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
CUBN	8029	broad.mit.edu	37	10	17024512	17024512	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:17024512C>A	uc001ioo.2	-	c.4666G>T	c.(4666-4668)GAT>TAT	p.D1556Y		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1556	CUB 10.				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				0.087719	0.663958	20.26818	10	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17024512	17024512	4211	10	C	A	A	A	377	29	CUBN	2	2
C10orf140	387640	broad.mit.edu	37	10	21804176	21804176	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:21804176C>A	uc009xkd.2	-	c.2576G>T	c.(2575-2577)GGG>GTG	p.G859V		NM_207371	NP_997254	Q1XH10	DLN1_HUMAN	hypothetical protein LOC387640	778						nucleus	nucleotide binding			ovary(1)	1														0.258621	38.096058	41.158899	15	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21804176	21804176	1632	10	C	A	A	A	286	22	C10orf140	2	2
FAM13C	220965	broad.mit.edu	37	10	61112108	61112108	+	Silent	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:61112108G>C	uc010qif.1	-	c.312C>G	c.(310-312)CCC>CCG	p.P104P	FAM13C_uc001jkn.2_Silent_p.P82P|FAM13C_uc001jko.2_Silent_p.P82P|FAM13C_uc010qid.1_5'UTR|FAM13C_uc010qie.1_5'UTR|FAM13C_uc001jkp.2_5'UTR	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1	82										ovary(1)	1														0.113636	11.509706	24.449041	10	78	KEEP	---	---	---	---	capture		Silent	SNP	61112108	61112108	5651	10	G	C	C	C	600	47	FAM13C	3	3
TET1	80312	broad.mit.edu	37	10	70404986	70404986	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70404986T>G	uc001jok.3	+	c.2500T>G	c.(2500-2502)TCC>GCC	p.S834A		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	834					DNA demethylation|inner cell mass cell differentiation|oxidation-reduction process|stem cell maintenance	nucleus	iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)	5										280				0.062696	-11.16331	52.39548	20	299	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70404986	70404986	16296	10	T	G	G	G	806	62	TET1	4	4
TSPAN15	23555	broad.mit.edu	37	10	71265915	71265915	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:71265915C>A	uc001jpo.1	+	c.654C>A	c.(652-654)GGC>GGA	p.G218G		NM_012339	NP_036471	O95858	TSN15_HUMAN	transmembrane 4 superfamily member 15	218	Extracellular (Potential).					integral to plasma membrane|membrane fraction					0														0.086957	2.008566	25.833673	12	126	KEEP	---	---	---	---	capture		Silent	SNP	71265915	71265915	17190	10	C	A	A	A	353	28	TSPAN15	2	2
FUT11	170384	broad.mit.edu	37	10	75532609	75532609	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75532609G>A	uc001jva.2	+	c.518G>A	c.(517-519)CGC>CAC	p.R173H	FUT11_uc001juy.1_Missense_Mutation_p.R173H|FUT11_uc001juz.1_Missense_Mutation_p.R173H	NM_173540	NP_775811	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3)	173	Lumenal (Potential).				protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity				0	Prostate(51;0.0112)													0.3	38.519248	40.298759	15	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75532609	75532609	6354	10	G	A	A	A	494	38	FUT11	1	1
MYST4	23522	broad.mit.edu	37	10	76781967	76781967	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:76781967A>T	uc001jwn.1	+	c.3350A>T	c.(3349-3351)CAG>CTG	p.Q1117L	MYST4_uc001jwm.1_Missense_Mutation_p.Q825L|MYST4_uc001jwo.1_Missense_Mutation_p.Q825L|MYST4_uc001jwp.1_Missense_Mutation_p.Q934L	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1117					histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription activator activity|transcription factor binding|transcription repressor activity|zinc ion binding			central_nervous_system(5)|ovary(3)|breast(1)	9	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)									319		OREG0020273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.156951	69.778341	94.819128	35	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76781967	76781967	10500	10	A	T	T	T	91	7	MYST4	3	3
CDHR1	92211	broad.mit.edu	37	10	85973997	85973997	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85973997C>A	uc001kcv.2	+	c.2200C>A	c.(2200-2202)CTG>ATG	p.L734M	CDHR1_uc001kcw.2_Intron|CDHR1_uc009xst.2_Missense_Mutation_p.L438M|CDHR1_uc001kcx.2_Missense_Mutation_p.L48M	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	734	Cytoplasmic (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1														0.16	18.245363	26.531742	12	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85973997	85973997	3247	10	C	A	A	A	311	24	CDHR1	2	2
GRID1	2894	broad.mit.edu	37	10	87373323	87373323	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:87373323G>T	uc001kdl.1	-	c.2442C>A	c.(2440-2442)ACC>ACA	p.T814T	GRID1_uc009xsu.1_Non-coding_Transcript|GRID1_uc010qmf.1_Silent_p.T385T	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	814	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|large_intestine(2)	7					L-Glutamic Acid(DB00142)						Multiple Myeloma(13;0.14)			0.216216	34.558884	40.06028	16	58	KEEP	---	---	---	---	capture		Silent	SNP	87373323	87373323	7049	10	G	T	T	T	600	47	GRID1	2	2
BTAF1	9044	broad.mit.edu	37	10	93749274	93749274	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:93749274C>G	uc001khr.2	+	c.2791C>G	c.(2791-2793)CCA>GCA	p.P931A	BTAF1_uc001khs.1_Missense_Mutation_p.P601A|BTAF1_uc001kht.1_Missense_Mutation_p.P369A	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription	931					negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0846)												0.084112	4.399259	23.183497	9	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93749274	93749274	1568	10	C	G	G	G	286	22	BTAF1	3	3
CYP2C19	1557	broad.mit.edu	37	10	96534881	96534881	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:96534881G>T	uc010qnz.1	+	c.235G>T	c.(235-237)GGA>TGA	p.G79*	CYP2C19_uc009xus.1_Intron|CYP2C19_uc010qny.1_Nonsense_Mutation_p.G57*	NM_000769	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C,	79					exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidation-reduction process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding|steroid hydroxylase activity			ovary(4)|central_nervous_system(1)	5		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Adinazolam(DB00546)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Arformoterol(DB01274)|Bortezomib(DB00188)|Carisoprodol(DB00395)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Desipramine(DB01151)|Desloratadine(DB00967)|Diclofenac(DB00586)|Diltiazem(DB00343)|Efavirenz(DB00625)|Esomeprazole(DB00736)|Famotidine(DB00927)|Felbamate(DB00949)|Finasteride(DB01216)|Flunitrazepam(DB01544)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Guanfacine(DB01018)|Imipramine(DB00458)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Loratadine(DB00455)|Melatonin(DB01065)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nilutamide(DB00665)|Norgestrel(DB00506)|Omeprazole(DB00338)|Oxcarbazepine(DB00776)|Pantoprazole(DB00213)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Quinidine(DB00908)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Temazepam(DB00231)|Teniposide(DB00444)|Terfenadine(DB00342)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tolbutamide(DB01124)|Topiramate(DB00273)|Tranylcypromine(DB00752)|Troglitazone(DB00197)|Troleandomycin(DB01361)|Voriconazole(DB00582)									0.190789	62.377512	75.967932	29	123	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	96534881	96534881	4331	10	G	T	T	T	611	47	CYP2C19	5	2
NPAT	4863	broad.mit.edu	37	11	108057265	108057265	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108057265C>T	uc001pjz.3	-	c.670G>A	c.(670-672)GGC>AGC	p.G224S	NPAT_uc001pka.2_Missense_Mutation_p.G19S	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	224	Interaction with MIZF.				regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)						345				0.08	-0.885287	17.118675	8	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108057265	108057265	10970	11	C	T	T	T	273	21	NPAT	2	2
DSCAML1	57453	broad.mit.edu	37	11	117395626	117395626	+	Silent	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117395626T>C	uc001prh.1	-	c.1011A>G	c.(1009-1011)ACA>ACG	p.T337T	DSCAML1_uc001pri.1_Silent_p.T141T	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	277	Ig-like C2-type 3.|Extracellular (Potential).				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)	5	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)										0.12	5.311547	8.848677	3	22	KEEP	---	---	---	---	capture		Silent	SNP	117395626	117395626	4953	11	T	C	C	C	704	55	DSCAML1	4	4
OR8D1	283159	broad.mit.edu	37	11	124180365	124180365	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124180365G>T	uc010sag.1	-	c.298C>A	c.(298-300)CAG>AAG	p.Q100K		NM_001002917	NP_001002917	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D,	100	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)										0.1	2.00137	6.797746	3	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124180365	124180365	11642	11	G	T	T	T	611	47	OR8D1	2	2
PRDM10	56980	broad.mit.edu	37	11	129801996	129801996	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:129801996C>A	uc001qfm.2	-	c.1287_splice	c.e10+1	p.Q429_splice	PRDM10_uc001qfj.2_Splice_Site_SNP_p.Q343_splice|PRDM10_uc001qfk.2_Splice_Site_SNP_p.Q343_splice|PRDM10_uc001qfl.2_Splice_Site_SNP_p.Q343_splice|PRDM10_uc010sbx.1_Splice_Site_SNP_p.Q343_splice|PRDM10_uc001qfn.2_Splice_Site_SNP_p.Q429_splice|PRDM10_uc009zct.1_Splice_Site_SNP_p.Q461_splice	NM_020228	NP_064613			PR domain containing 10 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)										0.145299	28.592816	42.757161	17	100	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	129801996	129801996	12893	11	C	A	A	A	234	18	PRDM10	5	2
ABCC8	6833	broad.mit.edu	37	11	17419905	17419905	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17419905C>G	uc001mnc.2	-	c.3734G>C	c.(3733-3735)AGA>ACA	p.R1245T		NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	1245	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)									0.111111	11.489141	20.89844	7	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17419905	17419905	59	11	C	G	G	G	416	32	ABCC8	3	3
LSP1	4046	broad.mit.edu	37	11	1905541	1905541	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1905541C>A	uc001luj.2	+	c.1007C>A	c.(1006-1008)TCC>TAC	p.S336Y	LSP1_uc001lui.2_Missense_Mutation_p.S208Y|LSP1_uc001luk.2_Missense_Mutation_p.S146Y|LSP1_uc001lul.2_Missense_Mutation_p.S146Y|LSP1_uc001lum.2_Missense_Mutation_p.S146Y	NM_001013255	NP_001013273	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 2	208					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)						91				0.046296	-14.473	9.205439	5	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1905541	1905541	9439	11	C	A	A	A	390	30	LSP1	2	2
OR52K1	390036	broad.mit.edu	37	11	4510393	4510393	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4510393G>T	uc001lza.1	+	c.263G>T	c.(262-264)TGG>TTG	p.W88L		NM_001005171	NP_001005171	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K,	88	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)										0.119048	11.585641	23.559503	10	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4510393	4510393	11533	11	G	T	T	T	611	47	OR52K1	2	2
OR51F2	119694	broad.mit.edu	37	11	4843600	4843600	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4843600A>T	uc010qyn.1	+	c.985A>T	c.(985-987)AAT>TAT	p.N329Y		NM_001004753	NP_001004753	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F,	329	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.188406	23.02745	29.310601	13	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4843600	4843600	11507	11	A	T	T	T	169	13	OR51F2	3	3
OR51L1	119682	broad.mit.edu	37	11	5020470	5020470	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5020470G>T	uc010qyu.1	+	c.258G>T	c.(256-258)GTG>GTT	p.V86V		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	86	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.043716	-25.959684	14.876939	8	175	KEEP	---	---	---	---	capture		Silent	SNP	5020470	5020470	11512	11	G	T	T	T	613	48	OR51L1	2	2
OR52A5	390054	broad.mit.edu	37	11	5153561	5153561	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5153561C>A	uc010qyx.1	-	c.312G>T	c.(310-312)TGG>TGT	p.W104C		NM_001005160	NP_001005160	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A,	104	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(1)|central_nervous_system(1)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)										0.23913	25.09916	27.959803	11	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5153561	5153561	11520	11	C	A	A	A	338	26	OR52A5	2	2
OR51V1	283111	broad.mit.edu	37	11	5221508	5221508	+	Silent	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5221508A>G	uc010qyz.1	-	c.423T>C	c.(421-423)TAT>TAC	p.Y141Y		NM_001004760	NP_001004760	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V,	141	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.084337	5.06434	19.616079	7	76	KEEP	---	---	---	---	capture		Silent	SNP	5221508	5221508	11517	11	A	G	G	G	50	4	OR51V1	4	4
OR4C15	81309	broad.mit.edu	37	11	55322475	55322475	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55322475G>C	uc010rig.1	+	c.693G>C	c.(691-693)ATG>ATC	p.M231I		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.186667	35.903724	42.805168	14	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55322475	55322475	11454	11	G	C	C	C	624	48	OR4C15	3	3
OR8I2	120586	broad.mit.edu	37	11	55860901	55860901	+	Silent	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55860901T>C	uc010rix.1	+	c.118T>C	c.(118-120)TTG>CTG	p.L40L		NM_001003750	NP_001003750	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1	Esophageal squamous(21;0.00693)													0.144681	79.497722	108.038948	34	201	KEEP	---	---	---	---	capture		Silent	SNP	55860901	55860901	11651	11	T	C	C	C	829	64	OR8I2	4	4
CTNND1	1500	broad.mit.edu	37	11	57563083	57563083	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57563083G>C	uc001nmc.3	+	c.302G>C	c.(301-303)AGG>ACG	p.R101T	CTNND1_uc001nlf.1_Missense_Mutation_p.R101T|CTNND1_uc001nlh.1_Missense_Mutation_p.R101T|CTNND1_uc001nlu.3_5'UTR|CTNND1_uc001nlt.3_5'UTR|CTNND1_uc001nls.3_5'UTR|CTNND1_uc001nlw.3_5'UTR|CTNND1_uc001nmf.3_Missense_Mutation_p.R101T|CTNND1_uc001nmd.3_Missense_Mutation_p.R47T|CTNND1_uc001nlk.3_Missense_Mutation_p.R47T|CTNND1_uc001nme.3_Missense_Mutation_p.R101T|CTNND1_uc001nll.3_Missense_Mutation_p.R47T|CTNND1_uc001nmg.3_Missense_Mutation_p.R47T|CTNND1_uc001nlj.3_Missense_Mutation_p.R47T|CTNND1_uc001nlr.3_Missense_Mutation_p.R47T|CTNND1_uc001nlp.3_Missense_Mutation_p.R47T|CTNND1_uc001nlx.3_Intron|CTNND1_uc001nlz.3_Intron|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Missense_Mutation_p.R101T|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_5'UTR|CTNND1_uc001nmh.3_Missense_Mutation_p.R101T|CTNND1_uc001nlq.3_5'UTR|CTNND1_uc001nln.3_Missense_Mutation_p.R101T|CTNND1_uc001nli.3_Missense_Mutation_p.R101T|CTNND1_uc001nlo.3_5'UTR|CTNND1_uc001nlv.3_5'UTR	NM_001085458	NP_001078927	O60716	CTND1_HUMAN	catenin, delta 1 isoform 1ABC	101					adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)												0.069767	-0.609924	7.607356	3	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57563083	57563083	4178	11	G	C	C	C	455	35	CTNND1	3	3
OR5AN1	390195	broad.mit.edu	37	11	59132051	59132051	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59132051G>T	uc010rks.1	+	c.120G>T	c.(118-120)CTG>CTT	p.L40L		NM_001004729	NP_001004729	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.065744	-15.928109	40.649247	19	270	KEEP	---	---	---	---	capture		Silent	SNP	59132051	59132051	11553	11	G	T	T	T	600	47	OR5AN1	2	2
OR4D10	390197	broad.mit.edu	37	11	59245669	59245669	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59245669A>G	uc001nnz.1	+	c.767A>G	c.(766-768)TAT>TGT	p.Y256C		NM_001004705	NP_001004705	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D,	256	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.103586	37.402134	76.636555	26	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59245669	59245669	11461	11	A	G	G	G	208	16	OR4D10	4	4
MYEOV	26579	broad.mit.edu	37	11	69062910	69062910	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:69062910C>T	uc001oov.2	+	c.89C>T	c.(88-90)TCC>TTC	p.S30F	MYEOV_uc001oox.2_Intron|MYEOV_uc009ysl.2_Missense_Mutation_p.S30F|MYEOV_uc001oow.2_5'UTR	NM_138768	NP_620123	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	30											0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)										0.192308	41.412307	50.647478	20	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69062910	69062910	10420	11	C	T	T	T	390	30	MYEOV	2	2
TUB	7275	broad.mit.edu	37	11	8118969	8118969	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:8118969G>T	uc001mfy.2	+	c.1047G>T	c.(1045-1047)AAG>AAT	p.K349N	TUB_uc010rbk.1_Missense_Mutation_p.K300N|TUB_uc001mga.2_Missense_Mutation_p.K294N	NM_003320	NP_003311	P50607	TUB_HUMAN	tubby isoform a	294					phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)										0.109244	9.278474	27.288932	13	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8118969	8118969	17297	11	G	T	T	T	425	33	TUB	2	2
FAT3	120114	broad.mit.edu	37	11	92525961	92525961	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92525961G>T	uc001pdj.3	+	c.4640G>T	c.(4639-4641)AGA>ATA	p.R1547I		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1547	Cadherin 14.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.056962	-15.56561	17.016534	9	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92525961	92525961	5927	11	G	T	T	T	429	33	FAT3	2	2
FAT3	120114	broad.mit.edu	37	11	92535011	92535011	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92535011C>A	uc001pdj.3	+	c.8832C>A	c.(8830-8832)GCC>GCA	p.A2944A		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2944	Cadherin 27.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.096774	6.825326	27.035098	12	112	KEEP	---	---	---	---	capture		Silent	SNP	92535011	92535011	5927	11	C	A	A	A	288	23	FAT3	1	1
TCHP	84260	broad.mit.edu	37	12	110348913	110348913	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:110348913G>T	uc001tpn.2	+	c.925G>T	c.(925-927)GAG>TAG	p.E309*	TCHP_uc001tpo.1_Non-coding_Transcript|TCHP_uc001tpp.2_Nonsense_Mutation_p.E309*	NM_001143852	NP_001137324	Q9BT92	TCHP_HUMAN	trichoplein	309	Trichohyalin/plectin homology domain.|Glu-rich.|Interaction with keratin proteins.|Potential.				apoptosis|negative regulation of cell growth	apical cortex|keratin filament|mitochondrion|plasma membrane	protein binding				0														0.1875	6.415963	7.878843	3	13	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	110348913	110348913	16228	12	G	T	T	T	481	37	TCHP	5	1
P2RX7	5027	broad.mit.edu	37	12	121600296	121600296	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121600296C>G	uc001tzm.2	+	c.506C>G	c.(505-507)CCC>CGC	p.P169R	P2RX7_uc001tzn.2_Missense_Mutation_p.P79R|P2RX7_uc001tzo.2_Non-coding_Transcript|P2RX7_uc001tzp.2_5'UTR|P2RX7_uc001tzq.2_Intron	NM_002562	NP_002553	A8K2Z0	A8K2Z0_HUMAN	purinergic receptor P2X7	169						integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)	4	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)									719				0.0625	-1.951973	10.812016	4	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121600296	121600296	11758	12	C	G	G	G	286	22	P2RX7	3	3
TMEM132B	114795	broad.mit.edu	37	12	126137173	126137173	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:126137173C>A	uc001uhe.1	+	c.2086C>A	c.(2086-2088)CAG>AAG	p.Q696K	TMEM132B_uc001uhf.1_Missense_Mutation_p.Q208K	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	696	Extracellular (Potential).					integral to membrane				ovary(5)|large_intestine(1)|breast(1)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)										0.066667	-4.626908	12.895084	6	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126137173	126137173	16577	12	C	A	A	A	221	17	TMEM132B	2	2
ERC1	23085	broad.mit.edu	37	12	1299084	1299084	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:1299084C>A	uc001qjb.2	+	c.2217C>A	c.(2215-2217)CAC>CAA	p.H739Q	ERC1_uc001qiz.2_Non-coding_Transcript|ERC1_uc001qjc.2_Missense_Mutation_p.H711Q|ERC1_uc001qja.2_Non-coding_Transcript|ERC1_uc001qjd.2_Non-coding_Transcript|ERC1_uc001qjf.2_Missense_Mutation_p.H739Q|ERC1_uc010sdv.1_Missense_Mutation_p.H487Q|ERC1_uc009zdp.2_Missense_Mutation_p.H379Q|ERC1_uc001qje.2_Non-coding_Transcript	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	739	Potential.				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				0.162162	24.451622	32.483205	12	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1299084	1299084	5403	12	C	A	A	A	259	20	ERC1	2	2
RIMBP2	23504	broad.mit.edu	37	12	130912844	130912844	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:130912844G>T	uc001uil.2	-	c.2241C>A	c.(2239-2241)AGC>AGA	p.S747R		NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	747						cell junction|synapse				ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)										0.127273	14.335105	29.331802	14	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130912844	130912844	13838	12	G	T	T	T	594	46	RIMBP2	2	2
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:25398285C>A	uc001rgp.1	-	c.34G>T	c.(34-36)GGT>TGT	p.G12C	KRAS_uc001rgq.1_Missense_Mutation_p.G12C|KRAS_uc001rgr.2_Non-coding_Transcript	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	12	GTP.		G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12C(2374)|p.G12S(1078)|p.G12R(674)|p.G12?(50)|p.G12F(33)|p.G12D(15)|p.G12N(6)|p.G12V(6)|p.G12L(5)|p.G12I(3)|p.G12W(3)|p.G12A(2)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12_G13insG(1)		large_intestine(11742)|pancreas(3256)|lung(2694)|biliary_tract(514)|ovary(437)|endometrium(339)|haematopoietic_and_lymphoid_tissue(303)|stomach(179)|thyroid(145)|prostate(85)|soft_tissue(75)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|breast(27)|liver(21)|testis(17)|oesophagus(15)|central_nervous_system(8)|peritoneum(5)|kidney(5)|salivary_gland(5)|thymus(5)|eye(4)|gastrointestinal_tract_(site_indeterminate)(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	20148	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12C(CALU1_LUNG)|G12C(NCIH2030_LUNG)|G12C(LU99_LUNG)|G12C(NCIH1792_LUNG)|G12R(KP2_PANCREAS)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(NCIH2122_LUNG)|G12C(NCIH358_LUNG)|G12R(PSN1_PANCREAS)|G12C(KYSE410_OESOPHAGUS)|G12S(A549_LUNG)|G12R(HUPT3_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12C(HCC44_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(SW1463_LARGE_INTESTINE)|G12C(NCIH23_LUNG)|G12C(LU65_LUNG)|G12C(NCIH1373_LUNG)|G12C(MIAPACA2_PANCREAS)|G12R(HS274T_BREAST)|G12S(LS123_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(OV56_OVARY)|G12C(IALM_LUNG)	119	p.G12R(PSN1-Tumor)|p.G12C(NCIH1373-Tumor)|p.G12C(NCIH1792-Tumor)|p.G12S(KMS20-Tumor)|p.G12C(HCC44-Tumor)|p.G12C(HCC1171-Tumor)|p.G12C(SW837-Tumor)|p.G12C(LU65-Tumor)|p.G12R(HUPT3-Tumor)|p.G12S(A549-Tumor)|p.G12C(NCIH2122-Tumor)|p.G12R(KP2-Tumor)|p.G12C(OV56-Tumor)|p.G12C(IALM-Tumor)|p.G12C(SW1463-Tumor)|p.G12C(SW1573-Tumor)|p.G12R(NCIH1339-Tumor)|p.G12C(NCIH23-Tumor)|p.G12C(MIAPACA2-Tumor)|p.G12C(CALU1-Tumor)|p.G12C(NCIH2030-Tumor)|p.G12S(LS123-Tumor)|p.G12C(KYSE410-Tumor)|p.G12C(UMUC3-Tumor)|p.G12C(NCIH2291-Tumor)|p.G12R(TCCPAN2-Tumor)|p.G12C(KHM1B-Tumor)|p.G12C(LU99-Tumor)|p.G12C(NCIH358-Tumor)|p.G12C(NCIH1385-Tumor)|p.G12R(CAL62-Tumor)	262	TSP Lung(1;<1E-8)|Multiple Myeloma(2;<1E-6)			0.272727	14.037958	15.063994	6	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25398285	25398285	8753	12	C	A	A	A	273	21	KRAS	2	2
TMTC1	83857	broad.mit.edu	37	12	29911688	29911688	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29911688G>T	uc001rjb.2	-	c.179C>A	c.(178-180)GCG>GAG	p.A60E	TMTC1_uc001rjc.1_Missense_Mutation_p.A60E	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	60	Helical; (Potential).					integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)													0.190476	8.187251	10.068673	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29911688	29911688	16801	12	G	T	T	T	494	38	TMTC1	1	1
MLL2	8085	broad.mit.edu	37	12	49435239	49435239	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49435239C>T	uc001rta.3	-	c.6314G>A	c.(6313-6315)CGC>CAC	p.R2105H		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	2105					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|promoter binding|protein binding|zinc ion binding			kidney(16)|lung(4)|skin(4)|ovary(3)|pancreas(2)	29														0.075758	-2.474063	9.703401	5	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49435239	49435239	10011	12	C	T	T	T	351	27	MLL2	1	1
KRT76	51350	broad.mit.edu	37	12	53170635	53170635	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53170635G>T	uc001sax.2	-	c.441C>A	c.(439-441)GGC>GGA	p.G147G		NM_015848	NP_056932	Q01546	K22O_HUMAN	keratin 76	147	Head.				cytoskeleton organization	keratin filament	structural molecule activity			breast(1)	1														0.125	5.548841	11.043977	5	35	KEEP	---	---	---	---	capture		Silent	SNP	53170635	53170635	8804	12	G	T	T	T	535	42	KRT76	2	2
PPP1R1A	5502	broad.mit.edu	37	12	54975870	54975870	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54975870C>A	uc001sgg.2	-	c.293G>T	c.(292-294)GGA>GTA	p.G98V		NM_006741	NP_006732	Q13522	PPR1A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	98					glycogen metabolic process|signal transduction		protein binding|protein serine/threonine phosphatase inhibitor activity				0														0.25974	46.375506	50.394247	20	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54975870	54975870	12802	12	C	A	A	A	390	30	PPP1R1A	2	2
