T	c.(517-519)CGT>TGT	p.R173C	PIGO_uc003zwc.1_Missense_Mutation_p.R173C|PIGO_uc003zwe.2_Missense_Mutation_p.R173C|PIGO_uc003zwf.2_Missense_Mutation_p.R173C|PIGO_uc003zwg.1_5'UTR	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	173					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)											0.112245	8.990354	23.526964	11	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35094351	35094351	12318	9	G	A	A	A	494	38	PIGO	1	1
DRP2	1821	broad.mit.edu	37	X	100491011	100491011	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100491011C>A	uc004egz.2	+	c.280C>A	c.(280-282)CGC>AGC	p.R94S	DRP2_uc011mrh.1_Missense_Mutation_p.R16S	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	94					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2														0.318182	62.958356	64.894106	21	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100491011	100491011	4948	23	C	A	A	A	299	23	DRP2	1	1
BTK	695	broad.mit.edu	37	X	100617171	100617171	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100617171T>A	uc010nno.2	-	c.680A>T	c.(679-681)GAG>GTG	p.E227V	BTK_uc004ehg.2_Missense_Mutation_p.E193V|BTK_uc010nnn.2_Missense_Mutation_p.E193V|BTK_uc004ehi.2_Missense_Mutation_p.E193V	NM_000061	NP_000052	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	193					calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding			central_nervous_system(2)|ovary(1)|lung(1)	4										247				0.259259	17.717752	19.131707	7	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100617171	100617171	1591	23	T	A	A	A	702	54	BTK	3	3
TEX13A	56157	broad.mit.edu	37	X	104463837	104463837	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:104463837C>A	uc004ema.2	-	c.1039G>T	c.(1039-1041)GGG>TGG	p.G347W	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Missense_Mutation_p.M347I	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	347						intracellular	zinc ion binding			ovary(2)	2														0.255814	25.497341	27.829738	11	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104463837	104463837	16303	23	C	A	A	A	273	21	TEX13A	2	2
MID1	4281	broad.mit.edu	37	X	10535314	10535314	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:10535314T>C	uc004cte.3	-	c.274A>G	c.(274-276)AGC>GGC	p.S92G	MID1_uc004ctd.3_5'Flank|MID1_uc004ctg.3_Missense_Mutation_p.S92G|MID1_uc004cth.3_Missense_Mutation_p.S92G|MID1_uc004ctk.3_Missense_Mutation_p.S92G|MID1_uc004cti.3_Missense_Mutation_p.S92G|MID1_uc004ctj.3_Missense_Mutation_p.S92G|MID1_uc011mie.1_Non-coding_Transcript|MID1_uc004ctm.1_Missense_Mutation_p.S92G|MID1_uc004ctn.1_Missense_Mutation_p.S92G|MID1_uc004cto.1_Missense_Mutation_p.S92G|MID1_uc010ndw.1_5'Flank|MID1_uc004cts.1_5'Flank|MID1_uc004ctt.2_Missense_Mutation_p.S92G|MID1_uc004ctu.2_Missense_Mutation_p.S92G|MID1_uc004ctv.2_Missense_Mutation_p.S92G|MID1_uc004ctw.2_Missense_Mutation_p.S92G|MID1_uc010ndy.1_Missense_Mutation_p.S92G|MID1_uc004cty.2_Missense_Mutation_p.S92G|MID1_uc004ctz.1_5'Flank|MID1_uc004cua.1_Non-coding_Transcript|MID1_uc004cub.1_Missense_Mutation_p.S92G|MID1_uc010nea.1_5'Flank|MID1_uc004cuc.1_Missense_Mutation_p.S92G|MID1_uc004cud.1_Missense_Mutation_p.S92G|MID1_uc004cue.1_Missense_Mutation_p.S92G|MID1_uc004cuf.1_Missense_Mutation_p.S92G|MID1_uc004cug.1_Missense_Mutation_p.S92G	NM_033290	NP_150632	O15344	TRI18_HUMAN	midline 1	92					microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3														0.183673	20.546928	25.146949	9	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10535314	10535314	9966	23	T	C	C	C	702	54	MID1	4	4
CXorf41	139212	broad.mit.edu	37	X	106462128	106462128	+	Silent	SNP	C	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:106462128C>T	uc004enc.2	+	c.261C>T	c.(259-261)GAC>GAT	p.D87D	CXorf41_uc004end.2_Silent_p.D87D	NM_173494	NP_775765	Q9NQM4	CX041_HUMAN	hypothetical protein LOC139212	87											0														0.085106	0.862302	9.070027	4	43	KEEP	---	---	---	---	capture		Silent	SNP	106462128	106462128	4271	23	C	T	T	T	220	17	CXorf41	2	2
GPR112	139378	broad.mit.edu	37	X	135405117	135405117	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135405117G>C	uc004ezu.1	+	c.251G>C	c.(250-252)GGC>GCC	p.G84A	GPR112_uc010nsb.1_Intron	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	84	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.484076	246.522499	246.555234	76	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135405117	135405117	6903	23	G	C	C	C	546	42	GPR112	3	3
