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
PNLIPRP3	119548	broad.mit.edu	37	10	118236232	118236232	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118236232C>A	uc001lcl.3	+	c.1241C>A	c.(1240-1242)ACA>AAA	p.T414K		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	414	PLAT.				lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)										0.186567	54.895258	67.229086	25	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118236232	118236232	12578	10	C	A	A	A	221	17	PNLIPRP3	2	2
CPXM2	119587	broad.mit.edu	37	10	125514203	125514203	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:125514203C>T	uc001lhk.1	-	c.1993G>A	c.(1993-1995)GGC>AGC	p.G665S	CPXM2_uc001lhj.2_Non-coding_Transcript	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	665					cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)										0.152542	17.935937	24.752326	9	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125514203	125514203	3977	10	C	T	T	T	312	24	CPXM2	2	2
CYP2E1	1571	broad.mit.edu	37	10	135346288	135346288	+	Silent	SNP	T	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:135346288T>C	uc001lnj.1	+	c.741T>C	c.(739-741)TCT>TCC	p.S247S	CYP2E1_uc001lnk.1_Silent_p.S110S|CYP2E1_uc009ybl.1_Silent_p.S48S|CYP2E1_uc009ybm.1_5'UTR|CYP2E1_uc001lnl.1_Silent_p.S48S	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	247					drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidation-reduction process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)									0.204545	14.939284	18.518674	9	35	KEEP	---	---	---	---	capture		Silent	SNP	135346288	135346288	4335	10	T	C	C	C	704	55	CYP2E1	4	4
PIP4K2A	5305	broad.mit.edu	37	10	22880659	22880659	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:22880659C>A	uc001irl.3	-	c.391G>T	c.(391-393)GGA>TGA	p.G131*	PIP4K2A_uc010qcu.1_5'UTR	NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	131	PIPK.						1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2										213				0.108108	4.171491	9.805786	4	33	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22880659	22880659	12360	10	C	A	A	A	273	21	PIP4K2A	5	2
ARMC3	219681	broad.mit.edu	37	10	23257339	23257339	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:23257339C>A	uc001irm.3	+	c.837C>A	c.(835-837)CTC>CTA	p.L279L	ARMC3_uc010qcv.1_Silent_p.L279L|ARMC3_uc010qcw.1_Silent_p.L16L	NM_173081	NP_775104	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	279	ARM 7.						binding				0														0.139535	6.141654	11.720414	6	37	KEEP	---	---	---	---	capture		Silent	SNP	23257339	23257339	970	10	C	A	A	A	379	30	ARMC3	2	2
ANKRD26	22852	broad.mit.edu	37	10	27322179	27322179	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27322179T>A	uc009xku.1	-	c.3782A>T	c.(3781-3783)AAG>ATG	p.K1261M	ANKRD26_uc001itg.2_Missense_Mutation_p.K947M|ANKRD26_uc001ith.2_Missense_Mutation_p.K1260M	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1260	Potential.									large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4														0.071429	-1.447141	9.153049	4	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27322179	27322179	659	10	T	A	A	A	728	56	ANKRD26	3	3
DIP2C	22982	broad.mit.edu	37	10	468956	468956	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:468956C>A	uc001ifp.2	-	c.412G>T	c.(412-414)GAA>TAA	p.E138*	DIP2C_uc009xhk.1_Missense_Mutation_p.Q139H	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	138						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)						1018				0.072464	-2.882028	10.101571	5	64	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	468956	468956	4708	10	C	A	A	A	416	32	DIP2C	5	2
ADAMTS14	140766	broad.mit.edu	37	10	72434397	72434397	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:72434397G>T	uc001jrg.2	+	c.168G>T	c.(166-168)GTG>GTT	p.V56V	ADAMTS14_uc001jrh.2_Silent_p.V56V	NM_139155	NP_631894	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	56					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)	5														0.172414	9.958133	12.897391	5	24	KEEP	---	---	---	---	capture		Silent	SNP	72434397	72434397	260	10	G	T	T	T	600	47	ADAMTS14	2	2