SLC39A5	283375	broad.mit.edu	37	12	56629470	56629470	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56629470C>T	uc010sqj.1	+	c.931C>T	c.(931-933)CGA>TGA	p.R311*	SLC39A5_uc010sqi.1_Nonsense_Mutation_p.R202*|SLC39A5_uc010sqk.1_Nonsense_Mutation_p.R311*	NM_173596	NP_775867	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (metal ion	311	Cytoplasmic (Potential).				zinc ion transport	basolateral plasma membrane|integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1														0.07	-19.901417	56.359143	28	372	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	56629470	56629470	15118	12	C	T	T	T	295	23	SLC39A5	5	1
ANO2	57101	broad.mit.edu	37	12	5687595	5687595	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5687595G>T	uc001qnm.2	-	c.2323C>A	c.(2323-2325)CTC>ATC	p.L775I		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	780	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.087719	1.628893	11.43088	5	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5687595	5687595	705	12	G	T	T	T	442	34	ANO2	2	2
TMTC2	160335	broad.mit.edu	37	12	83358817	83358817	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:83358817A>T	uc001szt.2	+	c.1613A>T	c.(1612-1614)CAG>CTG	p.Q538L	TMTC2_uc001szr.1_Missense_Mutation_p.Q538L|TMTC2_uc001szs.1_Missense_Mutation_p.Q538L|TMTC2_uc010suk.1_Missense_Mutation_p.Q293L	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat	538	TPR 3.					endoplasmic reticulum|integral to membrane	binding			ovary(2)	2														0.313253	78.517205	81.095943	26	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83358817	83358817	16802	12	A	T	T	T	91	7	TMTC2	3	3
ALX1	8092	broad.mit.edu	37	12	85695135	85695135	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85695135G>T	uc001tae.3	+	c.863G>T	c.(862-864)GGG>GTG	p.G288V		NM_006982	NP_008913	Q15699	ALX1_HUMAN	cartilage paired-class homeoprotein 1	288					brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription corepressor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(134;0.134)										0.094017	3.43354	22.81975	11	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85695135	85695135	559	12	G	T	T	T	559	43	ALX1	2	2
FLT3	2322	broad.mit.edu	37	13	28589815	28589815	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:28589815C>A	uc001urw.2	-	c.2565G>T	c.(2563-2565)ATG>ATT	p.M855I	FLT3_uc010aao.2_Non-coding_Transcript|FLT3_uc010tdn.1_Missense_Mutation_p.M814I	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor	855	Protein kinase.|Cytoplasmic (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8072)|ovary(2)|lung(1)|central_nervous_system(1)	8076	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)					630				0.158416	29.43547	40.668692	16	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28589815	28589815	6184	13	C	A	A	A	273	21	FLT3	2	2
ADSSL1	122622	broad.mit.edu	37	14	105201358	105201358	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105201358G>T	uc001ype.2	+	c.323G>T	c.(322-324)GGG>GTG	p.G108V	INF2_uc010tyi.1_Intron|ADSSL1_uc001ypd.2_Missense_Mutation_p.G65V|ADSSL1_uc001ypf.2_Non-coding_Transcript	NM_199165	NP_954634	Q8N142	PURA1_HUMAN	adenylosuccinate synthase like 1 isoform 1	65					AMP biosynthetic process|immune system process|purine base metabolic process	cytosol	adenylosuccinate synthase activity|GTP binding|magnesium ion binding|phosphate binding			ovary(1)|central_nervous_system(1)	2		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)	L-Aspartic Acid(DB00128)									0.166667	9.325136	13.121769	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105201358	105201358	349	14	G	T	T	T	559	43	ADSSL1	2	2
POTEG	404785	broad.mit.edu	37	14	19553724	19553724	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:19553724G>T	uc001vuz.1	+	c.308G>T	c.(307-309)TGC>TTC	p.C103F	POTEG_uc001vva.1_Non-coding_Transcript|POTEG_uc010ahc.1_Non-coding_Transcript	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	103										ovary(1)	1														0.076923	-12.987069	72.89334	36	432	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19553724	19553724	12696	14	G	T	T	T	598	46	POTEG	2	2
IL25	64806	broad.mit.edu	37	14	23842381	23842381	+	Silent	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23842381A>T	uc001wjr.2	+	c.54A>T	c.(52-54)CTA>CTT	p.L18L	IL25_uc001wjq.2_Intron	NM_022789	NP_073626	Q9H293	IL25_HUMAN	interleukin 25 isoform 1 precursor	18					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)										0.241135	80.37357	89.004554	34	107	KEEP	---	---	---	---	capture		Silent	SNP	23842381	23842381	7979	14	A	T	T	T	171	14	IL25	3	3
SYT16	83851	broad.mit.edu	37	14	62462844	62462844	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:62462844C>A	uc001xfu.1	+	c.107C>A	c.(106-108)TCT>TAT	p.S36Y	SYT16_uc010tsd.1_Missense_Mutation_p.S36Y	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	36										central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)										0.234568	41.177249	46.403993	19	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62462844	62462844	15993	14	C	A	A	A	416	32	SYT16	2	2
MOAP1	64112	broad.mit.edu	37	14	93649642	93649642	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:93649642C>G	uc001ybj.2	-	c.946G>C	c.(946-948)GAT>CAT	p.D316H	C14orf109_uc001ybk.3_5'Flank|C14orf109_uc010auo.2_5'Flank	NM_022151	NP_071434	Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	316					activation of caspase activity|apoptotic nuclear change	cytoplasm	protein homodimerization activity			ovary(1)	1		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)										0.296296	185.127778	192.141476	56	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93649642	93649642	10071	14	C	G	G	G	390	30	MOAP1	3	3
TRPM1	4308	broad.mit.edu	37	15	31360169	31360169	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31360169G>T	uc001zfm.2	-	c.340C>A	c.(340-342)CCC>ACC	p.P114T	TRPM1_uc010azy.2_Missense_Mutation_p.P27T|TRPM1_uc001zfl.2_Non-coding_Transcript|MIR211_hsa-mir-211|MI0000287_5'Flank	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	114	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.09322	6.176339	45.379514	22	214	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31360169	31360169	17136	15	G	T	T	T	546	42	TRPM1	2	2
C15orf55	256646	broad.mit.edu	37	15	34640216	34640216	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:34640216C>T	uc010ucc.1	+	c.147C>T	c.(145-147)GCC>GCT	p.A49A	C15orf55_uc010ucd.1_Silent_p.A39A|C15orf55_uc001zif.2_Silent_p.A21A	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	21	Pro-rich.					cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)						408				0.108911	12.646387	27.953102	11	90	KEEP	---	---	---	---	capture		Silent	SNP	34640216	34640216	1853	15	C	T	T	T	275	22	C15orf55	2	2
CASC5	57082	broad.mit.edu	37	15	40912855	40912855	+	Silent	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40912855T>C	uc010bbs.1	+	c.471T>C	c.(469-471)CAT>CAC	p.H157H	CASC5_uc010ucq.1_5'UTR|CASC5_uc001zme.2_Silent_p.H131H|CASC5_uc010bbt.1_Silent_p.H131H	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	157	Interaction with BUB1 and BUB1B.				acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(1)|central_nervous_system(1)	2		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)						629				0.111111	10.084207	19.498036	7	56	KEEP	---	---	---	---	capture		Silent	SNP	40912855	40912855	2782	15	T	C	C	C	634	49	CASC5	4	4
MAP1A	4130	broad.mit.edu	37	15	43819588	43819588	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43819588C>A	uc001zrt.2	+	c.5917C>A	c.(5917-5919)CAG>AAG	p.Q1973K		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1973						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)									0.043103	-16.630412	9.34499	5	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43819588	43819588	9610	15	C	A	A	A	325	25	MAP1A	2	2
DUOX2	50506	broad.mit.edu	37	15	45387725	45387725	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45387725C>A	uc010bea.2	-	c.4149G>T	c.(4147-4149)GTG>GTT	p.V1383V	DUOX2_uc001zun.2_Silent_p.V1383V	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1383	Cytoplasmic (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|pancreas(1)	3		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)										0.061947	-8.9469	13.653744	7	106	KEEP	---	---	---	---	capture		Silent	SNP	45387725	45387725	4986	15	C	A	A	A	262	21	DUOX2	2	2
CPLX3	594855	broad.mit.edu	37	15	75119191	75119191	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75119191G>A	uc002ayu.1	+	c.147G>A	c.(145-147)AAG>AAA	p.K49K	LMAN1L_uc010bke.1_3'UTR	NM_001030005	NP_001025176	Q8WVH0	CPLX3_HUMAN	complexin 3 precursor	49	Potential.					cell junction|synapse	syntaxin binding				0														0.12	6.013538	13.099156	6	44	KEEP	---	---	---	---	capture		Silent	SNP	75119191	75119191	3944	15	G	A	A	A	438	34	CPLX3	2	2
ULK3	25989	broad.mit.edu	37	15	75134424	75134424	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75134424T>A	uc010ulq.1	-	c.389A>T	c.(388-390)CAG>CTG	p.Q130L	ULK3_uc010ulp.1_Missense_Mutation_p.Q29L|ULK3_uc010ulr.1_Missense_Mutation_p.Q2L|ULK3_uc010bkf.1_Missense_Mutation_p.Q119L|ULK3_uc002ayv.2_Missense_Mutation_p.Q119L|ULK3_uc010uls.1_Missense_Mutation_p.Q2L|ULK3_uc010ult.1_Missense_Mutation_p.Q29L|ULK3_uc010ulu.1_Missense_Mutation_p.Q29L	NM_001099436	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51-like kinase 3	119	Protein kinase.				protein phosphorylation	cytoplasm	ATP binding|protein serine/threonine kinase activity			breast(2)	2										352				0.08134	-0.472065	36.836088	17	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75134424	75134424	17535	15	T	A	A	A	715	55	ULK3	3	3
MYH11	4629	broad.mit.edu	37	16	15839064	15839064	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:15839064G>T	uc002ddx.2	-	c.2463C>A	c.(2461-2463)ACC>ACA	p.T821T	MYH11_uc002ddv.2_Silent_p.T821T|MYH11_uc002ddw.2_Silent_p.T814T|MYH11_uc002ddy.2_Silent_p.T814T|MYH11_uc010bvg.2_Silent_p.T646T	NM_001040114	NP_001035203	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	814	IQ.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(4)|skin(2)|lung(1)	7										1257				0.189873	30.077539	37.185028	15	64	KEEP	---	---	---	---	capture		Silent	SNP	15839064	15839064	10426	16	G	T	T	T	496	39	MYH11	1	1
USP31	57478	broad.mit.edu	37	16	23080502	23080502	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23080502C>T	uc002dll.2	-	c.2924G>A	c.(2923-2925)CGC>CAC	p.R975H	USP31_uc002dlk.2_Missense_Mutation_p.R247H|USP31_uc010vca.1_Missense_Mutation_p.R278H|USP31_uc010bxm.2_Missense_Mutation_p.R263H	NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31	975	Ser-rich.				ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0187)										0.123457	19.631566	42.081642	20	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23080502	23080502	17626	16	C	T	T	T	351	27	USP31	1	1
ITGAX	3687	broad.mit.edu	37	16	31391640	31391640	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31391640C>G	uc002ebt.2	+	c.3114C>G	c.(3112-3114)AGC>AGG	p.S1038R	ITGAX_uc002ebu.1_Missense_Mutation_p.S1038R	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	1038	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.105263	4.270172	10.158465	4	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31391640	31391640	8193	16	C	G	G	G	350	27	ITGAX	3	3
ZNF597	146434	broad.mit.edu	37	16	3490906	3490906	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:3490906C>G	uc002cvd.2	-	c.61G>C	c.(61-63)GTG>CTG	p.V21L	NAT15_uc002cvh.3_5'Flank|NAT15_uc010uxb.1_5'Flank	NM_152457	NP_689670	Q96LX8	ZN597_HUMAN	zinc finger protein 597	21	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.122449	22.726823	36.40416	12	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3490906	3490906	18622	16	C	G	G	G	221	17	ZNF597	3	3
CBLN1	869	broad.mit.edu	37	16	49313499	49313499	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:49313499A>C	uc002efq.2	-	c.398T>G	c.(397-399)CTA>CGA	p.L133R		NM_004352	NP_004343	P23435	CBLN1_HUMAN	cerebellin 1 precursor	133	C1q.|Necessary for interaction with CBLN3, and homotrimerization (By similarity).				nervous system development|synaptic transmission	cell junction|extracellular region|synapse					0		all_cancers(37;0.0766)|all_lung(18;0.24)												0.125	9.161853	17.952312	8	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49313499	49313499	2823	16	A	C	C	C	195	15	CBLN1	4	4
SALL1	6299	broad.mit.edu	37	16	51173271	51173271	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:51173271G>A	uc010vgs.1	-	c.2862C>T	c.(2860-2862)AGC>AGT	p.S954S	SALL1_uc010vgr.1_Silent_p.S857S|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	954					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			ovary(3)	3		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GBM(103;1352 1446 1855 4775 8890)								0.130435	12.12656	21.295367	9	60	KEEP	---	---	---	---	capture		Silent	SNP	51173271	51173271	14290	16	G	A	A	A	490	38	SALL1	1	1
RPGRIP1L	23322	broad.mit.edu	37	16	53706901	53706901	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:53706901C>A	uc002ehp.2	-	c.910G>T	c.(910-912)GAT>TAT	p.D304Y	RPGRIP1L_uc002eho.3_Missense_Mutation_p.D304Y|RPGRIP1L_uc010vgy.1_Missense_Mutation_p.D304Y|RPGRIP1L_uc010cbx.2_Missense_Mutation_p.D304Y|RPGRIP1L_uc010vgz.1_Missense_Mutation_p.D304Y|RPGRIP1L_uc002ehq.1_Missense_Mutation_p.D304Y	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	304					negative regulation of G-protein coupled receptor protein signaling pathway	centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)												0.103448	3.303228	7.843447	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53706901	53706901	14029	16	C	A	A	A	403	31	RPGRIP1L	1	1
SLC6A2	6530	broad.mit.edu	37	16	55728015	55728015	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55728015A>T	uc002eif.2	+	c.1012A>T	c.(1012-1014)AAC>TAC	p.N338Y	SLC6A2_uc010ccd.2_Missense_Mutation_p.N338Y|SLC6A2_uc002eig.2_Missense_Mutation_p.N338Y|SLC6A2_uc002eih.2_Missense_Mutation_p.N338Y|SLC6A2_uc002eii.2_Missense_Mutation_p.N233Y|SLC6A2_uc002eij.2_Missense_Mutation_p.N52Y	NM_001043	NP_001034	P23975	SC6A2_HUMAN	solute carrier family 6 member 2	338					synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			ovary(2)|pancreas(2)	4				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)									0.165803	56.177657	76.631323	32	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55728015	55728015	15180	16	A	T	T	T	65	5	SLC6A2	3	3
GNAO1	2775	broad.mit.edu	37	16	56377812	56377812	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56377812G>T	uc002eit.3	+	c.1015G>T	c.(1015-1017)GTG>TTG	p.V339L	GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha	339					dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity				0		all_neural(199;0.159)												0.129412	16.362167	27.729569	11	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56377812	56377812	6777	16	G	T	T	T	624	48	GNAO1	2	2
TMCO7	79613	broad.mit.edu	37	16	68894053	68894053	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68894053C>T	uc002ewi.3	+	c.361C>T	c.(361-363)CCC>TCC	p.P121S	TMCO7_uc002ewh.2_Missense_Mutation_p.P121S	NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	121						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)										0.141104	69.612948	110.14737	46	280	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68894053	68894053	16531	16	C	T	T	T	234	18	TMCO7	2	2
HYDIN	54768	broad.mit.edu	37	16	71019123	71019123	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71019123G>T	uc002ezr.2	-	c.4294C>A	c.(4294-4296)CTT>ATT	p.L1432I		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1433										ovary(1)	1		Ovarian(137;0.0654)												0.189189	14.100177	17.447451	7	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71019123	71019123	7767	16	G	T	T	T	455	35	HYDIN	2	2
CNTNAP4	85445	broad.mit.edu	37	16	76461392	76461392	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:76461392G>T	uc002fex.1	+	c.443G>T	c.(442-444)AGA>ATA	p.R148I	CNTNAP4_uc002feu.1_Missense_Mutation_p.R145I|CNTNAP4_uc002fev.1_Missense_Mutation_p.R57I|CNTNAP4_uc010chb.1_Missense_Mutation_p.R120I|CNTNAP4_uc002few.2_Missense_Mutation_p.R120I	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	145	Extracellular (Potential).|F5/8 type C.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2														0.17341	54.455872	71.871743	30	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76461392	76461392	3787	16	G	T	T	T	429	33	CNTNAP4	2	2
ADAMTS18	170692	broad.mit.edu	37	16	77317955	77317955	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:77317955G>T	uc002ffc.3	-	c.3564C>A	c.(3562-3564)TGC>TGA	p.C1188*		NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1188	PLAC.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|kidney(4)|skin(2)|pancreas(1)|ovary(1)	12										1451				0.057692	-9.039014	12.308998	6	98	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	77317955	77317955	264	16	G	T	T	T	490	38	ADAMTS18	5	1
CENPBD1	92806	broad.mit.edu	37	16	90038268	90038268	+	Silent	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:90038268C>G	uc002fpr.2	-	c.63G>C	c.(61-63)GCG>GCC	p.A21A	AFG3L1_uc002fps.1_5'Flank|AFG3L1_uc002fpt.1_5'Flank|AFG3L1_uc002fpu.1_5'Flank|AFG3L1_uc002fpv.1_5'Flank|AFG3L1_uc002fpw.1_5'Flank|AFG3L1_uc002fpx.1_5'Flank	NM_145039	NP_659476	B2RD01	CENP1_HUMAN	CENPB DNA-binding domains containing 1	21	HTH psq-type.					chromosome, centromeric region|nucleus	DNA binding				0														0.152542	22.552634	29.354411	9	50	KEEP	---	---	---	---	capture		Silent	SNP	90038268	90038268	3361	16	C	G	G	G	392	31	CENPBD1	3	3
GRIN2A	2903	broad.mit.edu	37	16	9857275	9857275	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9857275G>T	uc002czo.3	-	c.4126C>A	c.(4126-4128)CGC>AGC	p.R1376S	GRIN2A_uc010uym.1_Missense_Mutation_p.R1376S|GRIN2A_uc010uyn.1_Missense_Mutation_p.N1104K|GRIN2A_uc002czr.3_Missense_Mutation_p.N1261K	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1376	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.163462	35.310729	46.49919	17	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9857275	9857275	7058	16	G	T	T	T	520	40	GRIN2A	1	1
MYH8	4626	broad.mit.edu	37	17	10298575	10298575	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10298575C>G	uc002gmm.2	-	c.4837G>C	c.(4837-4839)GAT>CAT	p.D1613H		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1613	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(3)|breast(2)	5														0.10625	24.549537	49.185663	17	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10298575	10298575	10436	17	C	G	G	G	377	29	MYH8	3	3
MYH8	4626	broad.mit.edu	37	17	10301785	10301785	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10301785C>A	uc002gmm.2	-	c.4154G>T	c.(4153-4155)CGC>CTC	p.R1385L		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1385	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(3)|breast(2)	5														0.171533	93.530557	121.420988	47	227	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10301785	10301785	10436	17	C	A	A	A	351	27	MYH8	1	1
DNAH9	1770	broad.mit.edu	37	17	11757701	11757701	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11757701A>T	uc002gne.2	+	c.9889A>T	c.(9889-9891)ACA>TCA	p.T3297S	DNAH9_uc010coo.2_Missense_Mutation_p.T2591S	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3297	Stalk (By similarity).|Potential.				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.183099	26.041166	32.731293	13	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11757701	11757701	4791	17	A	T	T	T	78	6	DNAH9	3	3
MAPK7	5598	broad.mit.edu	37	17	19285382	19285382	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:19285382C>G	uc002gvn.2	+	c.1766C>G	c.(1765-1767)CCT>CGT	p.P589R	MAPK7_uc002gvo.2_Missense_Mutation_p.P450R|MAPK7_uc002gvq.2_Missense_Mutation_p.P589R|MAPK7_uc002gvp.2_Missense_Mutation_p.P589R	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	589	May not be required for kinase activity; required to stimulate MEF2C activity (By similarity).|Pro-rich.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(3)|lung(1)|skin(1)	5	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)									176				0.294118	12.668019	13.31311	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19285382	19285382	9665	17	C	G	G	G	312	24	MAPK7	3	3
CPD	1362	broad.mit.edu	37	17	28754530	28754530	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28754530C>T	uc002hfb.1	+	c.1971C>T	c.(1969-1971)AGC>AGT	p.S657S	CPD_uc010wbo.1_Silent_p.S410S|CPD_uc010wbp.1_Non-coding_Transcript	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor	657	Extracellular (Potential).|Carboxypeptidase-like 2.				proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)	1														0.118227	27.247108	56.327344	24	179	KEEP	---	---	---	---	capture		Silent	SNP	28754530	28754530	3936	17	C	T	T	T	363	28	CPD	2	2
MYO1D	4642	broad.mit.edu	37	17	31075963	31075963	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31075963C>A	uc002hho.1	-	c.1529G>T	c.(1528-1530)GGC>GTC	p.G510V	MYO1D_uc002hhp.1_Missense_Mutation_p.G510V	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	510	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)											0.128834	26.57822	48.44313	21	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31075963	31075963	10466	17	C	A	A	A	338	26	MYO1D	2	2
MYO1D	4642	broad.mit.edu	37	17	31075976	31075976	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31075976G>A	uc002hho.1	-	c.1516C>T	c.(1516-1518)CGA>TGA	p.R506*	MYO1D_uc002hhp.1_Nonsense_Mutation_p.R506*	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	506	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)											0.130178	29.930333	52.427071	22	147	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31075976	31075976	10466	17	G	A	A	A	480	37	MYO1D	5	1
CNTD1	124817	broad.mit.edu	37	17	40958759	40958759	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40958759C>T	uc002ibm.3	+	c.648C>T	c.(646-648)GTC>GTT	p.V216V	CNTD1_uc010wha.1_Silent_p.V133V	NM_173478	NP_775749	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	216											0		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)										0.093923	11.727709	41.736787	17	164	KEEP	---	---	---	---	capture		Silent	SNP	40958759	40958759	3773	17	C	T	T	T	405	32	CNTD1	2	2
ARL4D	379	broad.mit.edu	37	17	41477386	41477386	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41477386G>T	uc002idt.2	+	c.286G>T	c.(286-288)GGT>TGT	p.G96C		NM_001661	NP_001652	P49703	ARL4D_HUMAN	ADP-ribosylation factor-like 4D	96					protein secretion|small GTPase mediated signal transduction	cytoplasm|nucleolus|plasma membrane	GTP binding|GTPase activity|protein binding			ovary(1)	1		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.155)										0.16	28.860528	39.849267	16	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41477386	41477386	955	17	G	T	T	T	507	39	ARL4D	1	1
C17orf46	124783	broad.mit.edu	37	17	43332762	43332762	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43332762G>A	uc002iis.1	-	c.787C>T	c.(787-789)CAC>TAC	p.H263Y	LOC100133991_uc010dah.2_Intron|C17orf46_uc010wjk.1_Missense_Mutation_p.H242Y	NM_152343	NP_689556	Q96LK8	CQ046_HUMAN	hypothetical protein LOC124783	263										large_intestine(1)|ovary(1)	2														0.058252	-9.729883	11.338112	6	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43332762	43332762	1913	17	G	A	A	A	624	48	C17orf46	2	2
NXPH3	11248	broad.mit.edu	37	17	47656499	47656499	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:47656499G>T	uc010wlw.1	+	c.596G>T	c.(595-597)TGC>TTC	p.C199F	NXPH3_uc002ipa.2_Missense_Mutation_p.C199F	NM_007225	NP_009156	O95157	NXPH3_HUMAN	neurexophilin 3 precursor	199	V (Cys-rich).				neuropeptide signaling pathway	extracellular region				pancreas(1)	1	all_cancers(4;7.45e-14)|Breast(4;1.08e-27)|all_epithelial(4;2.27e-17)													0.153846	36.020375	53.901335	24	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47656499	47656499	11197	17	G	T	T	T	598	46	NXPH3	2	2
CHRNE	1145	broad.mit.edu	37	17	4804399	4804399	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4804399C>A	uc002fzk.1	-	c.688G>T	c.(688-690)GTC>TTC	p.V230F	C17orf107_uc002fzl.3_3'UTR	NM_000080	NP_000071	Q04844	ACHE_HUMAN	nicotinic acetylcholine receptor epsilon	230	Extracellular (Potential).				muscle contraction|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0														0.111111	14.064432	32.904643	14	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4804399	4804399	3529	17	C	A	A	A	247	19	CHRNE	1	1
LRRC59	55379	broad.mit.edu	37	17	48462617	48462617	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:48462617T>C	uc002iqt.2	-	c.538A>G	c.(538-540)AAG>GAG	p.K180E		NM_018509	NP_060979	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	180	Potential.|Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial nucleoid	protein binding			central_nervous_system(1)	1	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)											0.135135	70.88948	104.267576	35	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48462617	48462617	9390	17	T	C	C	C	793	61	LRRC59	4	4