VGLL1	51442	broad.mit.edu	37	X	135631059	135631059	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135631059A>T	uc004ezy.2	+	c.526A>T	c.(526-528)AGA>TGA	p.R176*	MIR934_hsa-mir-934|MI0005756_5'Flank	NM_016267	NP_057351	Q99990	VGLL1_HUMAN	vestigial like 1	176					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity|transcription regulator activity				0	Acute lymphoblastic leukemia(192;0.000127)													0.376147	125.659137	127.122447	41	68	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	135631059	135631059	17725	23	A	T	T	T	88	7	VGLL1	5	3
ZIC3	7547	broad.mit.edu	37	X	136652166	136652166	+	Silent	SNP	A	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:136652166A>C	uc004fak.2	+	c.1341A>C	c.(1339-1341)GCA>GCC	p.A447A		NM_003413	NP_003404	O60481	ZIC3_HUMAN	zinc finger protein of the cerebellum 3	447					cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)													0.144928	18.104515	26.47727	10	59	KEEP	---	---	---	---	capture		Silent	SNP	136652166	136652166	18271	23	A	C	C	C	80	7	ZIC3	4	4
MAGEC1	9947	broad.mit.edu	37	X	140994078	140994078	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140994078G>C	uc004fbt.2	+	c.888G>C	c.(886-888)GAG>GAC	p.E296D	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	296							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.151515	16.798737	24.48966	10	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140994078	140994078	9561	23	G	C	C	C	451	35	MAGEC1	3	3
MAGEC1	9947	broad.mit.edu	37	X	140994373	140994373	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140994373A>G	uc004fbt.2	+	c.1183A>G	c.(1183-1185)AGA>GGA	p.R395G	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	395							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.322785	152.156903	156.569754	51	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140994373	140994373	9561	23	A	G	G	G	140	11	MAGEC1	4	4
MAGEC2	51438	broad.mit.edu	37	X	141290890	141290891	+	Missense	DNP	GG	AT	AT			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:141290890G>A	uc004fbu.1	-	c.884C>T	c.(883-885)CCA>CTA	p.P295L		NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	295	MAGE.					cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.273973	98.629391	105.354608	40	106	KEEP	---	---	---	---	capture		Missense	DNP	141290890	141290891	9562	23	GG	AT	AT	A	611	47	MAGEC2	2	2
SCML1	6322	broad.mit.edu	37	X	17771464	17771464	+	Silent	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:17771464A>G	uc004cyb.2	+	c.942A>G	c.(940-942)CTA>CTG	p.L314L	SCML1_uc004cyc.2_Silent_p.L287L|SCML1_uc004cyd.2_Silent_p.L193L|SCML1_uc004cye.2_Silent_p.L193L	NM_001037540	NP_001032629	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 isoform a	314	SAM.				anatomical structure morphogenesis|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)	3	Hepatocellular(33;0.183)													0.296296	46.28094	48.283706	16	38	KEEP	---	---	---	---	capture		Silent	SNP	17771464	17771464	14391	23	A	G	G	G	197	16	SCML1	4	4
FAM47A	158724	broad.mit.edu	37	X	34149861	34149861	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34149861G>C	uc004ddg.2	-	c.535C>G	c.(535-537)CCT>GCT	p.P179A		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	179	Pro-rich.									ovary(4)|central_nervous_system(1)	5														0.328947	75.75745	77.724625	25	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34149861	34149861	5790	23	G	C	C	C	546	42	FAM47A	3	3
FAM47B	170062	broad.mit.edu	37	X	34961693	34961693	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34961693G>T	uc004ddi.1	+	c.745G>T	c.(745-747)GTG>TTG	p.V249L		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	249	Pro-rich.									ovary(3)|breast(1)	4														0.246154	41.574032	45.317272	16	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34961693	34961693	5791	23	G	T	T	T	520	40	FAM47B	1	1
MAOA	4128	broad.mit.edu	37	X	43590552	43590552	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:43590552A>G	uc004dfy.2	+	c.710A>G	c.(709-711)CAA>CGA	p.Q237R	MAOA_uc011mkw.1_Missense_Mutation_p.Q104R	NM_000240	NP_000231	P21397	AOFA_HUMAN	monoamine oxidase A	237	Cytoplasmic.				behavior|neurotransmitter biosynthetic process|neurotransmitter catabolic process|neurotransmitter secretion|oxidation-reduction process|xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	primary amine oxidase activity|protein binding			breast(2)|ovary(1)	3					Almotriptan(DB00918)|Carbidopa(DB00190)|Clonazepam(DB01068)|Dopamine(DB00988)|Fluvoxamine(DB00176)|Ginkgo biloba(DB01381)|Imipramine(DB00458)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Linezolid(DB00601)|Lorazepam(DB00186)|Moclobemide(DB01171)|Nicotine(DB00184)|Norepinephrine(DB00368)|Phenelzine(DB00780)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pseudoephedrine(DB00852)|Rasagiline(DB01367)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)									0.52	38.472923	38.481496	13	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43590552	43590552	9608	23	A	G	G	G	65	5	MAOA	4	4