ITIH5	80760	broad.mit.edu	37	10	7611732	7611732	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7611732T>A	uc001ijq.2	-	c.2048A>T	c.(2047-2049)CAC>CTC	p.H683L	ITIH5_uc001ijp.2_Missense_Mutation_p.H469L	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	683					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4														0.137931	5.69672	9.36038	4	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7611732	7611732	8211	10	T	A	A	A	767	59	ITIH5	3	3
NRG3	10718	broad.mit.edu	37	10	84718766	84718766	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:84718766C>T	uc001kco.2	+	c.1219C>T	c.(1219-1221)CTC>TTC	p.L407F	NRG3_uc010qlz.1_Missense_Mutation_p.L406F|NRG3_uc001kcp.2_Missense_Mutation_p.L186F|NRG3_uc001kcq.2_Missense_Mutation_p.L57F|NRG3_uc001kcr.2_Missense_Mutation_p.L57F	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	407	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity				0				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)										0.193548	34.78162	42.953647	18	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84718766	84718766	11054	10	C	T	T	T	416	32	NRG3	2	2
NRG3	10718	broad.mit.edu	37	10	84738849	84738849	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:84738849C>G	uc001kco.2	+	c.1556C>G	c.(1555-1557)CCA>CGA	p.P519R	NRG3_uc010qlz.1_Missense_Mutation_p.P518R|NRG3_uc001kcp.2_Missense_Mutation_p.P298R|NRG3_uc001kcq.2_Missense_Mutation_p.P169R|NRG3_uc001kcr.2_Missense_Mutation_p.P169R	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	519	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity				0				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)										0.186047	16.590364	20.550626	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84738849	84738849	11054	10	C	G	G	G	273	21	NRG3	3	3
DDI1	414301	broad.mit.edu	37	11	103908003	103908003	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103908003C>A	uc001phr.2	+	c.453C>A	c.(451-453)CTC>CTA	p.L151L	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	151					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)										0.130435	11.45017	20.5993	9	60	KEEP	---	---	---	---	capture		Silent	SNP	103908003	103908003	4499	11	C	A	A	A	405	32	DDI1	2	2
MRVI1	10335	broad.mit.edu	37	11	10648125	10648125	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:10648125G>T	uc010rcc.1	-	c.756C>A	c.(754-756)GTC>GTA	p.V252V	MRVI1_uc001miw.2_Silent_p.V243V|MRVI1_uc010rcb.1_Silent_p.V244V|MRVI1_uc009ygb.1_5'UTR|MRVI1_uc001mix.2_5'UTR|MRVI1_uc001miz.2_Silent_p.V161V|MRVI1_uc009ygc.1_Silent_p.V161V|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_5'UTR|MRVI1_uc010rce.1_Intron	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c	225					platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)										0.1	2.782652	9.165194	4	36	KEEP	---	---	---	---	capture		Silent	SNP	10648125	10648125	10246	11	G	T	T	T	522	41	MRVI1	2	2
C11orf53	341032	broad.mit.edu	37	11	111154946	111154946	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:111154946C>A	uc001plc.2	+	c.153C>A	c.(151-153)AGC>AGA	p.S51R		NM_198498	NP_940900	Q8IXP5	CK053_HUMAN	hypothetical protein LOC341032	51											0		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)										0.184932	50.603526	64.150584	27	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111154946	111154946	1687	11	C	A	A	A	337	26	C11orf53	2	2
CEP164	22897	broad.mit.edu	37	11	117241905	117241905	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117241905G>A	uc001prc.2	+	c.875G>A	c.(874-876)AGT>AAT	p.S292N	CEP164_uc001prb.2_Missense_Mutation_p.S292N|CEP164_uc010rxk.1_Missense_Mutation_p.S266N|CEP164_uc001prf.2_Non-coding_Transcript|CEP164_uc009yzp.1_Non-coding_Transcript	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	292					cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)										0.04918	-13.812588	12.487026	6	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117241905	117241905	3382	11	G	A	A	A	468	36	CEP164	2	2