CA10	56934	broad.mit.edu	37	17	49710858	49710858	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:49710858C>A	uc002itv.3	-	c.961G>T	c.(961-963)GCC>TCC	p.A321S	CA10_uc002itu.3_Missense_Mutation_p.A244S|CA10_uc002itw.3_Missense_Mutation_p.A315S|CA10_uc002itx.3_Missense_Mutation_p.A315S|CA10_uc002ity.3_Missense_Mutation_p.A315S|CA10_uc002itz.2_Missense_Mutation_p.A315S	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	315					brain development					ovary(1)	1			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)											0.056604	-9.140561	12.755583	6	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49710858	49710858	2627	17	C	A	A	A	364	28	CA10	2	2
TANC2	26115	broad.mit.edu	37	17	61498459	61498459	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61498459C>T	uc002jal.3	+	c.5116C>T	c.(5116-5118)CGA>TGA	p.R1706*	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Nonsense_Mutation_p.R817*	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1706							binding			ovary(2)	2														0.063758	-13.204364	45.781929	19	279	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	61498459	61498459	16066	17	C	T	T	T	295	23	TANC2	5	1
ABCA9	10350	broad.mit.edu	37	17	66986013	66986013	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:66986013C>A	uc002jhu.2	-	c.3896G>T	c.(3895-3897)TGC>TTC	p.C1299F	ABCA9_uc010dez.2_Missense_Mutation_p.C1261F	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1299	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|central_nervous_system(1)	5	Breast(10;1.47e-12)													0.109244	12.284009	30.28387	13	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66986013	66986013	40	17	C	A	A	A	325	25	ABCA9	2	2
ABCA5	23461	broad.mit.edu	37	17	67243691	67243691	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:67243691C>T	uc002jif.2	-	c.4916G>A	c.(4915-4917)AGA>AAA	p.R1639K	ABCA10_uc010dfa.1_5'Flank|ABCA5_uc002jib.2_Missense_Mutation_p.R605K|ABCA5_uc002jic.2_Missense_Mutation_p.R862K|ABCA5_uc002jid.2_Missense_Mutation_p.R556K|ABCA5_uc002jie.2_Non-coding_Transcript|ABCA5_uc002jig.2_Missense_Mutation_p.R1639K	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	1639					cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation|reverse cholesterol transport	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)	3	Breast(10;3.72e-11)													0.068966	-5.19921	17.082331	8	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67243691	67243691	36	17	C	T	T	T	416	32	ABCA5	2	2
ABCA5	23461	broad.mit.edu	37	17	67309240	67309240	+	Silent	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:67309240T>C	uc002jif.2	-	c.300A>G	c.(298-300)CTA>CTG	p.L100L	ABCA5_uc002jig.2_Silent_p.L100L|ABCA5_uc002jih.2_Silent_p.L100L|ABCA5_uc010dfe.2_Silent_p.L100L	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	100					cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation|reverse cholesterol transport	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)	3	Breast(10;3.72e-11)													0.070423	-0.576589	12.933983	5	66	KEEP	---	---	---	---	capture		Silent	SNP	67309240	67309240	36	17	T	C	C	C	730	57	ABCA5	4	4
TP53	7157	broad.mit.edu	37	17	7577535	7577535	+	Missense_Mutation	SNP	C	A	A	rs67185453		TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577535C>A	uc002gim.2	-	c.746G>T	c.(745-747)AGG>ATG	p.R249M	TP53_uc002gig.1_Missense_Mutation_p.R249M|TP53_uc002gih.2_Missense_Mutation_p.R249M|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R117M|TP53_uc010cng.1_Missense_Mutation_p.R117M|TP53_uc002gii.1_Missense_Mutation_p.R117M|TP53_uc010cnh.1_Missense_Mutation_p.R249M|TP53_uc010cni.1_Missense_Mutation_p.R249M|TP53_uc002gij.2_Missense_Mutation_p.R249M|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R156M|TP53_uc002gio.2_Missense_Mutation_p.R117M	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	249	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).|R -> T (in sporadic cancers; somatic mutation).|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> I (in a sporadic cancer; somatic mutation).|R -> M (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> K (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.R249M(25)|p.R249T(15)|p.R249K(14)|p.0?(6)|p.R249fs*96(4)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.R249_I251delRPI(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.236111	37.434674	42.023261	17	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577535	7577535	16923	17	C	A	A	A	312	24	TP53	2	2
P4HB	5034	broad.mit.edu	37	17	79813036	79813036	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:79813036C>A	uc002kbn.1	-	c.606G>T	c.(604-606)GGG>GGT	p.G202G	P4HB_uc002kbm.1_5'UTR	NM_000918	NP_000909	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta subunit precursor	202					cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline	cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane	electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			Colon(49;444 983 1296 7887 42561)				156				0.145833	71.927922	112.516224	49	287	KEEP	---	---	---	---	capture		Silent	SNP	79813036	79813036	11772	17	C	A	A	A	275	22	P4HB	2	2
FAM38B	63895	broad.mit.edu	37	18	10680359	10680359	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:10680359G>T	uc002kor.3	-	c.1321C>A	c.(1321-1323)CAA>AAA	p.Q441K	FAM38B_uc002koq.2_Missense_Mutation_p.Q276K	NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	family with sequence similarity 38, member B	2484						integral to membrane	ion channel activity			ovary(1)	1														0.061856	-6.632441	12.793809	6	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10680359	10680359	5776	18	G	T	T	T	598	46	FAM38B	2	2
CEP192	55125	broad.mit.edu	37	18	13095519	13095519	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:13095519G>T	uc010xac.1	+	c.6272G>T	c.(6271-6273)GGG>GTG	p.G2091V	CEP192_uc010dlf.1_Non-coding_Transcript|CEP192_uc010xad.1_Missense_Mutation_p.G1616V|CEP192_uc002kru.2_Non-coding_Transcript|CEP192_uc002krv.2_Missense_Mutation_p.G513V|CEP192_uc002krw.2_Missense_Mutation_p.G240V|CEP192_uc002krx.2_Missense_Mutation_p.G95V|CEP192_uc002kry.2_Non-coding_Transcript	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	2091										ovary(4)|pancreas(1)	5														0.293375	238.929312	251.056821	93	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13095519	13095519	3384	18	G	T	T	T	559	43	CEP192	2	2
DSG3	1830	broad.mit.edu	37	18	29054280	29054280	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29054280G>T	uc002kws.2	+	c.2298G>T	c.(2296-2298)ATG>ATT	p.M766I	DSG3_uc002kwt.2_Missense_Mutation_p.M48I	NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	766	Cytoplasmic (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.151515	33.70623	49.066208	20	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29054280	29054280	4962	18	G	T	T	T	585	45	DSG3	2	2
DYM	54808	broad.mit.edu	37	18	46783444	46783444	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:46783444C>T	uc002ldi.1	-	c.1396G>A	c.(1396-1398)GCT>ACT	p.A466T	DYM_uc010xdf.1_Missense_Mutation_p.A276T|DYM_uc002ldj.3_Missense_Mutation_p.A288T|DYM_uc010dov.1_Missense_Mutation_p.A16T	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin	466						Golgi apparatus					0														0.065789	-4.689418	10.184416	5	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46783444	46783444	5026	18	C	T	T	T	364	28	DYM	2	2
ALPK2	115701	broad.mit.edu	37	18	56202933	56202933	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:56202933G>T	uc002lhj.3	-	c.4486C>A	c.(4486-4488)CAA>AAA	p.Q1496K	ALPK2_uc002lhk.1_Missense_Mutation_p.Q827K	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1496					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11										343				0.059259	-10.72013	16.738272	8	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56202933	56202933	548	18	G	T	T	T	598	46	ALPK2	2	2
ZCCHC2	54877	broad.mit.edu	37	18	60243765	60243765	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:60243765G>C	uc002lip.3	+	c.3490G>C	c.(3490-3492)GCA>CCA	p.A1164P	ZCCHC2_uc002lio.2_Non-coding_Transcript|ZCCHC2_uc002liq.2_Missense_Mutation_p.A634P	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	1164					cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding				0														0.090909	2.199638	7.766798	3	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60243765	60243765	18175	18	G	C	C	C	494	38	ZCCHC2	3	3
TSHZ1	10194	broad.mit.edu	37	18	72998565	72998565	+	Silent	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:72998565C>G	uc002lly.2	+	c.1068C>G	c.(1066-1068)GGC>GGG	p.G356G		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	401					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)										0.086207	1.465604	11.496717	5	53	KEEP	---	---	---	---	capture		Silent	SNP	72998565	72998565	17174	18	C	G	G	G	340	27	TSHZ1	3	3
TRMT1	55621	broad.mit.edu	37	19	13223573	13223573	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13223573C>A	uc002mwj.2	-	c.816G>T	c.(814-816)ACG>ACT	p.T272T	TRMT1_uc002mwk.2_Silent_p.T272T|TRMT1_uc002mwl.3_Silent_p.T272T|TRMT1_uc010xmz.1_Silent_p.T58T	NM_017722	NP_060192	Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 isoform 1	272							RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)										0.131148	12.563502	20.627366	8	53	KEEP	---	---	---	---	capture		Silent	SNP	13223573	13223573	17111	19	C	A	A	A	236	19	TRMT1	1	1
SLC27A1	376497	broad.mit.edu	37	19	17599848	17599848	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17599848C>T	uc002ngu.1	+	c.918C>T	c.(916-918)ATC>ATT	p.I306I	SLC27A1_uc002ngt.1_Silent_p.I38I|SLC27A1_uc010xpp.1_Silent_p.I127I	NM_198580	NP_940982	Q6PCB7	S27A1_HUMAN	solute carrier family 27, member 1	306	Sufficient for oligomerization (By similarity).|Cytoplasmic (Potential).				cardiolipin biosynthetic process|fatty acid metabolic process|long-chain fatty acid transport|negative regulation of phospholipid biosynthetic process|phosphatidic acid biosynthetic process|phosphatidylcholine biosynthetic process|phosphatidylethanolamine biosynthetic process|phosphatidylinositol biosynthetic process|phosphatidylserine biosynthetic process|transmembrane transport	endomembrane system|integral to membrane	fatty acid transporter activity|nucleotide binding				0														0.131148	10.953878	19.02655	8	53	KEEP	---	---	---	---	capture		Silent	SNP	17599848	17599848	15022	19	C	T	T	T	408	32	SLC27A1	2	2
ZNF492	57615	broad.mit.edu	37	19	22847799	22847799	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22847799A>G	uc002nqw.3	+	c.1328A>G	c.(1327-1329)CAT>CGT	p.H443R		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	443	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)												0.155556	14.896982	19.994253	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22847799	22847799	18537	19	A	G	G	G	104	8	ZNF492	4	4
TLE6	79816	broad.mit.edu	37	19	2989238	2989238	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:2989238G>T	uc002lwt.2	+	c.920G>T	c.(919-921)AGA>ATA	p.R307I	TLE6_uc002lwu.2_Missense_Mutation_p.R184I|TLE6_uc010dtg.2_Missense_Mutation_p.R307I|TLE6_uc002lwv.2_Missense_Mutation_p.R88I	NM_001143986	NP_001137458	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6 isoform 1	184	WD 1.					nucleus				ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.08	-1.441098	7.561324	4	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2989238	2989238	16472	19	G	T	T	T	429	33	TLE6	2	2
MIER2	54531	broad.mit.edu	37	19	313534	313534	+	Silent	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:313534C>G	uc002lok.1	-	c.765G>C	c.(763-765)GGG>GGC	p.G255G		NM_017550	NP_060020	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family	255	ELM2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.059829	-8.428952	15.298103	7	110	KEEP	---	---	---	---	capture		Silent	SNP	313534	313534	9971	19	C	G	G	G	327	26	MIER2	3	3
TSHZ3	57616	broad.mit.edu	37	19	31768256	31768256	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31768256G>T	uc002nsy.3	-	c.2443C>A	c.(2443-2445)CCG>ACG	p.P815T		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	815					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.196078	41.637402	50.422196	20	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31768256	31768256	17176	19	G	T	T	T	559	43	TSHZ3	2	2
GPI	2821	broad.mit.edu	37	19	34859562	34859562	+	Missense_Mutation	SNP	G	T	T	rs11548996		TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:34859562G>T	uc002nvf.2	+	c.474G>T	c.(472-474)ATG>ATT	p.M158I	GPI_uc010xrv.1_Missense_Mutation_p.M158I|GPI_uc002nvg.1_Missense_Mutation_p.M119I|GPI_uc010xrw.1_Missense_Mutation_p.M119I|GPI_uc010edl.1_Missense_Mutation_p.M119I|GPI_uc002nvh.1_3'UTR	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	119					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)													0.138298	18.620051	30.505754	13	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34859562	34859562	6885	19	G	T	T	T	598	46	GPI	2	2
ATP1A3	478	broad.mit.edu	37	19	42480646	42480646	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42480646C>T	uc010xwh.1	-	c.2055G>A	c.(2053-2055)CTG>CTA	p.L685L	ATP1A3_uc010xwf.1_Silent_p.L683L|ATP1A3_uc010xwg.1_Silent_p.L642L|ATP1A3_uc002osg.2_Silent_p.L672L|ATP1A3_uc002osh.2_Silent_p.L672L	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	672	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2														0.153846	22.188443	32.618334	14	77	KEEP	---	---	---	---	capture		Silent	SNP	42480646	42480646	1149	19	C	T	T	T	314	25	ATP1A3	2	2
PSG5	5673	broad.mit.edu	37	19	43683099	43683099	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43683099G>T	uc002ovv.2	-	c.641C>A	c.(640-642)CCC>CAC	p.P214H	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovu.2_Intron|PSG5_uc002ovx.2_Intron|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	119	Ig-like V-type.				female pregnancy	extracellular region					0		Prostate(69;0.00899)												0.159151	102.633711	144.314588	60	317	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43683099	43683099	13111	19	G	T	T	T	547	43	PSG5	2	2
ZNF221	7638	broad.mit.edu	37	19	44471333	44471333	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44471333G>T	uc002oxx.2	+	c.1679G>T	c.(1678-1680)CGA>CTA	p.R560L	ZNF221_uc010ejb.1_Missense_Mutation_p.R560L|ZNF221_uc010xws.1_Missense_Mutation_p.R560L	NM_013359	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	560					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)												0.183099	52.75962	66.15438	26	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44471333	44471333	18366	19	G	T	T	T	481	37	ZNF221	1	1
SHANK1	50944	broad.mit.edu	37	19	51220030	51220030	+	Silent	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51220030A>G	uc002psx.1	-	c.147T>C	c.(145-147)GGT>GGC	p.G49G		NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	49					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)										0.27451	44.040606	46.36813	14	37	KEEP	---	---	---	---	capture		Silent	SNP	51220030	51220030	14756	19	A	G	G	G	171	14	SHANK1	4	4
ZNF813	126017	broad.mit.edu	37	19	53994225	53994225	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53994225G>T	uc002qbu.2	+	c.739G>T	c.(739-741)GTA>TTA	p.V247L	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	247	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)										0.166667	29.064365	38.550954	15	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53994225	53994225	18773	19	G	T	T	T	624	48	ZNF813	2	2
PRKCG	5582	broad.mit.edu	37	19	54396639	54396639	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54396639G>T	uc010yeg.1	+	c.933G>T	c.(931-933)TTG>TTT	p.L311F	PRKCG_uc010eqz.1_Missense_Mutation_p.L311F|PRKCG_uc010yef.1_Missense_Mutation_p.C282F|PRKCG_uc002qcq.1_Missense_Mutation_p.L311F|PRKCG_uc010yeh.1_Missense_Mutation_p.L198F	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma	311					activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|protein phosphorylation|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)						505				0.171053	29.625293	37.401927	13	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54396639	54396639	12955	19	G	T	T	T	620	48	PRKCG	2	2
LILRB5	10990	broad.mit.edu	37	19	54760185	54760185	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54760185G>T	uc002qey.2	-	c.376C>A	c.(376-378)CTT>ATT	p.L126I	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Intron|LILRB5_uc002qex.2_Missense_Mutation_p.L126I|LILRB5_uc002qez.2_Intron|LILRB5_uc002qfa.1_Intron|LILRB5_uc010yes.1_Intron	NM_001081442	NP_001074911	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	126	Extracellular (Potential).|Ig-like C2-type 2.				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.192661	35.983195	45.637658	21	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54760185	54760185	9120	19	G	T	T	T	429	33	LILRB5	2	2
LILRA3	11026	broad.mit.edu	37	19	54801976	54801976	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54801976G>A	uc002qfd.2	-	c.1212C>T	c.(1210-1212)AAC>AAT	p.N404N	LILRA6_uc002qew.1_Intron|LILRA3_uc010erk.2_Silent_p.N340N	NM_006865	NP_006856	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor,	404	Ig-like C2-type 4.				defense response	extracellular region|plasma membrane	antigen binding|receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.092683	7.78117	41.908905	19	186	KEEP	---	---	---	---	capture		Silent	SNP	54801976	54801976	9112	19	G	A	A	A	568	44	LILRA3	2	2
NLRP2	55655	broad.mit.edu	37	19	55501959	55501959	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55501959C>A	uc002qij.2	+	c.2627C>A	c.(2626-2628)GCC>GAC	p.A876D	NLRP2_uc010yfp.1_Missense_Mutation_p.A853D|NLRP2_uc010esn.2_Missense_Mutation_p.A852D|NLRP2_uc010eso.2_Missense_Mutation_p.A873D|NLRP2_uc010esp.2_Missense_Mutation_p.A854D	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	876	LRR 3.				apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)										0.061069	-10.554234	15.753838	8	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55501959	55501959	10880	19	C	A	A	A	338	26	NLRP2	2	2
XAB2	56949	broad.mit.edu	37	19	7684528	7684528	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7684528G>T	uc002mgx.2	-	c.2512C>A	c.(2512-2514)CGG>AGG	p.R838R		NM_020196	NP_064581	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	838					nuclear mRNA splicing, via spliceosome|transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4														0.102564	0.90388	7.041539	4	35	KEEP	---	---	---	---	capture		Silent	SNP	7684528	7684528	17992	19	G	T	T	T	480	37	XAB2	1	1
MUC16	94025	broad.mit.edu	37	19	9064438	9064438	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9064438G>T	uc002mkp.2	-	c.23008C>A	c.(23008-23010)CCT>ACT	p.P7670T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7672	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.088235	-0.693134	10.969786	6	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9064438	9064438	10367	19	G	T	T	T	533	41	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9073402	9073402	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9073402G>T	uc002mkp.2	-	c.14044C>A	c.(14044-14046)CAG>AAG	p.Q4682K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4684	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														0.162281	64.936001	89.690377	37	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9073402	9073402	10367	19	G	T	T	T	611	47	MUC16	2	2
VAV3	10451	broad.mit.edu	37	1	108507486	108507486	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:108507486C>T	uc010ouw.1	-	c.6G>A	c.(4-6)GAG>GAA	p.E2E	VAV3_uc001dvk.1_Silent_p.E2E|VAV3_uc001dvl.1_5'Flank|VAV3_uc010oux.1_Silent_p.E2E	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	2	CH.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(4)|lung(2)|breast(2)	8		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)										0.375	9.422911	9.53271	3	5	KEEP	---	---	---	---	capture		Silent	SNP	108507486	108507486	17698	1	C	T	T	T	363	28	VAV3	2	2
WARS2	10352	broad.mit.edu	37	1	119576771	119576771	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:119576771T>A	uc001ehn.2	-	c.581A>T	c.(580-582)CAA>CTA	p.Q194L	WARS2_uc010oxf.1_Missense_Mutation_p.Q100L|WARS2_uc001ehm.2_Missense_Mutation_p.Q194L|WARS2_uc010oxg.1_Missense_Mutation_p.Q137L|WARS2_uc010oxh.1_Silent_p.T165T|WARS2_uc010oxi.1_Silent_p.T71T	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2	194					tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity				0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)									0.116788	15.798018	35.600184	16	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119576771	119576771	17822	1	T	A	A	A	819	63	WARS2	3	3
FLG2	388698	broad.mit.edu	37	1	152326733	152326733	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152326733T>C	uc001ezw.3	-	c.3529A>G	c.(3529-3531)ACA>GCA	p.T1177A		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1177	Ser-rich.						calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.104478	25.140683	56.402548	21	180	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152326733	152326733	6161	1	T	C	C	C	767	59	FLG2	4	4
FLG2	388698	broad.mit.edu	37	1	152329975	152329975	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152329975G>T	uc001ezw.3	-	c.287C>A	c.(286-288)GCT>GAT	p.A96D		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	96							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.035088	-18.999218	7.789602	4	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152329975	152329975	6161	1	G	T	T	T	442	34	FLG2	2	2
CD1C	911	broad.mit.edu	37	1	158261156	158261156	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158261156G>A	uc001fru.2	+	c.294G>A	c.(292-294)GAG>GAA	p.E98E	CD1C_uc001frv.2_5'Flank	NM_001765	NP_001756	P29017	CD1C_HUMAN	CD1C antigen precursor	98	Extracellular (Potential).				antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding			ovary(2)|pancreas(1)	3	all_hematologic(112;0.0378)													0.214286	83.786431	95.397003	33	121	KEEP	---	---	---	---	capture		Silent	SNP	158261156	158261156	3103	1	G	A	A	A	425	33	CD1C	2	2
CD1E	913	broad.mit.edu	37	1	158325701	158325701	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158325701C>A	uc001fse.2	+	c.710C>A	c.(709-711)CCA>CAA	p.P237Q	CD1E_uc010pid.1_Missense_Mutation_p.P235Q|CD1E_uc010pie.1_Missense_Mutation_p.P138Q|CD1E_uc010pif.1_Missense_Mutation_p.P48Q|CD1E_uc001fsd.2_Missense_Mutation_p.P237Q|CD1E_uc001fsk.2_Missense_Mutation_p.P147Q|CD1E_uc001fsj.2_Missense_Mutation_p.P147Q|CD1E_uc001fsc.2_Missense_Mutation_p.P48Q|CD1E_uc010pig.1_Non-coding_Transcript|CD1E_uc001fsa.2_Missense_Mutation_p.P48Q|CD1E_uc001fsf.2_Missense_Mutation_p.P237Q|CD1E_uc001fry.2_Missense_Mutation_p.P237Q|CD1E_uc001fsg.2_Missense_Mutation_p.P48Q|CD1E_uc001fsh.2_Missense_Mutation_p.P48Q|CD1E_uc001fsi.2_Missense_Mutation_p.P237Q|CD1E_uc009wsv.2_Missense_Mutation_p.P138Q|CD1E_uc001frz.2_Missense_Mutation_p.P147Q|CD1E_uc009wsw.2_5'UTR	NM_030893	NP_112155	P15812	CD1E_HUMAN	CD1E antigen isoform a precursor	237	Ig-like.				antigen processing and presentation|immune response	early endosome|Golgi membrane|integral to plasma membrane|late endosome|lysosomal lumen					0	all_hematologic(112;0.0378)													0.230769	62.858774	70.635528	27	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158325701	158325701	3105	1	C	A	A	A	273	21	CD1E	2	2
OR10R2	343406	broad.mit.edu	37	1	158450421	158450421	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158450421G>T	uc010pik.1	+	c.754G>T	c.(754-756)GAG>TAG	p.E252*		NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	252	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)	2	all_hematologic(112;0.0378)													0.175	40.194936	52.15702	21	99	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	158450421	158450421	11323	1	G	T	T	T	585	45	OR10R2	5	2
RGS5	8490	broad.mit.edu	37	1	163138072	163138073	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:163138072_163138073GG>TT	uc001gcn.2	-	c.130_131CC>AA	c.(130-132)CCA>AAA	p.P44K	RGS5_uc009wvb.2_Intron	NM_003617	NP_003608	O15539	RGS5_HUMAN	regulator of G-protein signalling 5	44					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)											0.175758	57.39028	73.735109	29	136	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	163138072	163138073	13782	1	GG	TT	TT	TT	611	47	RGS5	2	2
ILDR2	387597	broad.mit.edu	37	1	166905836	166905836	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:166905836G>T	uc001gdx.1	-	c.695C>A	c.(694-696)CCT>CAT	p.P232H		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	232	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1														0.088889	0.187213	7.85371	4	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166905836	166905836	8011	1	G	T	T	T	455	35	ILDR2	2	2
GPA33	10223	broad.mit.edu	37	1	167025041	167025041	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167025041G>T	uc001gea.1	-	c.617C>A	c.(616-618)TCG>TAG	p.S206*		NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor	206	Ig-like C2-type.|Extracellular (Potential).					integral to plasma membrane	receptor activity				0														0.241135	81.074571	89.69951	34	107	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	167025041	167025041	6860	1	G	T	T	T	481	37	GPA33	5	1
PAPPA2	60676	broad.mit.edu	37	1	176668684	176668684	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176668684G>T	uc001gkz.2	+	c.3195G>T	c.(3193-3195)TTG>TTT	p.L1065F	PAPPA2_uc009www.2_Non-coding_Transcript	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1065					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|lung(1)|breast(1)	14														0.241158	185.585397	204.586208	75	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176668684	176668684	11850	1	G	T	T	T	594	46	PAPPA2	2	2