SHROOM4	57477	broad.mit.edu	37	X	50378521	50378521	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:50378521G>T	uc004dpe.2	-	c.552C>A	c.(550-552)AAC>AAA	p.N184K	SHROOM4_uc004dpd.3_Non-coding_Transcript|SHROOM4_uc004dpf.1_Missense_Mutation_p.N68K	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4	184					actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding				0	Ovarian(276;0.236)													0.272727	7.519436	8.032087	3	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50378521	50378521	14791	23	G	T	T	T	568	44	SHROOM4	2	2
HEPH	9843	broad.mit.edu	37	X	65392258	65392258	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:65392258A>G	uc011moz.1	+	c.238A>G	c.(238-240)ATC>GTC	p.I80V	HEPH_uc004dwn.2_Missense_Mutation_p.I80V|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Missense_Mutation_p.I80V|HEPH_uc011mpa.1_Missense_Mutation_p.I80V	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	77	Extracellular (Potential).|Plastocyanin-like 1.				cellular iron ion homeostasis|copper ion transport|oxidation-reduction process|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9										386				0.078947	-0.005005	6.875656	3	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65392258	65392258	7337	23	A	G	G	G	104	8	HEPH	4	4
DACH2	117154	broad.mit.edu	37	X	85404023	85404023	+	Silent	SNP	G	A	A			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:85404023G>A	uc004eew.2	+	c.399G>A	c.(397-399)GGG>GGA	p.G133G	DACH2_uc004eex.2_Silent_p.G133G|DACH2_uc010nmq.2_5'UTR	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	133	DACHbox-N.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5														0.375	31.294708	31.732431	12	20	KEEP	---	---	---	---	capture		Silent	SNP	85404023	85404023	4387	23	G	A	A	A	535	42	DACH2	2	2
KIAA0754	643314	broad.mit.edu	37	1	39879036	39879037	+	Frame_Shift_Ins	INS	-	C	C			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:39879036_39879037insC	uc009vvt.1	+	c.3099_3100insC	c.(3097-3102)GTGCCCfs	p.V1033fs	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc010oiu.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	897_898	Ala-rich.|2.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)											0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	39879036	39879037	8499	1	-	C	C	C	587	46	KIAA0754	5	5
FAT1	2195	broad.mit.edu	37	4	187542211	187542211	+	Frame_Shift_Del	DEL	A	-	-			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187542211_187542211delA	uc003izf.2	-	c.5529_5529delT	c.(5527-5529)TTTfs	p.F1843fs		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1843	Extracellular (Potential).|Cadherin 16.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						Colon(197;1040 2055 4143 4984 49344)								0.34			20	38		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	187542211	187542211	5925	4	A	-	-	-	115	9	FAT1	5	5
EEF1D	1936	broad.mit.edu	37	8	144663326	144663327	+	Splice_Site_Ins	INS	-	G	G			TCGA-17-Z003-01	TCGA-17-Z003-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144663326_144663327insG	uc003yyq.1	-	c.1538_splice	c.e5-1	p.V513_splice	NAPRT1_uc003yym.3_5'Flank|NAPRT1_uc003yyn.3_5'Flank|NAPRT1_uc011lkh.1_5'Flank|NAPRT1_uc003yyo.3_5'Flank|EEF1D_uc003yyp.1_Splice_Site_Ins_p.V439_splice|EEF1D_uc011lki.1_Splice_Site_Ins_p.V97_splice|EEF1D_uc011lkj.1_Splice_Site_Ins_p.V462_splice|EEF1D_uc003yyr.2_Splice_Site_Ins_p.V463_splice|EEF1D_uc003yyt.2_Splice_Site_Ins_p.V463_splice|EEF1D_uc011lkk.1_Splice_Site_Ins_p.V97_splice|EEF1D_uc003yys.2_Splice_Site_Ins_p.V97_splice|EEF1D_uc003yyv.2_Splice_Site_Ins_p.V73_splice|EEF1D_uc003yyu.2_Splice_Site_Ins_p.V97_splice|EEF1D_uc011lkl.1_Splice_Site_Ins_p.V78_splice	NM_032378	NP_115754			eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)							610				0.36			4	7		---	---	---	---	capture_indel		Splice_Site_Ins	INS	144663326	144663327	5113	8	-	G	G	G	715	55	EEF1D	5	5