CD3D	915	broad.mit.edu	37	11	118210558	118210558	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118210558A>G	uc001pss.1	-	c.338T>C	c.(337-339)ATT>ACT	p.I113T	CD3D_uc001pst.1_Intron	NM_000732	NP_000723	P04234	CD3D_HUMAN	CD3 antigen, delta subunit isoform A precursor	113	Helical; (Potential).				positive thymic T cell selection|T cell costimulation|T cell receptor signaling pathway	cytoplasm|integral to membrane	protein heterodimerization activity|transmembrane receptor activity			ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)										0.076923	0.101249	7.240459	3	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118210558	118210558	3138	11	A	G	G	G	52	4	CD3D	4	4
GRIK4	2900	broad.mit.edu	37	11	120673557	120673557	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:120673557G>T	uc001pxn.2	+	c.238G>T	c.(238-240)GCA>TCA	p.A80S	GRIK4_uc009zav.1_Missense_Mutation_p.A80S|GRIK4_uc009zaw.1_Missense_Mutation_p.A80S|GRIK4_uc009zax.1_Missense_Mutation_p.A80S	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	80	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)							OREG0021427	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.081395	-0.88402	14.42393	7	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120673557	120673557	7055	11	G	T	T	T	598	46	GRIK4	2	2
PIK3C2A	5286	broad.mit.edu	37	11	17169144	17169144	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17169144G>C	uc001mmq.3	-	c.1480C>G	c.(1480-1482)CAA>GAA	p.Q494E	PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Missense_Mutation_p.Q114E|PIK3C2A_uc001mmr.3_Intron|PIK3C2A_uc010rcx.1_Missense_Mutation_p.Q494E|PIK3C2A_uc009ygv.1_Missense_Mutation_p.Q494E	NM_002645	NP_002636	O00443	P3C2A_HUMAN	phosphoinositide-3-kinase, class 2 alpha	494					cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			central_nervous_system(4)|lung(2)|ovary(1)	7					Phosphatidylserine(DB00144)					733				0.115385	4.405267	8.193926	3	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17169144	17169144	12333	11	G	C	C	C	585	45	PIK3C2A	3	3
SYT13	57586	broad.mit.edu	37	11	45265822	45265822	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45265822G>T	uc001myq.2	-	c.1062C>A	c.(1060-1062)CCC>CCA	p.P354P	SYT13_uc009yku.1_Silent_p.P210P	NM_020826	NP_065877	Q7L8C5	SYT13_HUMAN	synaptotagmin XIII	354	C2 2.|Cytoplasmic (Potential).					transport vesicle				ovary(1)	1														0.133333	9.331464	15.192613	6	39	KEEP	---	---	---	---	capture		Silent	SNP	45265822	45265822	15990	11	G	T	T	T	496	39	SYT13	1	1
OR51G1	79324	broad.mit.edu	37	11	4944831	4944831	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4944831T>C	uc010qyr.1	-	c.739A>G	c.(739-741)ATC>GTC	p.I247V		NM_001005237	NP_001005237	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.074074	-1.477052	13.600898	6	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4944831	4944831	11508	11	T	C	C	C	637	49	OR51G1	4	4
LRP5	4041	broad.mit.edu	37	11	68115425	68115425	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:68115425G>T	uc001ont.2	+	c.202G>T	c.(202-204)GTG>TTG	p.V68L	LRP5_uc009ysg.2_5'UTR	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	68	Beta-propeller 1.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(1)|pancreas(1)	2														0.169811	15.764045	21.227517	9	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68115425	68115425	9333	11	G	T	T	T	468	36	LRP5	2	2
CAPN5	726	broad.mit.edu	37	11	76834890	76834890	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:76834890A>G	uc009yup.2	+	c.2017A>G	c.(2017-2019)AGC>GGC	p.S673G	CAPN5_uc001oxx.2_Missense_Mutation_p.S633G|CAPN5_uc009yuq.2_Missense_Mutation_p.S669G|CAPN5_uc001oxy.2_Missense_Mutation_p.S673G|CAPN5_uc001oya.2_Missense_Mutation_p.S195G	NM_004055	NP_004046	O15484	CAN5_HUMAN	calpain 5	633					proteolysis|signal transduction	intracellular	calcium-dependent cysteine-type endopeptidase activity				0														0.173913	4.372414	6.708464	4	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76834890	76834890	2747	11	A	G	G	G	91	7	CAPN5	4	4