CFHR2	3080	broad.mit.edu	37	1	196928066	196928066	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196928066G>A	uc001gtq.1	+	c.669G>A	c.(667-669)TGG>TGA	p.W223*	CFHR2_uc001gtr.1_Nonsense_Mutation_p.W99*	NM_005666	NP_005657	P36980	FHR2_HUMAN	H factor (complement)-like 3 precursor	223	Sushi 4.					extracellular region				ovary(1)	1														0.075	-0.708073	6.706037	3	37	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	196928066	196928066	3418	1	G	A	A	A	533	41	CFHR2	5	2
LHX9	56956	broad.mit.edu	37	1	197898182	197898182	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197898182G>T	uc001guk.1	+	c.987G>T	c.(985-987)CAG>CAT	p.Q329H	LHX9_uc001gui.1_Missense_Mutation_p.Q320H|LHX9_uc001guj.1_Intron	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1	329					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														0.333333	78.141071	80.28379	29	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197898182	197898182	9103	1	G	T	T	T	451	35	LHX9	2	2
USH2A	7399	broad.mit.edu	37	1	216019167	216019167	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216019167C>A	uc001hku.1	-	c.9054G>T	c.(9052-9054)GGG>GGT	p.G3018G		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3018	Extracellular (Potential).				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)										0.132075	7.079354	14.070681	7	46	KEEP	---	---	---	---	capture		Silent	SNP	216019167	216019167	17598	1	C	A	A	A	275	22	USH2A	2	2
HHIPL2	79802	broad.mit.edu	37	1	222717100	222717100	+	Silent	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222717100C>G	uc001hnh.1	-	c.753G>C	c.(751-753)CTG>CTC	p.L251L		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	251					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)										0.159574	66.224065	86.977623	30	158	KEEP	---	---	---	---	capture		Silent	SNP	222717100	222717100	7378	1	C	G	G	G	262	21	HHIPL2	3	3
ITPKB	3707	broad.mit.edu	37	1	226836376	226836376	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:226836376C>T	uc010pvo.1	-	c.2029G>A	c.(2029-2031)GCA>ACA	p.A677T		NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	677							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				Colon(84;110 1851 5306 33547)								0.054645	-20.580922	17.654318	10	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	226836376	226836376	8222	1	C	T	T	T	351	27	ITPKB	1	1
PRSS38	339501	broad.mit.edu	37	1	228033666	228033666	+	Silent	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228033666G>C	uc001hrh.2	+	c.738G>C	c.(736-738)GGG>GGC	p.G246G		NM_183062	NP_898885	A1L453	PRS38_HUMAN	marapsin 2 precursor	246	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2														0.173333	25.839319	33.390079	13	62	KEEP	---	---	---	---	capture		Silent	SNP	228033666	228033666	13077	1	G	C	C	C	548	43	PRSS38	3	3
HNRNPR	10236	broad.mit.edu	37	1	23648100	23648100	+	Silent	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23648100T>A	uc001bgp.3	-	c.732A>T	c.(730-732)GCA>GCT	p.A244A	HNRNPR_uc001bgr.3_Silent_p.A244A|HNRNPR_uc009vqk.2_Silent_p.A143A|HNRNPR_uc001bgs.3_Silent_p.A143A|HNRNPR_uc010odw.1_Silent_p.A206A|HNRNPR_uc010odx.1_Silent_p.A84A|HNRNPR_uc009vql.2_Silent_p.A105A	NM_001102398	NP_001095868	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	244	RRM 1.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)										0.190871	98.411349	119.93623	46	195	KEEP	---	---	---	---	capture		Silent	SNP	23648100	23648100	7564	1	T	A	A	A	808	63	HNRNPR	3	3
TCEA3	6920	broad.mit.edu	37	1	23743829	23743829	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23743829T>A	uc001bgx.1	-	c.293A>T	c.(292-294)AAG>ATG	p.K98M	TCEA3_uc009vqn.1_Missense_Mutation_p.K77M|TCEA3_uc010ody.1_Missense_Mutation_p.K61M	NM_003196	NP_003187	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	98					regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	nucleus	DNA binding|RNA polymerase II transcription factor activity|transcription elongation regulator activity|translation elongation factor activity|zinc ion binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)										0.091603	2.993759	25.016793	12	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23743829	23743829	16195	1	T	A	A	A	728	56	TCEA3	3	3
RYR2	6262	broad.mit.edu	37	1	237948095	237948095	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237948095G>T	uc001hyl.1	+	c.13083G>T	c.(13081-13083)GAG>GAT	p.E4361D	RYR2_uc010pya.1_Missense_Mutation_p.E776D	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4361					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.157895	28.3628	41.123498	18	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237948095	237948095	14249	1	G	T	T	T	451	35	RYR2	2	2
CNR2	1269	broad.mit.edu	37	1	24201701	24201701	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:24201701C>T	uc001bif.2	-	c.407G>A	c.(406-408)CGC>CAC	p.R136H		NM_001841	NP_001832	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	136	Cytoplasmic (Potential).				behavior|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response	dendrite|integral to plasma membrane|perikaryon	cannabinoid receptor activity			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Nabilone(DB00486)									0.164384	38.302417	53.937665	24	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24201701	24201701	3770	1	C	T	T	T	351	27	CNR2	1	1
OR1C1	26188	broad.mit.edu	37	1	247921322	247921322	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247921322G>A	uc010pza.1	-	c.387C>T	c.(385-387)CCC>CCT	p.P129P		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)											0.144737	22.071123	31.302714	11	65	KEEP	---	---	---	---	capture		Silent	SNP	247921322	247921322	11358	1	G	A	A	A	444	35	OR1C1	2	2
OR2M5	127059	broad.mit.edu	37	1	248309050	248309050	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248309050A>T	uc010pze.1	+	c.601A>T	c.(601-603)ATC>TTC	p.I201F		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)											0.028986	-76.547103	24.455204	12	402	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248309050	248309050	11419	1	A	T	T	T	104	8	OR2M5	3	3
OR2G6	391211	broad.mit.edu	37	1	248685264	248685264	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248685264G>T	uc001ien.1	+	c.317G>T	c.(316-318)GGG>GTG	p.G106V		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	106	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.054054	-16.693873	14.324867	8	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248685264	248685264	11406	1	G	T	T	T	559	43	OR2G6	2	2
SH3BP5L	80851	broad.mit.edu	37	1	249110823	249110823	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:249110823C>A	uc001iew.1	-	c.285G>T	c.(283-285)TCG>TCT	p.S95S	SH3BP5L_uc010pzp.1_5'Flank|SH3BP5L_uc010pzq.1_Silent_p.S63S|SH3BP5L_uc001iev.1_5'UTR	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	95	Potential.										0	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;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)											0.063953	-12.393262	21.628384	11	161	KEEP	---	---	---	---	capture		Silent	SNP	249110823	249110823	14739	1	C	A	A	A	288	23	SH3BP5L	1	1
CCDC21	64793	broad.mit.edu	37	1	26566285	26566285	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26566285A>T	uc001bls.1	+	c.11A>T	c.(10-12)CAG>CTG	p.Q4L	CCDC21_uc001blr.2_Missense_Mutation_p.Q4L|CCDC21_uc010ofa.1_Missense_Mutation_p.Q4L	NM_022778	NP_073615	Q6P2H3	CCD21_HUMAN	coiled-coil domain containing 21	4											0		all_cancers(24;7e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.6e-26)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;9.48e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00917)|READ - Rectum adenocarcinoma(331;0.0649)										0.173469	35.82429	45.682782	17	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26566285	26566285	2918	1	A	T	T	T	91	7	CCDC21	3	3
WDTC1	23038	broad.mit.edu	37	1	27627736	27627736	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27627736G>T	uc009vst.2	+	c.1252G>T	c.(1252-1254)GCC>TCC	p.A418S	WDTC1_uc001bno.2_Missense_Mutation_p.A417S|WDTC1_uc001bnp.1_Non-coding_Transcript|WDTC1_uc001bnq.2_Missense_Mutation_p.A96S	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	418	TPR 2.						protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)								OREG0013280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.114754	7.879264	16.802744	7	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27627736	27627736	17916	1	G	T	T	T	598	46	WDTC1	2	2
RSPO1	284654	broad.mit.edu	37	1	38095323	38095323	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:38095323C>A	uc001cbl.1	-	c.11G>T	c.(10-12)GGG>GTG	p.G4V	RSPO1_uc001cbm.1_Missense_Mutation_p.G4V|RSPO1_uc009vvf.1_Intron|RSPO1_uc009vvg.1_Missense_Mutation_p.G4V	NM_001038633	NP_001033722	Q2MKA7	RSPO1_HUMAN	R-spondin1 precursor	4					positive regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization		heparin binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GBM(122;680 2230 27822 42821)								0.2	11.626409	14.545015	7	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38095323	38095323	14189	1	C	A	A	A	286	22	RSPO1	2	2
LRRC41	10489	broad.mit.edu	37	1	46746874	46746874	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46746874G>T	uc001cpn.2	-	c.1679C>A	c.(1678-1680)CCA>CAA	p.P560Q	LRRC41_uc010omb.1_Missense_Mutation_p.P560Q	NM_006369	NP_006360	Q15345	LRC41_HUMAN	MUF1 protein	560										ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(166;0.155)													0.075949	-6.105684	8.849024	6	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46746874	46746874	9374	1	G	T	T	T	611	47	LRRC41	2	2
SLC44A5	204962	broad.mit.edu	37	1	75708683	75708683	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75708683T>A	uc010oqz.1	-	c.476A>T	c.(475-477)AAG>ATG	p.K159M	SLC44A5_uc001dgt.2_Missense_Mutation_p.K120M|SLC44A5_uc001dgs.2_Missense_Mutation_p.K78M|SLC44A5_uc001dgr.2_Missense_Mutation_p.K78M|SLC44A5_uc001dgu.2_Missense_Mutation_p.K120M|SLC44A5_uc010ora.1_Missense_Mutation_p.K114M|SLC44A5_uc010orb.1_De_novo_Start_InFrame	NM_001130058	NP_001123530	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform B	120	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)	2														0.218182	55.337955	63.392362	24	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75708683	75708683	15136	1	T	A	A	A	728	56	SLC44A5	3	3
MACROD2	140733	broad.mit.edu	37	20	16025241	16025241	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:16025241G>T	uc002wou.2	+	c.1257G>T	c.(1255-1257)AAG>AAT	p.K419N	MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Missense_Mutation_p.K184N|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.2_Missense_Mutation_p.K70N	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1	419											0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)												0.270833	33.953602	36.227302	13	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16025241	16025241	9523	20	G	T	T	T	451	35	MACROD2	2	2
KIF16B	55614	broad.mit.edu	37	20	16360585	16360585	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:16360585G>T	uc010gci.1	-	c.2062C>A	c.(2062-2064)CAG>AAG	p.Q688K	KIF16B_uc002wpe.1_Missense_Mutation_p.Q70K|KIF16B_uc002wpf.1_Missense_Mutation_p.Q70K|KIF16B_uc002wpg.1_Missense_Mutation_p.Q688K|KIF16B_uc010gch.1_Missense_Mutation_p.Q688K|KIF16B_uc010gcj.1_Missense_Mutation_p.Q699K	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	688	Glu-rich.|Potential.				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7														0.082317	0.998104	59.200722	27	301	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16360585	16360585	8589	20	G	T	T	T	598	46	KIF16B	2	2
SIRPA	140885	broad.mit.edu	37	20	1896081	1896081	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:1896081G>A	uc002wft.2	+	c.416G>A	c.(415-417)GGC>GAC	p.G139D	SIRPA_uc002wfq.2_Missense_Mutation_p.G139D|SIRPA_uc010zps.1_Missense_Mutation_p.G119D|SIRPA_uc002wfr.2_Missense_Mutation_p.G139D|SIRPA_uc002wfs.2_Missense_Mutation_p.G139D	NM_080792	NP_542970	P78324	SHPS1_HUMAN	signal-regulatory protein alpha precursor	139	Extracellular (Potential).				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding			ovary(1)	1				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GBM(155;1668 1920 5945 42733 48121)								0.146497	36.518991	55.378201	23	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1896081	1896081	14827	20	G	A	A	A	546	42	SIRPA	2	2
SSTR4	6754	broad.mit.edu	37	20	23016906	23016906	+	Silent	SNP	G	T	T	rs72547257	byFrequency	TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23016906G>T	uc002wsr.2	+	c.786G>T	c.(784-786)CTG>CTT	p.L262L		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	262	Helical; Name=6; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity				0	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					Esophageal Squamous(15;850 1104 16640)								0.312057	109.61939	114.071113	44	97	KEEP	---	---	---	---	capture		Silent	SNP	23016906	23016906	15716	20	G	T	T	T	574	45	SSTR4	2	2
TGM6	343641	broad.mit.edu	37	20	2411621	2411621	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2411621T>A	uc002wfy.1	+	c.1915T>A	c.(1915-1917)TGT>AGT	p.C639S	TGM6_uc010gal.1_Intron	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	639					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)	3					L-Glutamine(DB00130)									0.315353	221.028818	228.329664	76	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2411621	2411621	16362	20	T	A	A	A	715	55	TGM6	3	3
CPXM1	56265	broad.mit.edu	37	20	2779518	2779518	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2779518C>A	uc002wgu.2	-	c.194G>T	c.(193-195)CGG>CTG	p.R65L	CPXM1_uc010gas.2_Missense_Mutation_p.R65L	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor	65					cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2														0.305221	218.210317	226.634829	76	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2779518	2779518	3976	20	C	A	A	A	299	23	CPXM1	1	1
CDK5RAP1	51654	broad.mit.edu	37	20	31973519	31973519	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31973519C>A	uc010gek.2	-	c.813G>T	c.(811-813)CGG>CGT	p.R271R	CDK5RAP1_uc002wyy.2_Silent_p.R181R|CDK5RAP1_uc002wyz.2_Silent_p.R271R|CDK5RAP1_uc002wza.2_Silent_p.R271R|CDK5RAP1_uc010gel.2_Silent_p.R180R|CDK5RAP1_uc010gem.2_Silent_p.R271R|CDK5RAP1_uc002wzc.1_Silent_p.R271R|CDK5RAP1_uc010gen.2_Silent_p.R271R	NM_016408	NP_057492	Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	271					brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5														0.11194	14.022293	33.965144	15	119	KEEP	---	---	---	---	capture		Silent	SNP	31973519	31973519	3274	20	C	A	A	A	275	22	CDK5RAP1	2	2
ZNF831	128611	broad.mit.edu	37	20	57766620	57766620	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:57766620G>T	uc002yan.2	+	c.546G>T	c.(544-546)AAG>AAT	p.K182N		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	182	C2H2-type 2.					intracellular	nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(29;0.0085)													0.368821	253.877565	257.865779	97	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57766620	57766620	18784	20	G	T	T	T	425	33	ZNF831	2	2
ZBTB46	140685	broad.mit.edu	37	20	62421767	62421767	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62421767G>T	uc002ygv.1	-	c.344C>A	c.(343-345)ACG>AAG	p.T115K	ZBTB46_uc002ygu.2_Non-coding_Transcript	NM_025224	NP_079500	Q6ZMU8	Q6ZMU8_HUMAN	zinc finger and BTB domain containing 46	115						nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)													0.125	4.308172	7.605339	3	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62421767	62421767	18134	20	G	T	T	T	520	40	ZBTB46	1	1
ZNF295	49854	broad.mit.edu	37	21	43414063	43414063	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43414063A>C	uc002zab.3	-	c.142T>G	c.(142-144)TTG>GTG	p.L48V	ZNF295_uc002yzz.3_Missense_Mutation_p.L48V|ZNF295_uc002yzy.3_Missense_Mutation_p.L48V|ZNF295_uc002zaa.3_Missense_Mutation_p.L48V|ZNF295_uc010gov.1_Missense_Mutation_p.L48V|ZNF295_uc002zac.2_Missense_Mutation_p.L48V	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	48	Mediates homodimerization.|BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methyl-CpG binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.118182	12.482248	28.282084	13	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43414063	43414063	18419	21	A	C	C	C	37	3	ZNF295	4	4
CECR2	27443	broad.mit.edu	37	22	18020342	18020342	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:18020342C>T	uc010gqw.1	+	c.1671C>T	c.(1669-1671)CCC>CCT	p.P557P	CECR2_uc010gqv.1_Silent_p.P416P|CECR2_uc002zml.2_Silent_p.P416P	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	599					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)										0.080645	-0.556087	10.544635	5	57	KEEP	---	---	---	---	capture		Silent	SNP	18020342	18020342	3339	22	C	T	T	T	262	21	CECR2	2	2
HIRA	7290	broad.mit.edu	37	22	19365417	19365417	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:19365417C>G	uc002zpf.1	-	c.1588G>C	c.(1588-1590)GCA>CCA	p.A530P	HIRA_uc011agx.1_Missense_Mutation_p.A396P|HIRA_uc010grn.1_Missense_Mutation_p.A530P|HIRA_uc010gro.1_Missense_Mutation_p.A486P|HIRA_uc010grp.2_Non-coding_Transcript	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	530	Interaction with CCNA1.				chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulator activity			ovary(1)	1	Colorectal(54;0.0993)													0.048951	-14.398963	16.517312	7	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19365417	19365417	7405	22	C	G	G	G	325	25	HIRA	3	3
MYO18B	84700	broad.mit.edu	37	22	26165096	26165096	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26165096G>C	uc003abz.1	+	c.1213G>C	c.(1213-1215)GCA>CCA	p.A405P	MYO18B_uc003aca.1_Missense_Mutation_p.A286P|MYO18B_uc010guy.1_Missense_Mutation_p.A286P|MYO18B_uc010guz.1_Missense_Mutation_p.A286P|MYO18B_uc011aka.1_5'UTR|MYO18B_uc011akb.1_5'Flank	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	405						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12									p.A405T(MFE296-Tumor)|p.A405T(CAMA1-Tumor)	968				0.075	0.292495	7.705983	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26165096	26165096	10461	22	G	C	C	C	494	38	MYO18B	3	3
HPS4	89781	broad.mit.edu	37	22	26868863	26868863	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26868863G>A	uc003acl.2	-	c.319C>T	c.(319-321)CGG>TGG	p.R107W	HPS4_uc003aci.2_Missense_Mutation_p.R102W|HPS4_uc003acj.2_5'UTR|HPS4_uc003ack.2_5'UTR|HPS4_uc003acn.2_5'UTR|HPS4_uc010gvd.1_Missense_Mutation_p.R107W|HPS4_uc003ach.2_5'Flank	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	107					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														0.060606	-13.888548	19.404802	10	155	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26868863	26868863	7633	22	G	A	A	A	493	38	HPS4	1	1
MYH9	4627	broad.mit.edu	37	22	36708162	36708162	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36708162G>T	uc003apg.2	-	c.1660C>A	c.(1660-1662)CCC>ACC	p.P554T	MYH9_uc003aph.1_Missense_Mutation_p.P418T	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	554	Myosin head-like.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	10										1624				0.072464	-5.60125	20.308104	10	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36708162	36708162	10437	22	G	T	T	T	559	43	MYH9	2	2
TTLL1	25809	broad.mit.edu	37	22	43460246	43460246	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:43460246G>T	uc003bdi.2	-	c.588C>A	c.(586-588)GAC>GAA	p.D196E	TTLL1_uc010gzh.2_Missense_Mutation_p.D196E|TTLL1_uc003bdj.2_Missense_Mutation_p.D82E|TTLL1_uc003bdh.2_Missense_Mutation_p.D158E	NM_012263	NP_036395	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	196	TTL.				protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity				0		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)										0.076923	-1.602565	15.032902	7	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43460246	43460246	17277	22	G	T	T	T	568	44	TTLL1	2	2
LRP1B	53353	broad.mit.edu	37	2	140992421	140992421	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:140992421G>T	uc002tvj.1	-	c.13593C>A	c.(13591-13593)TTC>TTA	p.F4531L		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4531	Cytoplasmic (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.266667	38.969037	41.922595	16	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140992421	140992421	9328	2	G	T	T	T	581	45	LRP1B	2	2
NEB	4703	broad.mit.edu	37	2	152527689	152527689	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:152527689T>C	uc010fnx.2	-	c.4354A>G	c.(4354-4356)ATT>GTT	p.I1452V		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	1452	Nebulin 37.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(1)|skin(1)|pancreas(1)	19				BRCA - Breast invasive adenocarcinoma(221;0.219)										0.224138	36.784969	40.81239	13	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152527689	152527689	10701	2	T	C	C	C	637	49	NEB	4	4
TBR1	10716	broad.mit.edu	37	2	162274750	162274750	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:162274750G>A	uc002ubw.1	+	c.886G>A	c.(886-888)GGG>AGG	p.G296R	TBR1_uc010foy.2_Missense_Mutation_p.G9R	NM_006593	NP_006584	Q16650	TBR1_HUMAN	T-box, brain, 1	296	T-box.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.206186	45.139486	52.908446	20	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	162274750	162274750	16173	2	G	A	A	A	611	47	TBR1	2	2
KCNH7	90134	broad.mit.edu	37	2	163374483	163374483	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:163374483T>C	uc002uch.1	-	c.649A>G	c.(649-651)AAA>GAA	p.K217E	KCNH7_uc002uci.2_Missense_Mutation_p.K217E	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	217	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)	3					Ibutilide(DB00308)	GBM(196;1492 2208 17507 24132 45496)								0.118012	34.431648	57.496155	19	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	163374483	163374483	8342	2	T	C	C	C	832	64	KCNH7	4	4
SCN3A	6328	broad.mit.edu	37	2	166019136	166019136	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166019136C>A	uc002ucx.2	-	c.897G>T	c.(895-897)ATG>ATT	p.M299I	SCN3A_uc002ucy.2_Missense_Mutation_p.M299I|SCN3A_uc002ucz.2_Missense_Mutation_p.M299I|SCN3A_uc002uda.1_Missense_Mutation_p.M168I|SCN3A_uc002udb.1_Missense_Mutation_p.M168I	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	299						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.07	-4.161273	14.931161	7	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166019136	166019136	14400	2	C	A	A	A	273	21	SCN3A	2	2
XIRP2	129446	broad.mit.edu	37	2	168102744	168102744	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168102744C>A	uc002udx.2	+	c.4842C>A	c.(4840-4842)TCC>TCA	p.S1614S	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.S1439S|XIRP2_uc010fpq.2_Silent_p.S1392S|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1439					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.095238	3.998546	14.360788	6	57	KEEP	---	---	---	---	capture		Silent	SNP	168102744	168102744	18011	2	C	A	A	A	262	21	XIRP2	2	2
TTN	7273	broad.mit.edu	37	2	179397726	179397726	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179397726G>T	uc010zfg.1	-	c.95912C>A	c.(95911-95913)CCT>CAT	p.P31971H	TTN_uc010zfh.1_Missense_Mutation_p.P25666H|TTN_uc010zfi.1_Missense_Mutation_p.P25599H|TTN_uc010zfj.1_Missense_Mutation_p.P25474H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1890										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				0.166667	100.10318	134.88473	55	275	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179397726	179397726	17290	2	G	T	T	T	455	35	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179412988	179412988	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179412988A>T	uc010zfg.1	-	c.85661T>A	c.(85660-85662)GTT>GAT	p.V28554D	TTN_uc010zfh.1_Missense_Mutation_p.V22249D|TTN_uc010zfi.1_Missense_Mutation_p.V22182D|TTN_uc010zfj.1_Missense_Mutation_p.V22057D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3260										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				0.051546	-21.308873	19.979648	10	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179412988	179412988	17290	2	A	T	T	T	26	2	TTN	3	3
TTN	7273	broad.mit.edu	37	2	179459084	179459084	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179459084G>T	uc010zfg.1	-	c.50433C>A	c.(50431-50433)TGC>TGA	p.C16811*	TTN_uc010zfh.1_Nonsense_Mutation_p.C10506*|TTN_uc010zfi.1_Nonsense_Mutation_p.C10439*|TTN_uc010zfj.1_Nonsense_Mutation_p.C10314*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	97										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				0.096774	2.597013	12.711827	6	56	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	179459084	179459084	17290	2	G	T	T	T	594	46	TTN	5	2
ITGA4	3676	broad.mit.edu	37	2	182359483	182359483	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:182359483G>C	uc002unu.2	+	c.1283G>C	c.(1282-1284)AGT>ACT	p.S428T		NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	428	FG-GAP 7.|Extracellular (Potential).				B cell differentiation|blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)									0.215827	89.071634	99.428903	30	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	182359483	182359483	8182	2	G	C	C	C	468	36	ITGA4	3	3
PDE1A	5136	broad.mit.edu	37	2	183051238	183051238	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:183051238C>A	uc002uoq.1	-	c.1333G>T	c.(1333-1335)GAG>TAG	p.E445*	PDE1A_uc010zfp.1_Nonsense_Mutation_p.E341*|PDE1A_uc010zfq.1_Nonsense_Mutation_p.E445*|PDE1A_uc002uor.2_Nonsense_Mutation_p.E429*|PDE1A_uc002uos.2_Nonsense_Mutation_p.E445*|PDE1A_uc002uou.2_Nonsense_Mutation_p.E411*	NM_005019	NP_005010	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 1	445	Catalytic (By similarity).				activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.061)											0.079365	-2.170297	9.214598	5	58	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	183051238	183051238	12054	2	C	A	A	A	416	32	PDE1A	5	2
COL3A1	1281	broad.mit.edu	37	2	189868184	189868184	+	Silent	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:189868184T>C	uc002uqj.1	+	c.2601T>C	c.(2599-2601)GGT>GGC	p.G867G		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	867	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)					1079				0.130435	8.919763	15.030492	6	40	KEEP	---	---	---	---	capture		Silent	SNP	189868184	189868184	3826	2	T	C	C	C	756	59	COL3A1	4	4
INO80D	54891	broad.mit.edu	37	2	206869874	206869874	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:206869874T>A	uc002vaz.3	-	c.2302A>T	c.(2302-2304)ACT>TCT	p.T768S		NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	768										ovary(1)	1														0.06383	-4.919273	13.677443	6	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206869874	206869874	8050	2	T	A	A	A	767	59	INO80D	3	3
MYL1	4632	broad.mit.edu	37	2	211158990	211158990	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:211158990G>T	uc002vec.2	-	c.457C>A	c.(457-459)CGC>AGC	p.R153S	MYL1_uc002veb.2_Missense_Mutation_p.R109S	NM_079420	NP_524144	P05976	MYL1_HUMAN	fast skeletal myosin alkali light chain 1	153	EF-hand 2.				muscle filament sliding|muscle organ development	cytosol|muscle myosin complex|sarcomere	calcium ion binding|motor activity|structural constituent of muscle			ovary(1)	1				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)										0.128205	7.461042	12.702867	5	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	211158990	211158990	10438	2	G	T	T	T	507	39	MYL1	1	1
APOB	338	broad.mit.edu	37	2	21235206	21235206	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21235206C>A	uc002red.2	-	c.4534G>T	c.(4534-4536)GGC>TGC	p.G1512C		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1512					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.131868	17.038625	29.020724	12	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21235206	21235206	796	2	C	A	A	A	273	21	APOB	2	2
VWC2L	402117	broad.mit.edu	37	2	215279062	215279062	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:215279062C>A	uc002vet.2	+	c.145C>A	c.(145-147)CGA>AGA	p.R49R	VWC2L_uc010zjl.1_Silent_p.R49R	NM_001080500	NP_001073969	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain-containing	49						extracellular region					0														0.171429	11.827375	15.400275	6	29	KEEP	---	---	---	---	capture		Silent	SNP	215279062	215279062	17815	2	C	A	A	A	399	31	VWC2L	1	1
CYP27A1	1593	broad.mit.edu	37	2	219674425	219674425	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219674425G>T	uc002viz.3	+	c.381G>T	c.(379-381)CGG>CGT	p.R127R		NM_000784	NP_000775	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A,	127					bile acid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	mitochondrial matrix	cholestanetriol 26-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Cholecalciferol(DB00169)									0.108333	9.780167	28.035732	13	107	KEEP	---	---	---	---	capture		Silent	SNP	219674425	219674425	4323	2	G	T	T	T	522	41	CYP27A1	2	2
CHRNG	1146	broad.mit.edu	37	2	233404770	233404770	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:233404770C>A	uc002vsx.1	+	c.124C>A	c.(124-126)CGG>AGG	p.R42R	CHRNG_uc010fyd.2_Silent_p.R42R|CHRNG_uc010fye.1_Silent_p.R42R	NM_005199	NP_005190	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma	42	Extracellular (Potential).				muscle contraction	cell junction|postsynaptic membrane	acetylcholine receptor activity				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)										0.095238	3.702804	14.061679	6	57	KEEP	---	---	---	---	capture		Silent	SNP	233404770	233404770	3530	2	C	A	A	A	347	27	CHRNG	1	1
DNAJB3	414061	broad.mit.edu	37	2	234652413	234652413	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234652413G>A	uc002vuz.2	-	c.150C>T	c.(148-150)GCC>GCT	p.A50A	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	50	J.				protein folding		heat shock protein binding|unfolded protein binding				0														0.067742	-17.622955	42.350842	21	289	KEEP	---	---	---	---	capture		Silent	SNP	234652413	234652413	4804	2	G	A	A	A	496	39	DNAJB3	1	1
OTOS	150677	broad.mit.edu	37	2	241078631	241078631	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241078631G>A	uc002vyv.2	-	c.226C>T	c.(226-228)CTG>TTG	p.L76L	MYEOV2_uc002vyu.1_5'Flank|MYEOV2_uc010zof.1_5'Flank	NM_148961	NP_683764	Q8NHW6	OTOSP_HUMAN	otospiralin precursor	76						extracellular region					0		all_epithelial(40;2.79e-15)|Breast(86;3.04e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|Hepatocellular(293;0.148)|all_hematologic(139;0.158)|Melanoma(123;0.16)		Epithelial(32;2.56e-30)|all cancers(36;7.18e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.37e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.07e-06)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)										0.223301	55.763103	63.021072	23	80	KEEP	---	---	---	---	capture		Silent	SNP	241078631	241078631	11721	2	G	A	A	A	451	35	OTOS	2	2
NEU4	129807	broad.mit.edu	37	2	242757727	242757727	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242757727C>A	uc002wcn.1	+	c.844C>A	c.(844-846)CCC>ACC	p.P282T	NEU4_uc002wcl.2_Non-coding_Transcript|NEU4_uc010fzr.2_Missense_Mutation_p.P270T|NEU4_uc002wcm.2_Missense_Mutation_p.P270T|NEU4_uc002wco.1_Missense_Mutation_p.P270T|NEU4_uc002wcp.1_Missense_Mutation_p.P282T	NM_080741	NP_542779	Q8WWR8	NEUR4_HUMAN	sialidase 4	270						lysosomal lumen|organelle inner membrane	exo-alpha-sialidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)										0.333333	13.169372	13.538696	5	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242757727	242757727	10743	2	C	A	A	A	338	26	NEU4	2	2
C2orf85	285093	broad.mit.edu	37	2	242814448	242814448	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242814448C>A	uc010fzu.1	+	c.741C>A	c.(739-741)TTC>TTA	p.F247L		NM_173821	NP_776182	Q14D33	CB085_HUMAN	hypothetical protein LOC285093	247						integral to membrane				ovary(1)	1														0.155556	9.99264	15.097643	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242814448	242814448	2292	2	C	A	A	A	389	30	C2orf85	2	2
ASXL2	55252	broad.mit.edu	37	2	25967101	25967101	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:25967101C>T	uc002rgs.2	-	c.2105G>A	c.(2104-2106)GGA>GAA	p.G702E	ASXL2_uc002rgt.1_Missense_Mutation_p.G442E	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	702	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.068063	-8.981603	27.895107	13	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25967101	25967101	1086	2	C	T	T	T	390	30	ASXL2	2	2
RASGRP3	25780	broad.mit.edu	37	2	33747045	33747045	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:33747045G>A	uc002rox.2	+	c.392G>A	c.(391-393)AGA>AAA	p.R131K	RASGRP3_uc010ync.1_Missense_Mutation_p.R131K|RASGRP3_uc002roy.2_Missense_Mutation_p.R131K	NM_170672	NP_733772	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and	131					MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|pancreas(1)	3	all_hematologic(175;0.115)													0.107914	14.8151	36.012068	15	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33747045	33747045	13537	2	G	A	A	A	429	33	RASGRP3	2	2
LRPPRC	10128	broad.mit.edu	37	2	44204192	44204192	+	Splice_Site_SNP	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44204192C>T	uc002rtr.2	-	c.592_splice	c.e5-1	p.V198_splice	LRPPRC_uc010yob.1_Splice_Site_SNP_p.V98_splice|LRPPRC_uc010faw.1_Splice_Site_SNP_p.V172_splice	NM_133259	NP_573566			leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)	2		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)												0.113636	6.240776	12.721546	5	39	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	44204192	44204192	9338	2	C	T	T	T	312	24	LRPPRC	5	2
AFTPH	54812	broad.mit.edu	37	2	64779295	64779295	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:64779295G>T	uc002sdc.2	+	c.687G>T	c.(685-687)GAG>GAT	p.E229D	AFTPH_uc002scz.2_Missense_Mutation_p.E229D|AFTPH_uc002sda.2_Missense_Mutation_p.E229D|AFTPH_uc002sdb.2_Missense_Mutation_p.E229D	NM_203437	NP_982261	Q6ULP2	AFTIN_HUMAN	aftiphilin protein isoform a	229					protein transport	AP-1 adaptor complex|cytosol|nucleus	clathrin binding			ovary(2)	2														0.227273	47.251023	53.261006	20	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64779295	64779295	365	2	G	T	T	T	451	35	AFTPH	2	2
MOGS	7841	broad.mit.edu	37	2	74688860	74688860	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74688860C>T	uc010ffj.2	-	c.2056G>A	c.(2056-2058)GTA>ATA	p.V686I	MOGS_uc010ffh.2_Missense_Mutation_p.V411I|MOGS_uc010yrt.1_Missense_Mutation_p.V567I|MOGS_uc010ffi.2_Missense_Mutation_p.V580I	NM_006302	NP_006293	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase isoform 1	686	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|membrane fraction	mannosyl-oligosaccharide glucosidase activity				0														0.108844	12.083717	34.382232	16	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74688860	74688860	10088	2	C	T	T	T	221	17	MOGS	2	2
LRRTM1	347730	broad.mit.edu	37	2	80530299	80530299	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:80530299G>T	uc002sok.1	-	c.646C>A	c.(646-648)CTC>ATC	p.L216I	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	216	LRR 6.|Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)	3														0.158974	49.182388	70.818564	31	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80530299	80530299	9415	2	G	T	T	T	455	35	LRRTM1	2	2
ATP2B2	491	broad.mit.edu	37	3	10381973	10381973	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10381973A>T	uc003bvt.2	-	c.3190T>A	c.(3190-3192)TGG>AGG	p.W1064R	ATP2B2_uc003bvv.2_Missense_Mutation_p.W1019R|ATP2B2_uc003bvw.2_Missense_Mutation_p.W1019R|ATP2B2_uc010hdo.2_Missense_Mutation_p.W769R	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	1064	Helical; (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|central_nervous_system(1)	4						Ovarian(125;1619 1709 15675 19819 38835)								0.195876	39.832525	48.252063	19	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10381973	10381973	1159	3	A	T	T	T	78	6	ATP2B2	3	3
CCDC80	151887	broad.mit.edu	37	3	112357838	112357838	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112357838G>T	uc003dzf.2	-	c.915C>A	c.(913-915)AGC>AGA	p.S305R	CCDC80_uc011bhv.1_Missense_Mutation_p.S305R|CCDC80_uc003dzg.2_Missense_Mutation_p.S305R|CCDC80_uc003dzh.1_Missense_Mutation_p.S305R	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	305										ovary(2)	2														0.204545	54.539765	65.170637	27	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112357838	112357838	2978	3	G	T	T	T	542	42	CCDC80	2	2
DRD3	1814	broad.mit.edu	37	3	113890615	113890615	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113890615G>T	uc003ebd.2	-	c.225C>A	c.(223-225)GAC>GAA	p.D75E	DRD3_uc010hqn.1_Missense_Mutation_p.D75E|DRD3_uc003ebb.1_Missense_Mutation_p.D75E|DRD3_uc003ebc.1_Missense_Mutation_p.D75E	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	75	Helical; Name=2.				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)									0.094828	5.038833	24.162804	11	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113890615	113890615	4942	3	G	T	T	T	464	36	DRD3	2	2
ZNF80	7634	broad.mit.edu	37	3	113955452	113955452	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113955452C>T	uc010hqo.2	-	c.470G>A	c.(469-471)GGA>GAA	p.G157E	ZNF80_uc003ebf.2_Non-coding_Transcript	NM_007136	NP_009067	P51504	ZNF80_HUMAN	zinc finger protein 80	157					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(201;0.0233)|all_neural(597;0.0837)				GBM(23;986 1114 21716)								0.084615	1.818034	24.589005	11	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113955452	113955452	18766	3	C	T	T	T	390	30	ZNF80	2	2
ARHGAP31	57514	broad.mit.edu	37	3	119133448	119133448	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:119133448A>T	uc003ecj.3	+	c.2672A>T	c.(2671-2673)GAT>GTT	p.D891V		NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein	891					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						Pancreas(7;176 297 5394 51128 51241)								0.173333	49.79127	64.881311	26	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119133448	119133448	892	3	A	T	T	T	156	12	ARHGAP31	3	3
MED12L	116931	broad.mit.edu	37	3	150881712	150881712	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:150881712G>T	uc003eyp.2	+	c.1140G>T	c.(1138-1140)GTG>GTT	p.V380V	MED12L_uc011bnz.1_Intron|MED12L_uc003eyn.2_Silent_p.V380V|MED12L_uc003eyo.2_Silent_p.V380V	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	380					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	RNA polymerase II transcription mediator activity			ovary(4)|large_intestine(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)							59				0.077586	0.076577	21.254423	9	107	KEEP	---	---	---	---	capture		Silent	SNP	150881712	150881712	9818	3	G	T	T	T	613	48	MED12L	2	2
PLCH1	23007	broad.mit.edu	37	3	155200774	155200774	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:155200774T>A	uc011bok.1	-	c.3065A>T	c.(3064-3066)AAC>ATC	p.N1022I	PLCH1_uc011boj.1_3'UTR|PLCH1_uc011bol.1_Missense_Mutation_p.N984I	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	1022					lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)											0.070312	-6.72759	17.667094	9	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155200774	155200774	12463	3	T	A	A	A	780	60	PLCH1	3	3
ALG3	10195	broad.mit.edu	37	3	183961588	183961588	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183961588C>A	uc003fne.2	-	c.923G>T	c.(922-924)AGG>ATG	p.R308M	ALG3_uc011brc.1_Missense_Mutation_p.R273M|ALG3_uc011brd.1_Missense_Mutation_p.R252M|ALG3_uc011bre.1_Missense_Mutation_p.R260M|ALG3_uc003fnf.1_Missense_Mutation_p.R268M	NM_005787	NP_005778	Q92685	ALG3_HUMAN	alpha-1,3-mannosyltransferase ALG3 isoform a	308	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity				0	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)											0.072727	-2.134192	8.188537	4	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183961588	183961588	523	3	C	A	A	A	312	24	ALG3	2	2
ATP13A4	84239	broad.mit.edu	37	3	193132540	193132540	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:193132540C>A	uc003ftd.2	-	c.2843_splice	c.e26-1	p.M948_splice	ATP13A4_uc010hzi.2_Splice_Site_SNP	NM_032279	NP_115655			ATPase type 13A4						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)										0.105882	7.005505	20.131021	9	76	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	193132540	193132540	1145	3	C	A	A	A	260	20	ATP13A4	5	2
KCNH8	131096	broad.mit.edu	37	3	19322780	19322780	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:19322780C>A	uc003cbk.1	+	c.401C>A	c.(400-402)ACA>AAA	p.T134K	KCNH8_uc011awe.1_Missense_Mutation_p.T134K|KCNH8_uc010hex.1_5'UTR	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	134	PAC.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity			ovary(1)	1						NSCLC(124;1625 1765 8018 24930 42026)								0.086957	0.489623	12.423241	6	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19322780	19322780	8343	3	C	A	A	A	221	17	KCNH8	2	2
CPN2	1370	broad.mit.edu	37	3	194062704	194062704	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:194062704A>T	uc003fts.2	-	c.728T>A	c.(727-729)CTA>CAA	p.L243Q		NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	243	LRR 7.				protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)										0.106383	4.545727	11.7717	5	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	194062704	194062704	3948	3	A	T	T	T	195	15	CPN2	3	3
SGOL1	151648	broad.mit.edu	37	3	20216127	20216127	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:20216127T>C	uc003cbs.2	-	c.896A>G	c.(895-897)AAC>AGC	p.N299S	SGOL1_uc003cbr.2_Intron|SGOL1_uc010hfa.2_Intron|SGOL1_uc003cbt.2_Intron|SGOL1_uc003cbu.2_Missense_Mutation_p.N299S|SGOL1_uc003cbv.2_Intron|SGOL1_uc003cbw.2_Intron|SGOL1_uc003cbx.2_Intron|SGOL1_uc003cby.2_Intron|SGOL1_uc003cbz.2_Missense_Mutation_p.N299S|SGOL1_uc003cca.2_Missense_Mutation_p.N299S|SGOL1_uc003ccb.2_Intron|SGOL1_uc003ccc.2_Intron	NM_001012410	NP_001012410	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 isoform A2	299	Potential.				attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding				0														0.098361	7.906054	17.747839	6	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20216127	20216127	14707	3	T	C	C	C	780	60	SGOL1	4	4
IL5RA	3568	broad.mit.edu	37	3	3136995	3136995	+	Silent	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:3136995A>G	uc011ask.1	-	c.843T>C	c.(841-843)AAT>AAC	p.N281N	IL5RA_uc010hbq.2_Intron|IL5RA_uc010hbr.2_Intron|IL5RA_uc010hbs.2_Silent_p.N281N|IL5RA_uc011asl.1_Silent_p.N281N|IL5RA_uc011asm.1_Silent_p.N281N|IL5RA_uc010hbt.2_Silent_p.N281N|IL5RA_uc011asn.1_Silent_p.N281N|IL5RA_uc010hbu.2_Silent_p.N281N|IL5RA_uc010hbp.2_5'Flank	NM_000564	NP_000555	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha isoform 1	281	Extracellular (Potential).				cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		GBM(169;430 2801 24955 28528)								0.163265	15.769317	21.048831	8	41	KEEP	---	---	---	---	capture		Silent	SNP	3136995	3136995	8001	3	A	G	G	G	102	8	IL5RA	4	4
DCLK3	85443	broad.mit.edu	37	3	36779774	36779774	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36779774C>T	uc003cgi.2	-	c.377G>A	c.(376-378)GGG>GAG	p.G126E		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	126					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|ovary(1)|breast(1)|kidney(1)	8									p.G126E(JHUEM2-Tumor)	128				0.107383	33.6063	79.155255	32	266	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36779774	36779774	4464	3	C	T	T	T	286	22	DCLK3	2	2
TDGF1	6997	broad.mit.edu	37	3	46621261	46621261	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:46621261G>T	uc003cpv.2	+	c.256G>T	c.(256-258)GGG>TGG	p.G86W	LRRC2_uc003cpu.3_Intron	NM_003212	NP_003203	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	86	EGF-like.				activation of MAPK activity|anterior/posterior axis specification, embryo|mammary gland development|morphogenesis of a branching structure|negative regulation of apoptosis|peptidyl-serine phosphorylation|positive regulation of cell migration|positive regulation of peptidyl-tyrosine phosphorylation	anchored to membrane|cell surface|extrinsic to plasma membrane	growth factor activity				0				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)										0.117391	31.017465	64.075956	27	203	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46621261	46621261	16252	3	G	T	T	T	611	47	TDGF1	2	2
WDR6	11180	broad.mit.edu	37	3	49052329	49052329	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49052329C>T	uc003cvj.2	+	c.3064C>T	c.(3064-3066)CGT>TGT	p.R1022C	WDR6_uc011bby.1_Missense_Mutation_p.R470C|WDR6_uc010hkn.2_Missense_Mutation_p.R966C|WDR6_uc011bbz.1_Missense_Mutation_p.R941C	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	992	WD 15.				cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)										0.12987	10.697421	20.969399	10	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49052329	49052329	17883	3	C	T	T	T	299	23	WDR6	1	1
CADPS	8618	broad.mit.edu	37	3	62478119	62478119	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:62478119G>T	uc003dll.2	-	c.2730C>A	c.(2728-2730)GCC>GCA	p.A910A	CADPS_uc003dlk.1_Silent_p.A407A|CADPS_uc003dlm.2_Silent_p.A920A|CADPS_uc003dln.2_Silent_p.A880A	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	910	Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)										0.04	-82.678116	37.115023	21	504	KEEP	---	---	---	---	capture		Silent	SNP	62478119	62478119	2686	3	G	T	T	T	444	35	CADPS	2	2
SLC25A26	115286	broad.mit.edu	37	3	66413339	66413339	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:66413339G>A	uc011bfq.1	+	c.554G>A	c.(553-555)TGT>TAT	p.C185Y	SLC25A26_uc011bfs.1_Missense_Mutation_p.C97Y|SLC25A26_uc011bft.1_Non-coding_Transcript|SLC25A26_uc011bfr.1_Missense_Mutation_p.C185Y|SLC25A26_uc003dmt.2_Missense_Mutation_p.C97Y	NM_173471	NP_775742	Q70HW3	SAMC_HUMAN	solute carrier family 25, member 26 isoform a	185	Helical; Name=5; (Potential).|Solcar 3.					integral to membrane|mitochondrial inner membrane|nucleus	S-adenosylmethionine transmembrane transporter activity			pancreas(1)	1		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)										0.227273	11.062066	12.565293	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66413339	66413339	14986	3	G	A	A	A	624	48	SLC25A26	2	2
CNTN3	5067	broad.mit.edu	37	3	74315728	74315728	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:74315728G>T	uc003dpm.1	-	c.2890C>A	c.(2890-2892)CTG>ATG	p.L964M		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	964	Fibronectin type-III 4.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)	4		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)										0.095694	8.810073	43.173342	20	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74315728	74315728	3780	3	G	T	T	T	438	34	CNTN3	2	2
LMCD1	29995	broad.mit.edu	37	3	8590464	8590464	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:8590464G>A	uc003bqq.2	+	c.598G>A	c.(598-600)GCC>ACC	p.A200T	LMCD1_uc011atd.1_Missense_Mutation_p.A127T|LMCD1_uc011ate.1_Missense_Mutation_p.A88T|LMCD1_uc011atf.1_Missense_Mutation_p.A127T	NM_014583	NP_055398	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	200	PET.				positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(96;0.124)										0.153333	32.451051	49.685775	23	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8590464	8590464	9173	3	G	A	A	A	546	42	LMCD1	2	2
PROS1	5627	broad.mit.edu	37	3	93605343	93605343	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:93605343G>A	uc003drb.3	-	c.1160C>T	c.(1159-1161)TCT>TTT	p.S387F	PROS1_uc010hoo.2_Missense_Mutation_p.S256F|PROS1_uc003dqz.3_Missense_Mutation_p.S256F	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	387	Laminin G-like 1.				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)									0.169492	58.045015	76.342305	30	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93605343	93605343	13001	3	G	A	A	A	429	33	PROS1	2	2
OGG1	4968	broad.mit.edu	37	3	9792684	9792684	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:9792684A>G	uc003bsm.2	+	c.193A>G	c.(193-195)ACA>GCA	p.T65A	OGG1_uc003bsh.2_Missense_Mutation_p.T65A|OGG1_uc003bsi.2_Missense_Mutation_p.T65A|OGG1_uc003bsj.2_Missense_Mutation_p.T65A|OGG1_uc003bsk.2_Missense_Mutation_p.T65A|OGG1_uc003bsl.2_Missense_Mutation_p.T65A|OGG1_uc003bsn.2_Missense_Mutation_p.T65A|OGG1_uc003bso.2_Missense_Mutation_p.T65A|OGG1_uc003bsp.1_5'Flank|OGG1_uc010hcm.1_5'Flank|OGG1_uc003bsq.1_5'Flank|OGG1_uc003bsr.1_5'Flank	NM_016821	NP_058214	O15527	OGG1_HUMAN	8-oxoguanine DNA-glycosylase 1 isoform 2a	65					depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)									40				0.095238	2.971194	9.875306	4	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9792684	9792684	11250	3	A	G	G	G	130	10	OGG1	4	4
AIMP1	9255	broad.mit.edu	37	4	107249400	107249400	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:107249400G>C	uc003hyh.2	+	c.463G>C	c.(463-465)GGA>CGA	p.G155R	AIMP1_uc011cfg.1_Missense_Mutation_p.G131R|AIMP1_uc003hyg.2_Missense_Mutation_p.G131R	NM_001142416	NP_001135888	Q12904	AIMP1_HUMAN	small inducible cytokine subfamily E, member 1	131	Interaction with HSP90B1 (By similarity).|Required for endothelial cell migration.				angiogenesis|apoptosis|cell adhesion|cell-cell signaling|chemotaxis|glucose metabolic process|inflammatory response|leukocyte migration|negative regulation of endothelial cell proliferation|signal transduction|tRNA aminoacylation for protein translation	aminoacyl-tRNA synthetase multienzyme complex|cytosol|endoplasmic reticulum|extracellular space|Golgi apparatus|nucleus|transport vesicle	cell surface binding|cytokine activity|protein homodimerization activity|tRNA binding				0														0.181818	8.385758	10.478917	4	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107249400	107249400	436	4	G	C	C	C	455	35	AIMP1	3	3
RRH	10692	broad.mit.edu	37	4	110763780	110763780	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:110763780C>A	uc003hzv.2	+	c.876C>A	c.(874-876)TGC>TGA	p.C292*		NM_006583	NP_006574	O14718	OPSX_HUMAN	peropsin	292	Helical; Name=7; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)										0.061404	-8.769477	14.124634	7	107	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	110763780	110763780	14160	4	C	A	A	A	324	25	RRH	5	2
C4orf21	55345	broad.mit.edu	37	4	113540185	113540185	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:113540185A>T	uc003iau.2	-	c.1013T>A	c.(1012-1014)ATA>AAA	p.I338K	C4orf21_uc003iaw.2_Missense_Mutation_p.I338K	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)										0.090226	6.409277	28.928698	12	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113540185	113540185	2349	4	A	T	T	T	208	16	C4orf21	3	3
ANK2	287	broad.mit.edu	37	4	114278877	114278877	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114278877A>G	uc003ibe.3	+	c.9103A>G	c.(9103-9105)ATC>GTC	p.I3035V	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Missense_Mutation_p.I337V|ANK2_uc011cgb.1_Missense_Mutation_p.I3050V	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3002					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.131148	40.979978	65.177246	24	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114278877	114278877	624	4	A	G	G	G	104	8	ANK2	4	4