FAM71C	196472	broad.mit.edu	37	12	100042223	100042223	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:100042223C>A	uc001tgn.2	+	c.271C>A	c.(271-273)CCA>ACA	p.P91T	ANKS1B_uc001tge.1_Intron|ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_153364	NP_699195	Q8NEG0	FA71C_HUMAN	hypothetical protein LOC196472	91											0				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)										0.1875	37.091363	45.878463	18	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100042223	100042223	5832	12	C	A	A	A	234	18	FAM71C	2	2
GOLGA3	2802	broad.mit.edu	37	12	133358913	133358913	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:133358913C>A	uc001ukz.1	-	c.3434G>T	c.(3433-3435)AGG>ATG	p.R1145M	GOLGA3_uc001ula.1_Missense_Mutation_p.R1145M	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1145	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)										0.171429	45.106663	59.407939	24	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133358913	133358913	6823	12	C	A	A	A	312	24	GOLGA3	2	2
ERP27	121506	broad.mit.edu	37	12	15073937	15073937	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:15073937T>C	uc001rco.2	-	c.379A>G	c.(379-381)ATT>GTT	p.I127V		NM_152321	NP_689534	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27 kDa precursor	127	Thioredoxin.					endoplasmic reticulum lumen				breast(1)	1														0.227273	51.720781	59.230818	25	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15073937	15073937	5434	12	T	C	C	C	663	51	ERP27	4	4
SLCO1B1	10599	broad.mit.edu	37	12	21325613	21325613	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21325613T>A	uc001req.3	+	c.114T>A	c.(112-114)TTT>TTA	p.F38L		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	38	Helical; Name=1; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)									0.261364	58.485295	63.0204	23	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21325613	21325613	15220	12	T	A	A	A	790	61	SLCO1B1	3	3
PCDH9	5101	broad.mit.edu	37	13	66878809	66878809	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:66878809C>T	uc001vik.2	-	c.3692G>A	c.(3691-3693)AGT>AAT	p.S1231N	PCDH9_uc010aei.2_Non-coding_Transcript|PCDH9_uc001vil.2_Missense_Mutation_p.S1197N|PCDH9_uc010thl.1_Missense_Mutation_p.S1189N	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1231	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)										0.043478	-12.560479	7.970439	4	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66878809	66878809	11938	13	C	T	T	T	260	20	PCDH9	2	2
RGS6	9628	broad.mit.edu	37	14	72932467	72932467	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:72932467C>A	uc010ttp.1	+	c.189C>A	c.(187-189)GCC>GCA	p.A63A	RGS6_uc010ttn.1_Silent_p.A132A|RGS6_uc001xna.3_Silent_p.A132A|RGS6_uc001xmx.3_Silent_p.A132A|RGS6_uc010tto.1_Non-coding_Transcript|RGS6_uc001xmy.3_Silent_p.A132A|RGS6_uc001xmz.1_5'UTR|RGS6_uc010arg.2_Non-coding_Transcript	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6	132					G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)	2				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		Ovarian(143;1926 2468 21071 48641)								0.120879	15.359028	28.181731	11	80	KEEP	---	---	---	---	capture		Silent	SNP	72932467	72932467	13783	14	C	A	A	A	262	21	RGS6	2	2
RPS6KL1	83694	broad.mit.edu	37	14	75386663	75386663	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75386663T>A	uc010tux.1	-	c.275A>T	c.(274-276)AAC>ATC	p.N92I	RPS6KL1_uc001xqw.2_Missense_Mutation_p.N92I|RPS6KL1_uc010asd.1_Non-coding_Transcript|RPS6KL1_uc001xqy.1_Missense_Mutation_p.N92I	NM_031464	NP_113652	Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	92	MIT.				protein phosphorylation	ribosome	ATP binding|protein serine/threonine kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00658)						524				0.107143	2.90528	7.192368	3	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75386663	75386663	14139	14	T	A	A	A	780	60	RPS6KL1	3	3