ANK2	287	broad.mit.edu	37	4	114279344	114279344	+	Silent	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114279344A>T	uc003ibe.3	+	c.9570A>T	c.(9568-9570)GTA>GTT	p.V3190V	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Silent_p.V492V|ANK2_uc011cgb.1_Silent_p.V3205V	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3157					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.117647	8.952104	18.724667	8	60	KEEP	---	---	---	---	capture		Silent	SNP	114279344	114279344	624	4	A	T	T	T	184	15	ANK2	3	3
FAT4	79633	broad.mit.edu	37	4	126411519	126411519	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126411519C>A	uc003ifj.3	+	c.13542C>A	c.(13540-13542)ACC>ACA	p.T4514T	FAT4_uc011cgp.1_Silent_p.T2755T|FAT4_uc003ifi.1_Silent_p.T1991T	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4514	Helical; (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.168067	39.72801	52.146418	20	99	KEEP	---	---	---	---	capture		Silent	SNP	126411519	126411519	5928	4	C	A	A	A	288	23	FAT4	1	1
CLGN	1047	broad.mit.edu	37	4	141331707	141331707	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:141331707C>A	uc011chi.1	-	c.218G>T	c.(217-219)GGA>GTA	p.G73V	CLGN_uc003iii.2_Missense_Mutation_p.G73V	NM_001130675	NP_001124147	O14967	CLGN_HUMAN	calmegin precursor	73	Lumenal (Potential).				protein folding	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|unfolded protein binding			ovary(2)	2	all_hematologic(180;0.162)													0.115385	3.205133	6.99466	3	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141331707	141331707	3662	4	C	A	A	A	286	22	CLGN	2	2
GALNTL6	442117	broad.mit.edu	37	4	173269702	173269702	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:173269702C>T	uc003isv.2	+	c.415C>T	c.(415-417)CTG>TTG	p.L139L		NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6	139	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)	3														0.15873	36.411389	50.404928	20	106	KEEP	---	---	---	---	capture		Silent	SNP	173269702	173269702	6489	4	C	T	T	T	363	28	GALNTL6	2	2
USP46	64854	broad.mit.edu	37	4	53468216	53468216	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:53468216T>A	uc003gzn.2	-	c.727A>T	c.(727-729)AGG>TGG	p.R243W	USP46_uc003gzm.3_Missense_Mutation_p.R236W|USP46_uc011bzr.1_Missense_Mutation_p.R220W|USP46_uc011bzs.1_Missense_Mutation_p.R127W	NM_022832	NP_073743	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46 isoform 1	243					behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0295)											0.108696	5.881968	19.848826	10	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53468216	53468216	17641	4	T	A	A	A	700	54	USP46	3	3
KDR	3791	broad.mit.edu	37	4	55968660	55968660	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55968660G>A	uc003has.2	-	c.2003C>T	c.(2002-2004)ACG>ATG	p.T668M	KDR_uc003hat.1_Missense_Mutation_p.T668M	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	668	Ig-like C2-type 7.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|protein phosphorylation|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(9)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|ovary(2)|kidney(1)	22	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)					1022	TSP Lung(20;0.16)			0.071429	-5.765066	12.83067	7	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55968660	55968660	8445	4	G	A	A	A	520	40	KDR	1	1
ZNF595	152687	broad.mit.edu	37	4	60022	60022	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:60022C>G	uc003fzv.1	+	c.202C>G	c.(202-204)CAT>GAT	p.H68D	ZNF595_uc003fzu.1_Non-coding_Transcript|ZNF718_uc003fzt.3_Missense_Mutation_p.H68D|ZNF595_uc010iay.1_Non-coding_Transcript|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595	68					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)										0.042373	-13.931682	12.599091	5	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60022	60022	18620	4	C	G	G	G	221	17	ZNF595	3	3
UGT2B4	7363	broad.mit.edu	37	4	70361472	70361472	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70361472C>A	uc003hek.3	-	c.108G>T	c.(106-108)TGG>TGT	p.W36C	UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_Missense_Mutation_p.W36C	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor	36					estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0														0.064356	-17.60513	22.342481	13	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70361472	70361472	17519	4	C	A	A	A	390	30	UGT2B4	2	2
LIN54	132660	broad.mit.edu	37	4	83905676	83905676	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:83905676C>A	uc003hnx.3	-	c.322G>T	c.(322-324)GTG>TTG	p.V108L	LIN54_uc003hnz.3_Intron|LIN54_uc003hny.3_Intron|LIN54_uc010ijt.2_Missense_Mutation_p.V108L|LIN54_uc010iju.2_5'UTR|LIN54_uc010ijv.2_Intron	NM_194282	NP_919258	Q6MZP7	LIN54_HUMAN	lin-54 homolog isoform a	108					cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)												0.071429	-5.419517	31.698947	14	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83905676	83905676	9136	4	C	A	A	A	221	17	LIN54	2	2
DSPP	1834	broad.mit.edu	37	4	88535090	88535090	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:88535090C>A	uc003hqu.2	+	c.1276C>A	c.(1276-1278)CCT>ACT	p.P426T		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	426					biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)										0.225806	51.32746	57.748102	21	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88535090	88535090	4966	4	C	A	A	A	234	18	DSPP	2	2
HERC6	55008	broad.mit.edu	37	4	89363544	89363544	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:89363544G>A	uc011cdi.1	+	c.3001G>A	c.(3001-3003)GAG>AAG	p.E1001K	HERC6_uc011cdj.1_Missense_Mutation_p.E965K|HERC6_uc011cdk.1_Non-coding_Transcript|HERC6_uc011cdl.1_Non-coding_Transcript	NM_017912	NP_060382	Q8IVU3	HERC6_HUMAN	hect domain and RLD 6 isoform 1	1001	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity			lung(1)|kidney(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)										0.129032	4.776406	8.933544	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89363544	89363544	7345	4	G	A	A	A	533	41	HERC6	2	2
C4orf37	285555	broad.mit.edu	37	4	98893504	98893504	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:98893504C>G	uc003htt.1	-	c.860G>C	c.(859-861)GGT>GCT	p.G287A		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	287											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)										0.134615	14.387357	21.118917	7	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98893504	98893504	2362	4	C	G	G	G	234	18	C4orf37	3	3
TSLP	85480	broad.mit.edu	37	5	110407675	110407675	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:110407675C>A	uc003kpb.2	+	c.87C>A	c.(85-87)TAC>TAA	p.Y29*	TSLP_uc003kpa.2_Non-coding_Transcript|TSLP_uc010jbt.1_5'Flank	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1	29						extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)										0.115385	27.847325	54.361608	21	161	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	110407675	110407675	17179	5	C	A	A	A	246	19	TSLP	5	1
AFF4	27125	broad.mit.edu	37	5	132232314	132232314	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:132232314C>T	uc003kyd.2	-	c.2008G>A	c.(2008-2010)GAG>AAG	p.E670K	AFF4_uc011cxk.1_Missense_Mutation_p.E348K|AFF4_uc003kye.1_Missense_Mutation_p.E670K	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	670					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			kidney(2)|ovary(1)|skin(1)	4		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			Ovarian(126;889 1733 2942 10745 11605)			p.E670K(HEC251-Tumor)	374				0.102564	9.208947	27.631778	12	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132232314	132232314	360	5	C	T	T	T	403	31	AFF4	1	1
TCERG1	10915	broad.mit.edu	37	5	145838723	145838723	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:145838723G>T	uc003lob.2	+	c.715G>T	c.(715-717)GCC>TCC	p.A239S	TCERG1_uc003loc.2_Missense_Mutation_p.A239S|TCERG1_uc011dbt.1_Missense_Mutation_p.A239S	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1	239	Potential.|Ala/Gln-rich.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|RNA polymerase II transcription factor activity|transcription coactivator activity				0		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.226415	26.169297	29.814337	12	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145838723	145838723	16211	5	G	T	T	T	546	42	TCERG1	2	2
SLIT3	6586	broad.mit.edu	37	5	168180932	168180932	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:168180932G>A	uc010jjg.2	-	c.1766C>T	c.(1765-1767)ACA>ATA	p.T589I	SLIT3_uc003mab.2_Missense_Mutation_p.T589I	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	589	LRR 14.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			Ovarian(29;311 847 10864 17279 24903)								0.244444	23.899106	26.580058	11	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168180932	168180932	15239	5	G	A	A	A	624	48	SLIT3	2	2
FOXI1	2299	broad.mit.edu	37	5	169533452	169533452	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169533452A>T	uc003mai.3	+	c.491A>T	c.(490-492)AAG>ATG	p.K164M	FOXI1_uc003maj.3_Missense_Mutation_p.K164M	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	164	Fork-head.				epidermal cell fate specification|negative regulation of gene-specific transcription from RNA polymerase II promoter|otic placode formation|pattern specification process|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.2	12.736869	15.245294	6	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169533452	169533452	6254	5	A	T	T	T	39	3	FOXI1	3	3
NSD1	64324	broad.mit.edu	37	5	176721186	176721186	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176721186T>G	uc003mfr.3	+	c.6817T>G	c.(6817-6819)TGT>GGT	p.C2273G	NSD1_uc003mft.3_Missense_Mutation_p.C2004G|NSD1_uc011dfx.1_Missense_Mutation_p.C1921G	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2273	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)						492				0.116183	41.038767	75.978573	28	213	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176721186	176721186	11074	5	T	G	G	G	819	63	NSD1	4	4
SCGB3A1	92304	broad.mit.edu	37	5	180017711	180017711	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:180017711C>A	uc003mly.2	-	c.180G>T	c.(178-180)CTG>CTT	p.L60L		NM_052863	NP_443095	Q96QR1	SG3A1_HUMAN	secretoglobin, family 3A, member 1 precursor	60					negative regulation of cell growth|regulation of cell proliferation	extracellular space	cytokine activity				0	all_cancers(89;7.5e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00658)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.454545	15.073589	15.09341	5	6	KEEP	---	---	---	---	capture		Silent	SNP	180017711	180017711	14382	5	C	A	A	A	314	25	SCGB3A1	2	2
PRDM9	56979	broad.mit.edu	37	5	23527621	23527621	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:23527621G>T	uc003jgo.2	+	c.2424G>T	c.(2422-2424)GAG>GAT	p.E808D		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	808	C2H2-type 12.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.040441	-44.112713	17.911079	11	261	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23527621	23527621	12906	5	G	T	T	T	464	36	PRDM9	2	2
ADAMTS12	81792	broad.mit.edu	37	5	33662100	33662100	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33662100A>T	uc003jia.1	-	c.961T>A	c.(961-963)TTC>ATC	p.F321I	ADAMTS12_uc010iuq.1_Missense_Mutation_p.F321I	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	321	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.410853	154.248974	155.144976	53	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33662100	33662100	258	5	A	T	T	T	39	3	ADAMTS12	3	3
UTP15	84135	broad.mit.edu	37	5	72863231	72863231	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:72863231A>T	uc003kcw.1	+	c.62A>T	c.(61-63)CAA>CTA	p.Q21L	UTP15_uc011cso.1_Missense_Mutation_p.Q21L|UTP15_uc011csp.1_Intron|UTP15_uc010ize.1_Missense_Mutation_p.Q21L|ANKRA2_uc003kcu.1_5'Flank|ANKRA2_uc003kcv.2_5'Flank	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,	21					rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)										0.206186	43.348534	51.111045	20	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72863231	72863231	17662	5	A	T	T	T	65	5	UTP15	3	3
CRHBP	1393	broad.mit.edu	37	5	76249973	76249973	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:76249973C>A	uc003ker.2	+	c.295C>A	c.(295-297)CAG>AAG	p.Q99K	CRHBP_uc010izx.2_Missense_Mutation_p.Q99K	NM_001882	NP_001873	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	99					female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)										0.069767	-4.52448	11.925984	6	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76249973	76249973	4009	5	C	A	A	A	273	21	CRHBP	2	2
FASTKD3	79072	broad.mit.edu	37	5	7866922	7866922	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:7866922G>T	uc003jeb.2	-	c.1275C>A	c.(1273-1275)GCC>GCA	p.A425A	FASTKD3_uc011cmp.1_Silent_p.A127A|FASTKD3_uc003jec.2_Intron|MTRR_uc010itn.1_5'Flank|MTRR_uc003jee.3_5'Flank|MTRR_uc003jed.2_5'Flank|MTRR_uc003jef.3_5'Flank|MTRR_uc003jeg.3_5'Flank|MTRR_uc010ito.2_5'Flank	NM_024091	NP_076996	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	425					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|breast(1)|pancreas(1)	4														0.073333	-4.601221	23.479857	11	139	KEEP	---	---	---	---	capture		Silent	SNP	7866922	7866922	5923	5	G	T	T	T	444	35	FASTKD3	2	2
CMYA5	202333	broad.mit.edu	37	5	79026350	79026350	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:79026350G>T	uc003kgc.2	+	c.1762G>T	c.(1762-1764)GTT>TTT	p.V588F		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	588	Glu-rich.					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)										0.150943	123.653026	173.121597	64	360	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79026350	79026350	3728	5	G	T	T	T	624	48	CMYA5	2	2
PCSK1	5122	broad.mit.edu	37	5	95761538	95761538	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:95761538G>A	uc003kls.1	-	c.382C>T	c.(382-384)CAG>TAG	p.Q128*		NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	128	Catalytic.				cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.145833	10.289308	16.083039	7	41	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	95761538	95761538	12020	5	G	A	A	A	585	45	PCSK1	5	2
C6orf182	285753	broad.mit.edu	37	6	109468107	109468107	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:109468107C>A	uc010kdk.2	+	c.307C>A	c.(307-309)CTG>ATG	p.L103M	C6orf182_uc003psv.3_Missense_Mutation_p.L103M|C6orf182_uc003psw.3_Missense_Mutation_p.L103M|C6orf182_uc003psx.3_Missense_Mutation_p.L103M|C6orf182_uc010kdl.2_Missense_Mutation_p.L103M|C6orf182_uc003psy.3_Missense_Mutation_p.L103M	NM_001083535	NP_001077004	Q8IYX8	CE57L_HUMAN	hypothetical protein LOC285753	103	Potential.					microtubule|microtubule organizing center					0		all_cancers(87;4.45e-07)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(75;3.25e-08)|all_epithelial(87;0.000254)|Colorectal(196;0.0293)|all_lung(197;0.11)		BRCA - Breast invasive adenocarcinoma(108;0.00123)|Epithelial(106;0.0022)|all cancers(137;0.00405)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)										0.111111	2.503564	6.543016	3	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109468107	109468107	2451	6	C	A	A	A	415	32	C6orf182	2	2
TRDN	10345	broad.mit.edu	37	6	123892215	123892215	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:123892215C>T	uc003pzj.1	-	c.85G>A	c.(85-87)GGA>AGA	p.G29R	TRDN_uc003pzk.1_Missense_Mutation_p.G29R|TRDN_uc003pzl.1_Missense_Mutation_p.G29R|TRDN_uc010ken.2_Missense_Mutation_p.G29R|TRDN_uc010keo.1_Missense_Mutation_p.G29R	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	29	Cytoplasmic.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)										0.111111	8.448927	19.213576	8	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123892215	123892215	17012	6	C	T	T	T	299	23	TRDN	1	1
THBS2	7058	broad.mit.edu	37	6	169626329	169626329	+	Silent	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:169626329A>T	uc003qwt.2	-	c.2484T>A	c.(2482-2484)GGT>GGA	p.G828G		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	828	TSP type-3 5.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(4)	4		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		Esophageal Squamous(91;219 1934 18562 44706)								0.170213	31.847383	41.514928	16	78	KEEP	---	---	---	---	capture		Silent	SNP	169626329	169626329	16382	6	A	T	T	T	67	6	THBS2	3	3
HDGFL1	154150	broad.mit.edu	37	6	22569972	22569972	+	Silent	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:22569972G>C	uc003nds.2	+	c.168G>C	c.(166-168)CTG>CTC	p.L56L		NM_138574	NP_612641	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	56	PWWP.										0	Ovarian(93;0.163)													0.121212	14.850999	24.131928	8	58	KEEP	---	---	---	---	capture		Silent	SNP	22569972	22569972	7302	6	G	C	C	C	613	48	HDGFL1	3	3
SLC17A1	6568	broad.mit.edu	37	6	25799037	25799037	+	Silent	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:25799037T>C	uc003nfh.3	-	c.1380A>G	c.(1378-1380)AAA>AAG	p.K460K	SLC17A1_uc011djy.1_Non-coding_Transcript|SLC17A1_uc010jqb.1_Silent_p.K458K|SLC17A1_uc010jqc.1_Silent_p.K404K	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	460					sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4														0.120968	27.934635	45.395567	15	109	KEEP	---	---	---	---	capture		Silent	SNP	25799037	25799037	14912	6	T	C	C	C	725	56	SLC17A1	4	4
NKAPL	222698	broad.mit.edu	37	6	28227314	28227314	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28227314G>T	uc003nkt.2	+	c.165G>T	c.(163-165)TGG>TGT	p.W55C	ZKSCAN4_uc011dlb.1_5'Flank	NM_001007531	NP_001007532	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	55										ovary(1)	1														0.120301	16.50827	35.316971	16	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28227314	28227314	10841	6	G	T	T	T	533	41	NKAPL	2	2
ZNF323	64288	broad.mit.edu	37	6	28294239	28294239	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28294239C>A	uc003nla.2	-	c.925G>T	c.(925-927)GGC>TGC	p.G309C	ZNF323_uc003nld.2_Missense_Mutation_p.G309C|ZNF323_uc010jra.2_Missense_Mutation_p.G309C|ZNF323_uc003nlb.2_Missense_Mutation_p.G150C|ZNF323_uc010jrb.2_Missense_Mutation_p.G150C|ZNF323_uc003nlc.2_Missense_Mutation_p.G309C	NM_001135216	NP_001128688	Q96LW9	ZN323_HUMAN	zinc finger protein 323	309	C2H2-type 3.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						Colon(115;1052 1587 16954 47314 53012)								0.152727	72.461636	104.206422	42	233	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28294239	28294239	18435	6	C	A	A	A	273	21	ZNF323	2	2
OR2J3	442186	broad.mit.edu	37	6	29079836	29079836	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29079836C>A	uc011dll.1	+	c.169C>A	c.(169-171)CAT>AAT	p.H57N		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	57	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.152355	92.942881	134.77664	55	306	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29079836	29079836	11410	6	C	A	A	A	273	21	OR2J3	2	2
ZFP57	346171	broad.mit.edu	37	6	29640787	29640787	+	Silent	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29640787C>T	uc011dlw.1	-	c.1101G>A	c.(1099-1101)CAG>CAA	p.Q367Q	ZFP57_uc003nnl.3_Silent_p.Q347Q	NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog	283					DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)	3														0.167587	184.731123	241.659449	91	452	KEEP	---	---	---	---	capture		Silent	SNP	29640787	29640787	18239	6	C	T	T	T	311	24	ZFP57	2	2
HSPA1L	3305	broad.mit.edu	37	6	31777930	31777930	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31777930G>A	uc003nxh.2	-	c.1820C>T	c.(1819-1821)CCT>CTT	p.P607L	HSPA1L_uc010jte.2_Missense_Mutation_p.P607L	NM_005527	NP_005518	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	607					response to unfolded protein		ATP binding			ovary(3)|kidney(1)|pleura(1)	5										2				0.052632	-13.825635	18.312335	8	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31777930	31777930	7709	6	G	A	A	A	455	35	HSPA1L	2	2
TTBK1	84630	broad.mit.edu	37	6	43221047	43221047	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43221047G>T	uc003ouq.1	+	c.275G>T	c.(274-276)AGG>ATG	p.R92M		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	92	Protein kinase.				protein phosphorylation	cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)							85				0.045455	-27.402246	16.338011	9	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43221047	43221047	17230	6	G	T	T	T	455	35	TTBK1	2	2
TDRD6	221400	broad.mit.edu	37	6	46658183	46658183	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:46658183C>T	uc003oyj.2	+	c.2318C>T	c.(2317-2319)ACA>ATA	p.T773I	TDRD6_uc010jze.2_Missense_Mutation_p.T767I	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	773					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)	5			Lung(136;0.192)											0.51145	195.627816	195.643018	67	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46658183	46658183	16261	6	C	T	T	T	221	17	TDRD6	2	2
PGK2	5232	broad.mit.edu	37	6	49754747	49754747	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49754747C>T	uc003ozu.2	-	c.154G>A	c.(154-156)GAC>AAC	p.D52N		NM_138733	NP_620061	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	52					glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1	Lung NSC(77;0.0402)													0.294643	178.855734	187.312112	66	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49754747	49754747	12214	6	C	T	T	T	390	30	PGK2	2	2
GFRAL	389400	broad.mit.edu	37	6	55214930	55214930	+	Silent	SNP	A	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55214930A>C	uc003pcm.1	+	c.357A>C	c.(355-357)ACA>ACC	p.T119T		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	119	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.206897	16.936306	19.243086	6	23	KEEP	---	---	---	---	capture		Silent	SNP	55214930	55214930	6619	6	A	C	C	C	67	6	GFRAL	4	4
OOEP	441161	broad.mit.edu	37	6	74078997	74078997	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:74078997C>A	uc003pgu.3	-	c.302G>T	c.(301-303)CGT>CTT	p.R101L	OOEP_uc003pgv.3_Missense_Mutation_p.R46L	NM_001080507	NP_001073976	A6NGQ2	OOEP_HUMAN	oocyte expressed protein homolog	101	KH; atypical.					cytoplasm					0														0.139535	10.820702	16.217346	6	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74078997	74078997	11276	6	C	A	A	A	247	19	OOEP	1	1
MYL10	93408	broad.mit.edu	37	7	101265451	101265451	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:101265451C>A	uc003uyr.2	-	c.379G>T	c.(379-381)GAG>TAG	p.E127*		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	127						mitochondrion	calcium ion binding			ovary(1)|breast(1)	2						Esophageal Squamous(24;575 709 17516 40384 51639)								0.12987	11.594861	21.865362	10	67	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	101265451	101265451	10439	7	C	A	A	A	390	30	MYL10	5	2
PTPRZ1	5803	broad.mit.edu	37	7	121651440	121651440	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121651440C>A	uc003vjy.2	+	c.2340C>A	c.(2338-2340)ATC>ATA	p.I780I	PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	780	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9														0.056537	-29.514174	28.958614	16	267	KEEP	---	---	---	---	capture		Silent	SNP	121651440	121651440	13272	7	C	A	A	A	382	30	PTPRZ1	2	2
CLCN1	1180	broad.mit.edu	37	7	143013364	143013364	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143013364C>A	uc003wcr.1	+	c.59C>A	c.(58-60)CCC>CAC	p.P20H	CLCN1_uc011ktc.1_5'UTR	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	20	Cytoplasmic (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)|breast(1)|central_nervous_system(1)	3	Melanoma(164;0.205)													0.107296	18.89769	54.581609	25	208	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143013364	143013364	3598	7	C	A	A	A	286	22	CLCN1	2	2
ABCB8	11194	broad.mit.edu	37	7	150732736	150732736	+	Silent	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150732736G>C	uc003wil.3	+	c.885G>C	c.(883-885)ACG>ACC	p.T295T	ABCB8_uc003wii.2_Silent_p.T315T|ABCB8_uc003wij.3_Silent_p.T278T|ABCB8_uc010lpw.1_Silent_p.T97T|ABCB8_uc010lpx.2_Silent_p.T278T|ABCB8_uc011kvd.1_Silent_p.T190T|ABCB8_uc003wim.3_Silent_p.T73T|ABCB8_uc003wik.3_Silent_p.T278T	NM_007188	NP_009119	Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B, member 8	295	ABC transmembrane type-1.					ATP-binding cassette (ABC) transporter complex|integral to membrane|membrane fraction|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(2)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.096491	12.854113	31.443081	11	103	KEEP	---	---	---	---	capture		Silent	SNP	150732736	150732736	48	7	G	C	C	C	483	38	ABCB8	3	3
ABCF2	10061	broad.mit.edu	37	7	150915920	150915920	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150915920C>A	uc003wjo.1	-	c.1057G>T	c.(1057-1059)GCC>TCC	p.A353S	ABCF2_uc003wjp.2_Missense_Mutation_p.A353S	NM_005692	NP_005683	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	353						ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.160256	40.48215	57.625631	25	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150915920	150915920	67	7	C	A	A	A	338	26	ABCF2	2	2