GABRB3	2562	broad.mit.edu	37	15	27184492	27184492	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:27184492A>T	uc001zbb.2	-	c.92T>A	c.(91-93)ATT>AAT	p.I31N	GABRA5_uc001zbd.1_Intron	NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	Error:Variant_position_missing_in_P28472_after_alignment					synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	4		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.129412	15.972098	27.332504	11	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27184492	27184492	6419	15	A	T	T	T	40	4	GABRB3	3	3
GABRA5	2558	broad.mit.edu	37	15	27185073	27185073	+	Silent	SNP	C	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:27185073C>G	uc001zbd.1	+	c.726C>G	c.(724-726)GGC>GGG	p.G242G	GABRB3_uc001zbb.2_5'Flank	NM_000810	NP_000801	P31644	GBRA5_HUMAN	gamma-aminobutyric acid A receptor, alpha 5	242	Extracellular (Potential).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.114286	8.667853	18.924236	8	62	KEEP	---	---	---	---	capture		Silent	SNP	27185073	27185073	6415	15	C	G	G	G	340	27	GABRA5	3	3
C15orf52	388115	broad.mit.edu	37	15	40631027	40631027	+	Silent	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40631027C>T	uc001zlh.3	-	c.441G>A	c.(439-441)GAG>GAA	p.E147E	C15orf52_uc001zli.1_Silent_p.E79E|C15orf52_uc010ucn.1_5'Flank	NM_207380	NP_997263	Q6ZUT6	CO052_HUMAN	hypothetical protein LOC388115	147										large_intestine(1)	1		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)										0.214286	29.078307	33.293477	12	44	KEEP	---	---	---	---	capture		Silent	SNP	40631027	40631027	1850	15	C	T	T	T	311	24	C15orf52	2	2
CCDC33	80125	broad.mit.edu	37	15	74554835	74554835	+	Silent	SNP	G	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:74554835G>C	uc002axo.2	+	c.240G>C	c.(238-240)GTG>GTC	p.V80V		NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	283	C2.						protein binding			ovary(3)	3														0.111111	4.005147	8.041807	3	24	KEEP	---	---	---	---	capture		Silent	SNP	74554835	74554835	2928	15	G	C	C	C	574	45	CCDC33	3	3
IL27	246778	broad.mit.edu	37	16	28515315	28515315	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28515315G>A	uc002dqc.2	-	c.88C>T	c.(88-90)CCA>TCA	p.P30S		NM_145659	NP_663634	Q8NEV9	IL27A_HUMAN	interleukin 27 precursor	30					inflammatory response|innate immune response|positive regulation of interferon-gamma biosynthetic process|regulation of defense response to virus|regulation of T cell proliferation|regulation of T-helper 1 cell differentiation	extracellular space	cytokine activity|interleukin-27 receptor binding				0														0.184211	15.502206	19.057142	7	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28515315	28515315	7981	16	G	A	A	A	559	43	IL27	2	2
ZNF423	23090	broad.mit.edu	37	16	49672250	49672250	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:49672250G>T	uc002efs.2	-	c.813C>A	c.(811-813)ACC>ACA	p.T271T	ZNF423_uc010vgn.1_Silent_p.T154T	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	271	C2H2-type 6.				cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription activator activity|transcription repressor activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)								386				0.1875	13.234994	16.158092	6	26	KEEP	---	---	---	---	capture		Silent	SNP	49672250	49672250	18491	16	G	T	T	T	444	35	ZNF423	2	2
MYH1	4619	broad.mit.edu	37	17	10403943	10403943	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10403943C>T	uc002gmo.2	-	c.3865G>A	c.(3865-3867)GGT>AGT	p.G1289S		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1289	Potential.			TESG -> QNQV (in Ref. 4; CAA27380).		muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.211268	36.785978	42.259758	15	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10403943	10403943	10424	17	C	T	T	T	312	24	MYH1	2	2
ZNF287	57336	broad.mit.edu	37	17	16456596	16456596	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16456596A>C	uc002gqi.2	-	c.860T>G	c.(859-861)ATT>AGT	p.I287S		NM_020653	NP_065704	Q9HBT7	ZN287_HUMAN	zinc finger protein 287	280					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)										0.158416	30.349559	41.572816	16	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16456596	16456596	18417	17	A	C	C	C	52	4	ZNF287	4	4