HTR5A	3361	broad.mit.edu	37	7	154862977	154862977	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:154862977T>C	uc003wlu.1	+	c.368T>C	c.(367-369)CTT>CCT	p.L123P		NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	123	Helical; Name=3; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)										0.238095	29.030804	31.660752	10	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154862977	154862977	7750	7	T	C	C	C	728	56	HTR5A	4	4
PTPRN2	5799	broad.mit.edu	37	7	157929352	157929352	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:157929352G>T	uc011kwa.1	-	c.1237C>A	c.(1237-1239)CAA>AAA	p.Q413K	PTPRN2_uc003wno.2_Missense_Mutation_p.Q390K|PTPRN2_uc003wnp.2_Missense_Mutation_p.Q373K|PTPRN2_uc003wnq.2_Missense_Mutation_p.Q390K|PTPRN2_uc003wnr.2_Missense_Mutation_p.Q352K	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	390	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.173913	46.806488	60.66438	24	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157929352	157929352	13265	7	G	T	T	T	611	47	PTPRN2	2	2
CPVL	54504	broad.mit.edu	37	7	29160641	29160641	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:29160641C>A	uc003szv.2	-	c.37G>T	c.(37-39)GTC>TTC	p.V13F	CPVL_uc003szw.2_Missense_Mutation_p.V13F|CPVL_uc003szx.2_Missense_Mutation_p.V13F	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like	13					proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2														0.125	10.998212	21.988285	10	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29160641	29160641	3974	7	C	A	A	A	234	18	CPVL	2	2
AKAP9	10142	broad.mit.edu	37	7	91609624	91609624	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91609624A>T	uc003ulg.2	+	c.328A>T	c.(328-330)ACA>TCA	p.T110S	AKAP9_uc003uld.3_Missense_Mutation_p.T110S|AKAP9_uc003ule.2_Missense_Mutation_p.T122S|AKAP9_uc003ulf.2_Missense_Mutation_p.T110S	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	122					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)							807				0.067797	-2.945602	8.460662	4	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91609624	91609624	462	7	A	T	T	T	78	6	AKAP9	3	3
GATAD1	57798	broad.mit.edu	37	7	92080020	92080020	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92080020C>G	uc003ulx.1	+	c.381C>G	c.(379-381)ATC>ATG	p.I127M	GATAD1_uc011khq.1_Non-coding_Transcript	NM_021167	NP_066990	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	127					regulation of transcription, DNA-dependent		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)											0.119266	26.394592	41.903767	13	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92080020	92080020	6523	7	C	G	G	G	369	29	GATAD1	3	3
SAMD9L	219285	broad.mit.edu	37	7	92762064	92762064	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92762064C>A	uc003umh.1	-	c.3221G>T	c.(3220-3222)GGA>GTA	p.G1074V	SAMD9L_uc003umj.1_Missense_Mutation_p.G1074V|SAMD9L_uc003umi.1_Missense_Mutation_p.G1074V|SAMD9L_uc010lfb.1_Missense_Mutation_p.G1074V|SAMD9L_uc003umk.1_Missense_Mutation_p.G1074V|SAMD9L_uc010lfc.1_Missense_Mutation_p.G1074V|SAMD9L_uc010lfd.1_Missense_Mutation_p.G1074V|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1074										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)											0.145695	33.468313	51.684232	22	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92762064	92762064	14307	7	C	A	A	A	390	30	SAMD9L	2	2
GNG11	2791	broad.mit.edu	37	7	93555509	93555509	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:93555509G>T	uc003und.2	+	c.203G>T	c.(202-204)GGC>GTC	p.G68V		NM_004126	NP_004117	P61952	GBG11_HUMAN	guanine nucleotide binding protein gamma 11	68					cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway	heterotrimeric G-protein complex	GTPase activity|signal transducer activity			kidney(1)	1	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)											0.081818	0.204443	19.774606	9	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93555509	93555509	6793	7	G	T	T	T	546	42	GNG11	2	2
PPP1R9A	55607	broad.mit.edu	37	7	94791228	94791228	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:94791228G>C	uc010lfj.2	+	c.1699G>C	c.(1699-1701)GGT>CGT	p.G567R	PPP1R9A_uc003unp.2_Missense_Mutation_p.G567R|PPP1R9A_uc011kif.1_Missense_Mutation_p.G567R|PPP1R9A_uc003unq.2_Missense_Mutation_p.G567R|PPP1R9A_uc011kig.1_Missense_Mutation_p.G567R	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	567	PDZ.					cell junction|synapse|synaptosome	actin binding			ovary(2)|skin(1)	3	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)											0.131579	4.543213	9.570928	5	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94791228	94791228	12814	7	G	C	C	C	559	43	PPP1R9A	3	3
TRRAP	8295	broad.mit.edu	37	7	98495465	98495465	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:98495465G>C	uc003upp.2	+	c.609G>C	c.(607-609)GAG>GAC	p.E203D	TRRAP_uc011kis.1_Missense_Mutation_p.E203D|TRRAP_uc003upr.2_5'Flank	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	203					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)							1847				0.16092	65.683448	84.724898	28	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98495465	98495465	17152	7	G	C	C	C	438	34	TRRAP	3	3
CYP3A5	1577	broad.mit.edu	37	7	99262907	99262907	+	Silent	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99262907A>G	uc003urq.2	-	c.552T>C	c.(550-552)ATT>ATC	p.I184I	ZNF498_uc003urn.2_Intron|CYP3A5_uc003urp.2_Silent_p.I4I|CYP3A5_uc003urr.2_Silent_p.I71I|CYP3A5_uc011kiy.1_Silent_p.I174I|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron	NM_000777	NP_000768	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A,	184					alkaloid catabolic process|drug catabolic process|oxidative demethylation|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				Alfentanil(DB00802)|Clopidogrel(DB00758)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Indinavir(DB00224)|Irinotecan(DB00762)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Mephenytoin(DB00532)|Midazolam(DB00683)|Mifepristone(DB00834)|Phenytoin(DB00252)|Quinine(DB00468)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Troleandomycin(DB01361)|Verapamil(DB00661)|Vincristine(DB00541)									0.144828	46.184789	63.778718	21	124	KEEP	---	---	---	---	capture		Silent	SNP	99262907	99262907	4345	7	A	G	G	G	164	13	CYP3A5	4	4
RP1L1	94137	broad.mit.edu	37	8	10470413	10470413	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10470413C>A	uc003wtc.2	-	c.1195G>T	c.(1195-1197)GGG>TGG	p.G399W		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	399					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.097345	4.129429	22.527907	11	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10470413	10470413	14012	8	C	A	A	A	299	23	RP1L1	1	1
TRPS1	7227	broad.mit.edu	37	8	116616574	116616574	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:116616574C>A	uc003yny.2	-	c.1622G>T	c.(1621-1623)TGT>TTT	p.C541F	TRPS1_uc011lhy.1_Missense_Mutation_p.C532F|TRPS1_uc010mcy.2_Missense_Mutation_p.C528F|TRPS1_uc003ynz.2_Missense_Mutation_p.C528F	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	528					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)							312				0.084967	3.183086	29.898931	13	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116616574	116616574	17144	8	C	A	A	A	221	17	TRPS1	2	2
SNTB1	6641	broad.mit.edu	37	8	121706136	121706136	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:121706136C>A	uc010mdg.2	-	c.584G>T	c.(583-585)CGA>CTA	p.R195L	SNTB1_uc003ype.2_Missense_Mutation_p.R195L	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin	195	PH 1.|PDZ.				muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(3)	3	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)											0.126437	16.764188	28.619292	11	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121706136	121706136	15372	8	C	A	A	A	403	31	SNTB1	1	1
C8orf79	57604	broad.mit.edu	37	8	12878877	12878877	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:12878877C>A	uc010lsq.2	+	c.689C>A	c.(688-690)TCT>TAT	p.S230Y	C8orf79_uc011kxw.1_Intron|C8orf79_uc003wwj.3_Missense_Mutation_p.S143Y|C8orf79_uc010lsr.2_Missense_Mutation_p.S104Y	NM_020844	NP_065895	Q9P272	K1456_HUMAN	hypothetical protein LOC57604 isoform 1	230							methyltransferase activity				0														0.072464	-5.458428	20.50697	10	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12878877	12878877	2550	8	C	A	A	A	416	32	C8orf79	2	2
TG	7038	broad.mit.edu	37	8	133953768	133953768	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133953768C>A	uc003ytw.2	+	c.5214C>A	c.(5212-5214)GTC>GTA	p.V1738V	TG_uc010mdw.2_Silent_p.V497V|TG_uc011ljb.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1738	Type IIIB.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.141304	16.421118	27.839698	13	79	KEEP	---	---	---	---	capture		Silent	SNP	133953768	133953768	16341	8	C	A	A	A	379	30	TG	2	2
FAM135B	51059	broad.mit.edu	37	8	139180236	139180236	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139180236C>A	uc003yuy.2	-	c.1160G>T	c.(1159-1161)AGC>ATC	p.S387I	FAM135B_uc003yux.2_Missense_Mutation_p.S288I|FAM135B_uc003yuz.2_Non-coding_Transcript	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	387										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)											0.173913	57.272776	75.75907	32	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139180236	139180236	5646	8	C	A	A	A	364	28	FAM135B	2	2
SPATC1	375686	broad.mit.edu	37	8	145095635	145095635	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145095635T>A	uc011lkw.1	+	c.933T>A	c.(931-933)AGT>AGA	p.S311R	SPATC1_uc011lkx.1_Missense_Mutation_p.S311R	NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	311										ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)											0.176471	17.745406	22.775977	9	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145095635	145095635	15527	8	T	A	A	A	764	59	SPATC1	3	3
HEATR7A	727957	broad.mit.edu	37	8	145235188	145235188	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145235188G>T	uc003zbk.3	+	c.408G>T	c.(406-408)GGG>GGT	p.G136G	HEATR7A_uc003zbg.2_Silent_p.G136G|HEATR7A_uc003zbh.3_Silent_p.G136G|HEATR7A_uc003zbi.3_Silent_p.G136G|HEATR7A_uc011lla.1_Silent_p.G136G|HEATR7A_uc010mft.2_Silent_p.G136G	NM_032450	NP_115826	Q8NDA8	HTR7A_HUMAN	HEAT repeat containing 7A isoform 1	136							binding				0														0.142857	5.41843	10.593155	6	36	KEEP	---	---	---	---	capture		Silent	SNP	145235188	145235188	7317	8	G	T	T	T	522	41	HEATR7A	2	2
CNOT7	29883	broad.mit.edu	37	8	17090038	17090038	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:17090038T>A	uc003wxf.1	-	c.627A>T	c.(625-627)TTA>TTT	p.L209F	CNOT7_uc003wxg.1_Missense_Mutation_p.L209F|CNOT7_uc003wxh.1_Missense_Mutation_p.L209F	NM_013354	NP_037486	Q9UIV1	CNOT7_HUMAN	CCR4-NOT transcription complex, subunit 7	209					carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)										0.082418	0.896674	33.172794	15	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17090038	17090038	3762	8	T	A	A	A	738	57	CNOT7	3	3
CNOT7	29883	broad.mit.edu	37	8	17090042	17090042	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:17090042C>A	uc003wxf.1	-	c.623G>T	c.(622-624)GGA>GTA	p.G208V	CNOT7_uc003wxg.1_Missense_Mutation_p.G208V|CNOT7_uc003wxh.1_Missense_Mutation_p.G208V	NM_013354	NP_037486	Q9UIV1	CNOT7_HUMAN	CCR4-NOT transcription complex, subunit 7	208					carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)										0.086207	0.687829	30.880945	15	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17090042	17090042	3762	8	C	A	A	A	390	30	CNOT7	2	2
CSMD1	64478	broad.mit.edu	37	8	2949091	2949091	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:2949091C>T	uc011kwk.1	-	c.7235G>A	c.(7234-7236)CGC>CAC	p.R2412H	CSMD1_uc011kwj.1_Missense_Mutation_p.R1741H|CSMD1_uc010lrg.2_Missense_Mutation_p.R480H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2412	CUB 14.|Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)										0.210526	17.779299	20.725077	8	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2949091	2949091	4085	8	C	T	T	T	351	27	CSMD1	1	1
AGPAT6	137964	broad.mit.edu	37	8	41476485	41476485	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41476485G>A	uc003xnz.2	+	c.1251G>A	c.(1249-1251)GTG>GTA	p.V417V		NM_178819	NP_848934	Q86UL3	GPAT4_HUMAN	lysophosphatidic acid acyltransferase zeta	417					acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity				0	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)											0.171429	23.655119	30.800746	12	58	KEEP	---	---	---	---	capture		Silent	SNP	41476485	41476485	394	8	G	A	A	A	600	47	AGPAT6	2	2
SNTG1	54212	broad.mit.edu	37	8	51362272	51362272	+	Silent	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:51362272C>G	uc010lxy.1	+	c.264C>G	c.(262-264)TCC>TCG	p.S88S	SNTG1_uc003xqs.1_Silent_p.S88S|SNTG1_uc010lxz.1_Silent_p.S88S|SNTG1_uc011ldl.1_Non-coding_Transcript	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	88	PDZ.				cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)												0.15625	8.953542	12.563923	5	27	KEEP	---	---	---	---	capture		Silent	SNP	51362272	51362272	15374	8	C	G	G	G	262	21	SNTG1	3	3
TRPA1	8989	broad.mit.edu	37	8	72942164	72942164	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:72942164T>A	uc003xza.2	-	c.2909A>T	c.(2908-2910)CAT>CTT	p.H970L		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	970	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)									0.207792	39.268962	45.350738	16	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72942164	72942164	17128	8	T	A	A	A	663	51	TRPA1	3	3
ZFHX4	79776	broad.mit.edu	37	8	77764254	77764254	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77764254G>T	uc003yav.2	+	c.4962G>T	c.(4960-4962)CAG>CAT	p.Q1654H	ZFHX4_uc003yau.1_Missense_Mutation_p.Q1699H|ZFHX4_uc003yaw.1_Missense_Mutation_p.Q1654H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1654	Gln-rich.				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)											0.072917	-3.757922	14.261618	7	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77764254	77764254	18223	8	G	T	T	T	438	34	ZFHX4	2	2
SLC7A13	157724	broad.mit.edu	37	8	87242421	87242421	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87242421G>T	uc003ydq.1	-	c.86C>A	c.(85-87)GCA>GAA	p.A29E	SLC7A13_uc003ydr.1_Missense_Mutation_p.A29E	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	29	Helical; Name=1; (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1														0.078431	-1.076545	17.446315	8	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87242421	87242421	15192	8	G	T	T	T	598	46	SLC7A13	2	2
ESRP1	54845	broad.mit.edu	37	8	95683790	95683790	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95683790G>T	uc003ygq.3	+	c.1343G>T	c.(1342-1344)CGC>CTC	p.R448L	ESRP1_uc003ygr.3_Missense_Mutation_p.R448L|ESRP1_uc003ygs.3_Missense_Mutation_p.R448L|ESRP1_uc003ygt.3_Missense_Mutation_p.R448L|ESRP1_uc003ygu.3_Missense_Mutation_p.R448L|ESRP1_uc003ygv.2_Missense_Mutation_p.R288L|ESRP1_uc003ygw.2_Missense_Mutation_p.R288L	NM_017697	NP_060167	Q6NXG1	ESRP1_HUMAN	RNA binding motif protein 35A isoform 1	448	RRM 3.				mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4														0.098361	0.857836	10.687453	6	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95683790	95683790	5451	8	G	T	T	T	494	38	ESRP1	1	1
TMEFF1	8577	broad.mit.edu	37	9	103279049	103279049	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:103279049G>T	uc004bay.1	+	c.778G>T	c.(778-780)GTT>TTT	p.V260F	TMEFF1_uc004baz.1_Missense_Mutation_p.V186F	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two	186	Kazal-like 2.|Extracellular (Potential).				multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)												0.146667	16.41048	25.549225	11	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103279049	103279049	16543	9	G	T	T	T	624	48	TMEFF1	2	2
PALM2-AKAP2	445815	broad.mit.edu	37	9	112898590	112898590	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:112898590C>A	uc004bei.2	+	c.1462C>A	c.(1462-1464)CAT>AAT	p.H488N	PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.H256N|PALM2-AKAP2_uc004bej.3_Missense_Mutation_p.H256N|PALM2-AKAP2_uc004bel.1_Missense_Mutation_p.H66N|AKAP2_uc011lwi.1_Missense_Mutation_p.H114N|AKAP2_uc004bem.2_Missense_Mutation_p.H114N|PALM2-AKAP2_uc010mtw.1_Missense_Mutation_p.H74N|AKAP2_uc011lwj.1_Missense_Mutation_p.H25N|PALM2-AKAP2_uc004ben.2_Missense_Mutation_p.H25N	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	25							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.171296	70.737627	92.806451	37	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112898590	112898590	11826	9	C	A	A	A	273	21	PALM2-AKAP2	2	2
OR1L8	138881	broad.mit.edu	37	9	125330565	125330565	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125330565C>A	uc004bmp.1	-	c.192G>T	c.(190-192)TTG>TTT	p.L64F		NM_001004454	NP_001004454	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L,	64	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3														0.1	4.700472	19.096658	9	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125330565	125330565	11373	9	C	A	A	A	376	29	OR1L8	2	2
SDCCAG3	10807	broad.mit.edu	37	9	139304594	139304594	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139304594C>A	uc004chi.2	-	c.168G>T	c.(166-168)CCG>CCT	p.P56P	SDCCAG3_uc004chj.2_Silent_p.P56P|SDCCAG3_uc004chk.2_Intron|PMPCA_uc011mdy.1_5'Flank|PMPCA_uc010nbk.2_5'Flank|PMPCA_uc004chl.2_5'Flank|PMPCA_uc010nbl.2_5'Flank|PMPCA_uc011mdz.1_5'Flank	NM_001039707	NP_001034796	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	56						cytoplasm					0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)										0.214286	14.936128	17.04556	6	22	KEEP	---	---	---	---	capture		Silent	SNP	139304594	139304594	14443	9	C	A	A	A	288	23	SDCCAG3	1	1
PNPLA7	375775	broad.mit.edu	37	9	140356755	140356755	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:140356755C>A	uc010ncj.1	-	c.3521G>T	c.(3520-3522)CGC>CTC	p.R1174L	C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_Intron|PNPLA7_uc004cne.1_Missense_Mutation_p.R415L|PNPLA7_uc011mfa.1_Missense_Mutation_p.R557L|PNPLA7_uc004cnf.2_Missense_Mutation_p.R1149L|NELF_uc004cna.2_5'Flank|NELF_uc011mez.1_5'Flank|NELF_uc004cmz.2_5'Flank|NELF_uc004cnc.2_5'Flank|NELF_uc004cnb.2_5'Flank	NM_001098537	NP_001092007	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1149					lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity				0	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)										0.108696	3.174284	17.193652	10	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140356755	140356755	12597	9	C	A	A	A	351	27	PNPLA7	1	1
KIAA1797	54914	broad.mit.edu	37	9	20717833	20717833	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:20717833G>T	uc003zog.1	+	c.98G>T	c.(97-99)GGT>GTT	p.G33V		NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914	33						integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)										0.170213	16.369351	21.206343	8	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20717833	20717833	8569	9	G	T	T	T	572	44	KIAA1797	2	2
KIAA1797	54914	broad.mit.edu	37	9	20926351	20926351	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:20926351A>T	uc003zog.1	+	c.3013A>T	c.(3013-3015)ACA>TCA	p.T1005S	KIAA1797_uc003zoh.1_Missense_Mutation_p.T441S	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914	1005						integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)										0.112069	11.798317	29.04296	13	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20926351	20926351	8569	9	A	T	T	T	182	14	KIAA1797	3	3
CCIN	881	broad.mit.edu	37	9	36170205	36170205	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:36170205G>T	uc003zzb.3	+	c.706G>T	c.(706-708)GCC>TCC	p.A236S		NM_005893	NP_005884	Q13939	CALI_HUMAN	calicin	236					cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			ovary(1)	1			STAD - Stomach adenocarcinoma(86;0.228)											0.208333	21.617228	25.406997	10	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36170205	36170205	3003	9	G	T	T	T	598	46	CCIN	2	2
FAM75A2	642265	broad.mit.edu	37	9	39888226	39888226	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:39888226C>A	uc004abp.2	+	c.1213C>A	c.(1213-1215)CAG>AAG	p.Q405K		NM_001040065	NP_001035154	Q5RGS2	F75A2_HUMAN	hypothetical protein LOC642265	405						integral to membrane					0				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)										0.171765	142.190684	185.486003	73	352	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39888226	39888226	5844	9	C	A	A	A	325	25	FAM75A2	2	2
FLJ46321	389763	broad.mit.edu	37	9	84606311	84606311	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:84606311G>T	uc004amn.2	+	c.926G>T	c.(925-927)TGC>TTC	p.C309F		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	309						integral to membrane					0														0.082474	2.277377	71.111005	32	356	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84606311	84606311	6174	9	G	T	T	T	598	46	FLJ46321	2	2
FLJ46321	389763	broad.mit.edu	37	9	84608122	84608122	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:84608122A>T	uc004amn.2	+	c.2737A>T	c.(2737-2739)AGG>TGG	p.R913W		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	913						integral to membrane					0														0.20339	27.066586	31.885848	12	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84608122	84608122	6174	9	A	T	T	T	140	11	FLJ46321	3	3
KIF27	55582	broad.mit.edu	37	9	86503486	86503486	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:86503486A>C	uc004ana.2	-	c.2001T>G	c.(1999-2001)ATT>ATG	p.I667M	KIF27_uc010mpw.2_Missense_Mutation_p.I667M|KIF27_uc010mpx.2_Missense_Mutation_p.I667M	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27	667					cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity				0														0.090909	6.100332	17.232845	6	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86503486	86503486	8607	9	A	C	C	C	112	9	KIF27	4	4
NTRK2	4915	broad.mit.edu	37	9	87636230	87636230	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:87636230T>A	uc004anz.1	+	c.2395T>A	c.(2395-2397)TAT>AAT	p.Y799N	NTRK2_uc004aoa.1_Missense_Mutation_p.Y783N	NM_006180	NP_006171	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	783	Protein kinase.|Cytoplasmic (Potential).				activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(1)|liver(1)|central_nervous_system(1)|skin(1)	12										348	TSP Lung(25;0.17)			0.112676	8.654611	19.165467	8	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87636230	87636230	11112	9	T	A	A	A	741	57	NTRK2	3	3
CSTF2	1478	broad.mit.edu	37	X	100086550	100086550	+	Silent	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100086550T>A	uc010nnd.2	+	c.996T>A	c.(994-996)CCT>CCA	p.P332P	CSTF2_uc004egh.2_Silent_p.P312P|CSTF2_uc004egi.2_Silent_p.P295P	NM_001325	NP_001316	P33240	CSTF2_HUMAN	cleavage stimulation factor subunit 2	312	Gly/Pro-rich.				mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	nucleotide binding|protein binding|protein binding|RNA binding				0														0.061303	-18.517778	33.997625	16	245	KEEP	---	---	---	---	capture		Silent	SNP	100086550	100086550	4125	23	T	A	A	A	704	55	CSTF2	3	3
BHLHB9	80823	broad.mit.edu	37	X	102004639	102004639	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:102004639C>T	uc010nog.2	+	c.716C>T	c.(715-717)TCT>TTT	p.S239F	BHLHB9_uc011mrq.1_Missense_Mutation_p.S239F|BHLHB9_uc011mrr.1_Missense_Mutation_p.S239F|BHLHB9_uc011mrs.1_Missense_Mutation_p.S239F|BHLHB9_uc011mrt.1_Missense_Mutation_p.S239F|BHLHB9_uc004ejo.2_Missense_Mutation_p.S239F|BHLHB9_uc011mru.1_Missense_Mutation_p.S239F|BHLHB9_uc011mrv.1_Missense_Mutation_p.S239F	NM_001142526	NP_001135998	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class	239						cytoplasm|nucleus	binding			ovary(2)	2														0.110599	26.628854	59.18683	24	193	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102004639	102004639	1445	23	C	T	T	T	416	32	BHLHB9	2	2
ATG4A	115201	broad.mit.edu	37	X	107381398	107381398	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107381398C>A	uc004enr.2	+	c.791C>A	c.(790-792)GCG>GAG	p.A264E	ATG4A_uc004ent.2_Intron|ATG4A_uc004ens.2_Missense_Mutation_p.A180E|ATG4A_uc011msl.1_Intron|ATG4A_uc010npi.2_Intron|ATG4A_uc004enu.2_Missense_Mutation_p.A180E	NM_052936	NP_443168	Q8WYN0	ATG4A_HUMAN	autophagy-related cysteine endopeptidase 2	264					autophagy|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity			pancreas(1)	1														0.131285	76.881892	124.1894	47	311	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107381398	107381398	1115	23	C	A	A	A	351	27	ATG4A	1	1
COL4A6	1288	broad.mit.edu	37	X	107424191	107424191	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107424191G>T	uc004enw.3	-	c.1962C>A	c.(1960-1962)ACC>ACA	p.T654T	COL4A6_uc004env.3_Silent_p.T653T|COL4A6_uc011msn.1_Silent_p.T653T|COL4A6_uc010npk.2_Silent_p.T653T	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	654	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.114754	7.978085	16.90263	7	54	KEEP	---	---	---	---	capture		Silent	SNP	107424191	107424191	3833	23	G	T	T	T	548	43	COL4A6	2	2
COL4A5	1287	broad.mit.edu	37	X	107821581	107821581	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107821581C>A	uc004enz.1	+	c.748C>A	c.(748-750)CCA>ACA	p.P250T	COL4A5_uc011mso.1_Missense_Mutation_p.P250T	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	250	Triple-helical region.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														0.11194	14.357885	34.271959	15	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107821581	107821581	3832	23	C	A	A	A	234	18	COL4A5	2	2
GUCY2F	2986	broad.mit.edu	37	X	108708514	108708514	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:108708514C>A	uc004eod.3	-	c.889G>T	c.(889-891)GTC>TTC	p.V297F	GUCY2F_uc011msq.1_Non-coding_Transcript	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	297	Extracellular (Potential).				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8									p.V297L(SKOV3-Tumor)	308				0.188341	88.414685	108.692979	42	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108708514	108708514	7178	23	C	A	A	A	234	18	GUCY2F	2	2
TRPC5	7224	broad.mit.edu	37	X	111090471	111090471	+	Missense_Mutation	SNP	T	A	A	rs3027722		TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:111090471T>A	uc004epl.1	-	c.1571A>T	c.(1570-1572)TAC>TTC	p.Y524F	TRPC5_uc004epm.1_Missense_Mutation_p.Y524F	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	524	Helical; (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1														0.122549	29.03953	57.50687	25	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111090471	111090471	17133	23	T	A	A	A	741	57	TRPC5	3	3
ZCCHC16	340595	broad.mit.edu	37	X	111698312	111698312	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:111698312G>C	uc004epo.1	+	c.356G>C	c.(355-357)AGT>ACT	p.S119T		NM_001004308	NP_001004308	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	119							nucleic acid binding|zinc ion binding			ovary(1)	1														0.089109	16.586851	51.032341	18	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111698312	111698312	18172	23	G	C	C	C	468	36	ZCCHC16	3	3
IL13RA2	3598	broad.mit.edu	37	X	114250291	114250291	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:114250291T>A	uc004epx.2	-	c.188A>T	c.(187-189)AAG>ATG	p.K63M	IL13RA2_uc010nqd.1_Missense_Mutation_p.K63M	NM_000640	NP_000631	Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2 precursor	63	Extracellular (Potential).|Fibronectin type-III 1.					extracellular space|integral to membrane|soluble fraction	cytokine receptor activity			ovary(1)|lung(1)	2														0.18018	37.826325	48.513644	20	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114250291	114250291	7931	23	T	A	A	A	728	56	IL13RA2	3	3
UPF3B	65109	broad.mit.edu	37	X	118975155	118975155	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:118975155C>A	uc004erz.1	-	c.691G>T	c.(691-693)GAA>TAA	p.E231*	UPF3B_uc004esa.1_Nonsense_Mutation_p.E231*	NM_080632	NP_542199	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B	231	Necessary for interaction with UPF2.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|termination of RNA polymerase II transcription	cytosol|exon-exon junction complex|nucleoplasm	mRNA binding|nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(2)|kidney(1)	3														0.140351	9.156469	16.2836	8	49	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	118975155	118975155	17566	23	C	A	A	A	416	32	UPF3B	5	2
THOC2	57187	broad.mit.edu	37	X	122765624	122765624	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:122765624G>T	uc004etu.2	-	c.2396C>A	c.(2395-2397)TCA>TAA	p.S799*	THOC2_uc011muh.1_Nonsense_Mutation_p.S724*	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2	799					intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3														0.082596	0.635659	60.717349	28	311	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	122765624	122765624	16393	23	G	T	T	T	585	45	THOC2	5	2
ODZ1	10178	broad.mit.edu	37	X	123515111	123515111	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123515111G>T	uc010nqy.2	-	c.7474C>A	c.(7474-7476)CAG>AAG	p.Q2492K	ODZ1_uc011muj.1_Missense_Mutation_p.Q2491K|ODZ1_uc004euj.2_Missense_Mutation_p.Q2485K	NM_001163278	NP_001156750	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 1	2485	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	22										623				0.123853	40.563317	70.731313	27	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123515111	123515111	11239	23	G	T	T	T	624	48	ODZ1	2	2
DCAF12L2	340578	broad.mit.edu	37	X	125298776	125298776	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:125298776G>A	uc004euk.1	-	c.1132C>T	c.(1132-1134)CGC>TGC	p.R378C		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	378	WD 4.									lung(2)|large_intestine(1)|ovary(1)|pancreas(1)	5														0.086124	5.022294	41.271683	18	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125298776	125298776	4436	23	G	A	A	A	507	39	DCAF12L2	1	1
RAB33A	9363	broad.mit.edu	37	X	129318306	129318306	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:129318306G>T	uc004evl.2	+	c.306G>T	c.(304-306)ATG>ATT	p.M102I	RAB33A_uc010nre.2_Non-coding_Transcript	NM_004794	NP_004785	Q14088	RB33A_HUMAN	Ras-related protein Rab-33A	102			M -> T.		protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding				0														0.140845	28.591401	46.287315	20	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129318306	129318306	13381	23	G	T	T	T	611	47	RAB33A	2	2
PHF6	84295	broad.mit.edu	37	X	133527957	133527957	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:133527957C>A	uc004exj.2	+	c.393C>A	c.(391-393)CAC>CAA	p.H131Q	PHF6_uc004exk.2_Missense_Mutation_p.H131Q|PHF6_uc011mvk.1_Missense_Mutation_p.H97Q|PHF6_uc004exh.2_Missense_Mutation_p.H131Q|PHF6_uc010nrr.2_Missense_Mutation_p.H131Q|PHF6_uc004exi.2_Missense_Mutation_p.H131Q	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1	131	Nuclear localization signal (Potential).|PHD-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					Colon(100;666 1493 6344 21231 35807)								0.176	47.86881	60.241814	22	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133527957	133527957	12261	23	C	A	A	A	220	17	PHF6	2	2
PHF6	84295	broad.mit.edu	37	X	133549067	133549067	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:133549067C>A	uc004exj.2	+	c.751C>A	c.(751-753)CAG>AAG	p.Q251K	PHF6_uc004exk.2_Missense_Mutation_p.Q251K|PHF6_uc011mvk.1_Missense_Mutation_p.Q217K|PHF6_uc004exh.2_Missense_Mutation_p.Q252K|PHF6_uc010nrr.2_Missense_Mutation_p.Q251K|PHF6_uc004exi.2_Missense_Mutation_p.Q252K	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1	251					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					Colon(100;666 1493 6344 21231 35807)								0.081633	0.662381	9.394137	4	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133549067	133549067	12261	23	C	A	A	A	273	21	PHF6	2	2
DDX26B	203522	broad.mit.edu	37	X	134681099	134681099	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:134681099T>A	uc004eyw.3	+	c.651T>A	c.(649-651)AAT>AAA	p.N217K		NM_182540	NP_872346	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	217	VWFA.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.144144	54.254481	81.317668	32	190	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134681099	134681099	4524	23	T	A	A	A	647	50	DDX26B	3	3
MAGEC1	9947	broad.mit.edu	37	X	140993253	140993253	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140993253T>A	uc004fbt.2	+	c.63T>A	c.(61-63)AGT>AGA	p.S21R	MAGEC1_uc010nsl.1_5'UTR	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	21							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.119048	21.086507	45.0266	20	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140993253	140993253	9561	23	T	A	A	A	751	58	MAGEC1	3	3
SLITRK4	139065	broad.mit.edu	37	X	142717965	142717965	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:142717965G>T	uc004fbx.2	-	c.960C>A	c.(958-960)GCC>GCA	p.A320A	SLITRK4_uc004fby.2_Silent_p.A320A	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	320	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.141667	42.356572	72.178932	34	206	KEEP	---	---	---	---	capture		Silent	SNP	142717965	142717965	15243	23	G	T	T	T	548	43	SLITRK4	2	2
SLITRK2	84631	broad.mit.edu	37	X	144906317	144906317	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:144906317C>G	uc004fcd.2	+	c.2374C>G	c.(2374-2376)CGC>GGC	p.R792G	SLITRK2_uc010nsp.2_Missense_Mutation_p.R792G|SLITRK2_uc010nso.2_Missense_Mutation_p.R792G|SLITRK2_uc011mwq.1_Missense_Mutation_p.R792G|SLITRK2_uc011mwr.1_Missense_Mutation_p.R792G|SLITRK2_uc011mws.1_Missense_Mutation_p.R792G|SLITRK2_uc004fcg.2_Missense_Mutation_p.R792G|SLITRK2_uc011mwt.1_Missense_Mutation_p.R792G|CXorf1_uc004fch.2_5'Flank	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	792	Cytoplasmic (Potential).					integral to membrane				ovary(4)|pancreas(1)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.178295	122.639144	147.73515	46	212	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144906317	144906317	15241	23	C	G	G	G	247	19	SLITRK2	3	3
MOSPD2	158747	broad.mit.edu	37	X	14934407	14934407	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:14934407G>A	uc004cwi.2	+	c.1275G>A	c.(1273-1275)CAG>CAA	p.Q425Q	MOSPD2_uc004cwj.2_Silent_p.Q362Q	NM_152581	NP_689794	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	425	MSP.					integral to membrane	structural molecule activity			lung(1)	1	Hepatocellular(33;0.183)													0.154472	68.782329	96.860243	38	208	KEEP	---	---	---	---	capture		Silent	SNP	14934407	14934407	10108	23	G	A	A	A	464	36	MOSPD2	2	2
MAMLD1	10046	broad.mit.edu	37	X	149638184	149638184	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149638184G>C	uc004fee.1	+	c.339G>C	c.(337-339)TTG>TTC	p.L113F	MAMLD1_uc011mxt.1_Missense_Mutation_p.L75F|MAMLD1_uc011mxu.1_Missense_Mutation_p.L88F|MAMLD1_uc011mxv.1_Missense_Mutation_p.L88F|MAMLD1_uc011mxw.1_Missense_Mutation_p.L40F	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	113					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.068783	-1.88077	34.492204	13	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149638184	149638184	9591	23	G	C	C	C	581	45	MAMLD1	3	3
MAMLD1	10046	broad.mit.edu	37	X	149638523	149638523	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149638523G>C	uc004fee.1	+	c.678G>C	c.(676-678)CAG>CAC	p.Q226H	MAMLD1_uc011mxt.1_Missense_Mutation_p.Q188H|MAMLD1_uc011mxu.1_Missense_Mutation_p.Q201H|MAMLD1_uc011mxv.1_Missense_Mutation_p.Q201H|MAMLD1_uc011mxw.1_Missense_Mutation_p.Q153H	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	226					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.06875	2.664957	94.955939	33	447	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149638523	149638523	9591	23	G	C	C	C	425	33	MAMLD1	3	3
MAMLD1	10046	broad.mit.edu	37	X	149638601	149638601	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149638601G>A	uc004fee.1	+	c.756G>A	c.(754-756)CAG>CAA	p.Q252Q	MAMLD1_uc011mxt.1_Silent_p.Q214Q|MAMLD1_uc011mxu.1_Silent_p.Q227Q|MAMLD1_uc011mxv.1_Silent_p.Q227Q|MAMLD1_uc011mxw.1_Silent_p.Q179Q	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	252					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.057402	-29.860798	38.211607	19	312	KEEP	---	---	---	---	capture		Silent	SNP	149638601	149638601	9591	23	G	A	A	A	425	33	MAMLD1	2	2
MAMLD1	10046	broad.mit.edu	37	X	149638622	149638622	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149638622G>A	uc004fee.1	+	c.777G>A	c.(775-777)GGG>GGA	p.G259G	MAMLD1_uc011mxt.1_Silent_p.G221G|MAMLD1_uc011mxu.1_Silent_p.G234G|MAMLD1_uc011mxv.1_Silent_p.G234G|MAMLD1_uc011mxw.1_Silent_p.G186G	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	259					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.059603	-25.250151	35.995104	18	284	KEEP	---	---	---	---	capture		Silent	SNP	149638622	149638622	9591	23	G	A	A	A	522	41	MAMLD1	2	2
MAMLD1	10046	broad.mit.edu	37	X	149638634	149638634	+	Silent	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149638634G>A	uc004fee.1	+	c.789G>A	c.(787-789)TCG>TCA	p.S263S	MAMLD1_uc011mxt.1_Silent_p.S225S|MAMLD1_uc011mxu.1_Silent_p.S238S|MAMLD1_uc011mxv.1_Silent_p.S238S|MAMLD1_uc011mxw.1_Silent_p.S190S	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	263					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.068841	-13.492913	39.554187	19	257	KEEP	---	---	---	---	capture		Silent	SNP	149638634	149638634	9591	23	G	A	A	A	470	37	MAMLD1	1	1
MAMLD1	10046	broad.mit.edu	37	X	149639226	149639226	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149639226G>C	uc004fee.1	+	c.1381G>C	c.(1381-1383)GAG>CAG	p.E461Q	MAMLD1_uc011mxt.1_Missense_Mutation_p.E423Q|MAMLD1_uc011mxu.1_Missense_Mutation_p.E436Q|MAMLD1_uc011mxv.1_Missense_Mutation_p.E436Q|MAMLD1_uc011mxw.1_Missense_Mutation_p.E388Q	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	461					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.089069	20.853031	62.987315	22	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149639226	149639226	9591	23	G	C	C	C	429	33	MAMLD1	3	3
PASD1	139135	broad.mit.edu	37	X	150841005	150841005	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150841005C>A	uc004fev.3	+	c.1788C>A	c.(1786-1788)CCC>CCA	p.P596P		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	596						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.097015	6.572022	28.379835	13	121	KEEP	---	---	---	---	capture		Silent	SNP	150841005	150841005	11888	23	C	A	A	A	275	22	PASD1	2	2
CNGA2	1260	broad.mit.edu	37	X	150912053	150912053	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150912053G>T	uc004fey.1	+	c.1078G>T	c.(1078-1080)GGC>TGC	p.G360C		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	360	Helical; Name=H5; (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.101695	11.55969	39.739381	18	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150912053	150912053	3735	23	G	T	T	T	611	47	CNGA2	2	2
MAGEA12	4111	broad.mit.edu	37	X	151899893	151899893	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:151899893G>T	uc010ntp.2	-	c.908C>A	c.(907-909)CCC>CAC	p.P303H	MAGEA12_uc004fgb.2_Intron|MAGEA12_uc004fgc.2_Missense_Mutation_p.P303H	NM_005367	NP_005358	P43365	MAGAC_HUMAN	melanoma antigen family A, 12	303	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.070111	-15.781012	35.918289	19	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151899893	151899893	9543	23	G	T	T	T	559	43	MAGEA12	2	2
SRPK3	26576	broad.mit.edu	37	X	153048470	153048470	+	Silent	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153048470C>A	uc004fik.2	+	c.843C>A	c.(841-843)CCC>CCA	p.P281P	SRPK3_uc010nul.2_Silent_p.P173P|SRPK3_uc004fin.2_Silent_p.P215P|SRPK3_uc004fil.2_Silent_p.P215P|SRPK3_uc004fim.2_Silent_p.P215P	NM_014370	NP_055185	Q9UPE1	SRPK3_HUMAN	serine arginine rich protein-specific kinase 3	215	Protein kinase.				cell differentiation|muscle organ development|muscle tissue development|protein phosphorylation		ATP binding|protein serine/threonine kinase activity			pancreas(2)|lung(1)	3	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					Esophageal Squamous(167;766 3400 32156)				307				0.104	11.590137	31.091114	13	112	KEEP	---	---	---	---	capture		Silent	SNP	153048470	153048470	15675	23	C	A	A	A	288	23	SRPK3	1	1
PDZD4	57595	broad.mit.edu	37	X	153069157	153069157	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153069157C>A	uc004fja.1	-	c.1979G>T	c.(1978-1980)CGG>CTG	p.R660L	PDZD4_uc004fiy.1_Missense_Mutation_p.R579L|PDZD4_uc004fiz.1_Missense_Mutation_p.R654L|PDZD4_uc004fix.2_Missense_Mutation_p.R558L|PDZD4_uc011mze.1_Missense_Mutation_p.R545L	NM_032512	NP_115901	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	654						cell cortex				breast(1)	1	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.148148	25.133885	37.96815	16	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153069157	153069157	12124	23	C	A	A	A	299	23	PDZD4	1	1
MPP1	4354	broad.mit.edu	37	X	154007556	154007556	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:154007556A>T	uc004fmp.1	-	c.1297T>A	c.(1297-1299)TCA>ACA	p.S433T	MPP1_uc010nvg.1_Missense_Mutation_p.S413T|MPP1_uc011mzv.1_Missense_Mutation_p.S403T|MPP1_uc004fmq.1_Missense_Mutation_p.S387T|MPP1_uc011mzw.1_Missense_Mutation_p.S416T	NM_002436	NP_002427	Q00013	EM55_HUMAN	palmitoylated membrane protein 1	433	Guanylate kinase-like.|Interaction with MPP5.				regulation of neutrophil chemotaxis|signal transduction	integral to plasma membrane|membrane fraction|stereocilium	guanylate kinase activity|protein binding			ovary(2)|central_nervous_system(1)	3	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.117647	19.638638	41.631301	18	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154007556	154007556	10125	23	A	T	T	T	143	11	MPP1	3	3
NHS	4810	broad.mit.edu	37	X	17744628	17744628	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:17744628T>C	uc011mix.1	+	c.2402T>C	c.(2401-2403)GTC>GCC	p.V801A	NHS_uc004cxx.2_Missense_Mutation_p.V780A|NHS_uc004cxy.2_Missense_Mutation_p.V624A|NHS_uc004cxz.2_Missense_Mutation_p.V603A|NHS_uc004cya.2_Missense_Mutation_p.V503A	NM_001136024	NP_001129496	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 2	780						nucleus				ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6	Hepatocellular(33;0.183)													0.114094	53.046048	96.79409	34	264	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17744628	17744628	10811	23	T	C	C	C	754	58	NHS	4	4
MXRA5	25878	broad.mit.edu	37	X	3235287	3235287	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3235287G>T	uc004crg.3	-	c.6435C>A	c.(6433-6435)AAC>AAA	p.N2145K		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2145						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.184211	14.000818	17.56046	7	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3235287	3235287	10397	23	G	T	T	T	516	40	MXRA5	1	1
CXorf59	286464	broad.mit.edu	37	X	36122683	36122683	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:36122683C>A	uc004ddk.1	+	c.920C>A	c.(919-921)ACA>AAA	p.T307K		NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464	307						integral to membrane				central_nervous_system(1)	1														0.053435	-12.890507	14.685374	7	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36122683	36122683	4279	23	C	A	A	A	221	17	CXorf59	2	2
CYBB	1536	broad.mit.edu	37	X	37658247	37658247	+	Silent	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37658247G>T	uc004ddr.2	+	c.714G>T	c.(712-714)GTG>GTT	p.V238V	CYBB_uc011mke.1_Non-coding_Transcript|CYBB_uc011mkf.1_Silent_p.V206V|CYBB_uc011mkg.1_5'UTR	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	238	Extracellular (Potential).|Ferric oxidoreductase.				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2														0.113636	5.44023	11.922074	5	39	KEEP	---	---	---	---	capture		Silent	SNP	37658247	37658247	4298	23	G	T	T	T	587	46	CYBB	2	2
RPGR	6103	broad.mit.edu	37	X	38132681	38132681	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:38132681G>T	uc004deb.2	-	c.2199C>A	c.(2197-2199)AAC>AAA	p.N733K	RPGR_uc004dea.2_Non-coding_Transcript|RPGR_uc004dec.2_Non-coding_Transcript	NM_000328	NP_000319	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform A	739	Glu-rich.				intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1														0.135135	5.926387	10.76049	5	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38132681	38132681	14027	23	G	T	T	T	620	48	RPGR	2	2
USP9X	8239	broad.mit.edu	37	X	41012324	41012324	+	Silent	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:41012324A>G	uc004dfb.2	+	c.1887A>G	c.(1885-1887)CTA>CTG	p.L629L	USP9X_uc004dfc.2_Silent_p.L629L	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	629					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			ovary(1)	1						Ovarian(172;1807 2695 35459 49286)								0.180451	66.925404	79.686543	24	109	KEEP	---	---	---	---	capture		Silent	SNP	41012324	41012324	17654	23	A	G	G	G	197	16	USP9X	4	4
ZNF674	641339	broad.mit.edu	37	X	46387869	46387869	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:46387869C>A	uc004dgr.2	-	c.154G>T	c.(154-156)GGG>TGG	p.G52W	ZNF674_uc011mlg.1_Missense_Mutation_p.G52W|ZNF674_uc010nhm.2_Missense_Mutation_p.G52W	NM_001039891	NP_001034980	Q2M3X9	ZN674_HUMAN	zinc finger family member 674 isoform 1	52	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)	2														0.129771	23.676649	41.160112	17	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46387869	46387869	18676	23	C	A	A	A	273	21	ZNF674	2	2
ZNF81	347344	broad.mit.edu	37	X	47774732	47774732	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47774732G>C	uc010nhy.1	+	c.687G>C	c.(685-687)CAG>CAC	p.Q229H		NM_007137	NP_009068	P51508	ZNF81_HUMAN	zinc finger protein 81	229					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)												0.082645	6.9493	28.3873	10	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47774732	47774732	18772	23	G	C	C	C	425	33	ZNF81	3	3
TIMM17B	10245	broad.mit.edu	37	X	48754088	48754088	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48754088C>A	uc004dla.1	-	c.80G>T	c.(79-81)GGT>GTT	p.G27V	PQBP1_uc004dle.2_5'Flank|PQBP1_uc004dlf.2_5'Flank|PQBP1_uc004dlg.2_5'Flank|PQBP1_uc004dld.2_5'Flank|PQBP1_uc004dlh.2_5'Flank|PQBP1_uc004dli.2_5'Flank|PQBP1_uc004dlj.1_5'Flank|PQBP1_uc004dln.2_5'Flank|PQBP1_uc010nih.2_5'Flank|PQBP1_uc010nii.2_5'Flank|PQBP1_uc004dlk.2_5'Flank|PQBP1_uc004dll.2_5'Flank|PQBP1_uc004dlm.2_5'Flank|PQBP1_uc010nij.2_5'Flank|TIMM17B_uc004dlb.1_Missense_Mutation_p.V13L|TIMM17B_uc004dlc.1_Missense_Mutation_p.G27V	NM_005834	NP_005825	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17	27	Helical; (Potential).				protein targeting to mitochondrion	integral to membrane|microtubule cytoskeleton|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1														0.090909	4.529146	19.378271	8	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48754088	48754088	16438	23	C	A	A	A	234	18	TIMM17B	2	2
DGKK	139189	broad.mit.edu	37	X	50119912	50119912	+	Silent	SNP	A	G	G			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:50119912A>G	uc010njr.1	-	c.3117T>C	c.(3115-3117)TTT>TTC	p.F1039F		NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa	1039					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)													0.209302	23.368325	26.719402	9	34	KEEP	---	---	---	---	capture		Silent	SNP	50119912	50119912	4651	23	A	G	G	G	63	5	DGKK	4	4
RRAGB	10325	broad.mit.edu	37	X	55784734	55784734	+	Silent	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:55784734G>C	uc004dup.2	+	c.1083G>C	c.(1081-1083)CTG>CTC	p.L361L	RRAGB_uc004duq.2_Silent_p.L333L	NM_016656	NP_057740	Q5VZM2	RRAGB_HUMAN	Ras-related GTP binding B long isoform	361					cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|signal transduction	Golgi apparatus|lysosome|nucleus	GTP binding|protein binding				0														0.136364	4.708288	7.527065	3	19	KEEP	---	---	---	---	capture		Silent	SNP	55784734	55784734	14153	23	G	C	C	C	600	47	RRAGB	3	3
SLC7A3	84889	broad.mit.edu	37	X	70149736	70149736	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70149736C>A	uc004dyn.2	-	c.112G>T	c.(112-114)GTG>TTG	p.V38L	SLC7A3_uc004dyo.2_Missense_Mutation_p.V38L	NM_032803	NP_116192	Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid	38	Helical; Name=1; (Potential).				cellular nitrogen compound metabolic process	integral to membrane|plasma membrane				ovary(1)|kidney(1)	2	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)									0.102041	4.336597	12.075196	5	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70149736	70149736	15195	23	C	A	A	A	260	20	SLC7A3	2	2
MED12	9968	broad.mit.edu	37	X	70342990	70342990	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70342990G>T	uc004dyy.2	+	c.1531G>T	c.(1531-1533)GCT>TCT	p.A511S	MED12_uc011mpq.1_Missense_Mutation_p.A511S|MED12_uc004dyz.2_Missense_Mutation_p.A511S|MED12_uc004dza.2_Missense_Mutation_p.A358S	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	511					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.142857	63.966012	97.500653	39	234	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70342990	70342990	9817	23	G	T	T	T	546	42	MED12	2	2
KIAA2022	340533	broad.mit.edu	37	X	73963899	73963899	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:73963899G>C	uc004eby.2	-	c.493C>G	c.(493-495)CTG>GTG	p.L165V		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	165					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|central_nervous_system(1)	14										126				0.07874	4.943675	27.968338	10	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73963899	73963899	8580	23	G	C	C	C	425	33	KIAA2022	3	3
MAGEE1	57692	broad.mit.edu	37	X	75649077	75649077	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:75649077C>A	uc004ecm.1	+	c.754C>A	c.(754-756)CGT>AGT	p.R252S		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	252	Pro-rich.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6														0.263158	21.361436	23.280338	10	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75649077	75649077	9568	23	C	A	A	A	299	23	MAGEE1	1	1
MAGT1	84061	broad.mit.edu	37	X	77086363	77086363	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77086363C>A	uc004fof.2	-	c.1027G>T	c.(1027-1029)GTA>TTA	p.V343L	MAGT1_uc004fog.3_Non-coding_Transcript	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	311	Helical; (Potential).		V -> G (in MRX95).		protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex					0														0.180328	23.887328	29.749138	11	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77086363	77086363	9579	23	C	A	A	A	221	17	MAGT1	2	2
ZCCHC5	203430	broad.mit.edu	37	X	77913592	77913592	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4430-01	TCGA-05-4430-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77913592G>A	uc004edc.1	-	c.326C>T	c.(325-327)CCA>CTA	p.P109L		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	109	Pro-rich.						nucleic acid binding|zinc ion binding			ovary(1)	1														0.232143	29.945009	33.626943	13	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77913592	77913592	18179	23	G	A	A	A	611	47	ZCCHC5	2	2