B9D1	27077	broad.mit.edu	37	17	19263678	19263678	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:19263678G>T	uc010cqn.1	-	c.239C>A	c.(238-240)ACT>AAT	p.T80N	B9D1_uc010cqm.1_Missense_Mutation_p.T5N|B9D1_uc002gvl.3_Missense_Mutation_p.T5N|B9D1_uc010vyr.1_Missense_Mutation_p.T49N|B9D1_uc010vys.1_Missense_Mutation_p.T80N|B9D1_uc002gvk.3_Nonsense_Mutation_p.Y29*	NM_015681	NP_056496	Q9UPM9	B9D1_HUMAN	B9 protein	Error:Variant_position_missing_in_Q9UPM9_after_alignment					cilium assembly	centrosome|microtubule basal body	protein binding				0	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)													0.076923	-0.291792	13.981894	6	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19263678	19263678	1298	17	G	T	T	T	464	36	B9D1	2	2
KCNJ12	3768	broad.mit.edu	37	17	21319507	21319507	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:21319507C>A	uc002gyv.1	+	c.853C>A	c.(853-855)CGG>AGG	p.R285R		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	285	Cytoplasmic (By similarity).			Missing (in Ref. 1; AAA65122).	blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)	3				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)						Prostate(3;0.18)			0.097561	3.07494	9.718597	4	37	KEEP	---	---	---	---	capture		Silent	SNP	21319507	21319507	8351	17	C	A	A	A	295	23	KCNJ12	1	1
ACCN1	40	broad.mit.edu	37	17	32483211	32483211	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:32483211A>T	uc002hhu.2	-	c.341T>A	c.(340-342)CTG>CAG	p.L114Q		NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal	114	Extracellular (By similarity).				central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)									0.115385	11.625175	22.983569	9	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32483211	32483211	129	17	A	T	T	T	91	7	ACCN1	3	3
KIAA1267	284058	broad.mit.edu	37	17	44109534	44109534	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:44109534C>A	uc002ikb.2	-	c.2969G>T	c.(2968-2970)AGG>ATG	p.R990M	KIAA1267_uc002ikc.2_Missense_Mutation_p.R990M|KIAA1267_uc002ikd.2_Missense_Mutation_p.R990M|KIAA1267_uc010dav.2_Missense_Mutation_p.R989M|KIAA1267_uc010wkb.1_Missense_Mutation_p.R321M|KIAA1267_uc010wkc.1_Missense_Mutation_p.R258M	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	990						MLL1 complex	protein binding				0		Melanoma(429;0.211)												0.188406	23.747049	30.013088	13	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44109534	44109534	8528	17	C	A	A	A	312	24	KIAA1267	2	2
TP53	7157	broad.mit.edu	37	17	7578479	7578479	+	Missense_Mutation	SNP	G	A	A	rs28934874		TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578479G>A	uc002gim.2	-	c.451C>T	c.(451-453)CCC>TCC	p.P151S	TP53_uc002gig.1_Missense_Mutation_p.P151S|TP53_uc002gih.2_Missense_Mutation_p.P151S|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.P19S|TP53_uc010cng.1_Missense_Mutation_p.P19S|TP53_uc002gii.1_Missense_Mutation_p.P19S|TP53_uc010cnh.1_Missense_Mutation_p.P151S|TP53_uc010cni.1_Missense_Mutation_p.P151S|TP53_uc002gij.2_Missense_Mutation_p.P151S|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.P58S|TP53_uc002gio.2_Missense_Mutation_p.P19S|TP53_uc010vug.1_Missense_Mutation_p.P112S	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	151	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		P -> R (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.P151S(60)|p.P151T(13)|p.P152fs*18(9)|p.P151A(7)|p.0?(6)|p.P151fs*30(6)|p.T150fs*16(3)|p.D148_T155delDSTPPPGT(1)|p.Q144_G154del11(1)|p.T150_P153delTPPP(1)|p.P152fs*28(1)|p.T150_P151delTP(1)|p.P151_V173del23(1)|p.P152fs*14(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.S149fs*17(1)|p.P151del(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.P151T(HPAFII-Tumor)|p.P151A(SNU119-Tumor)|p.P151T(SCC4-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.2	33.476424	40.55801	17	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7578479	7578479	16923	17	G	A	A	A	572	44	TP53	2	2
ALOXE3	59344	broad.mit.edu	37	17	8011889	8011889	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8011889C>A	uc002gka.2	-	c.2049G>T	c.(2047-2049)GTG>GTT	p.V683V	ALOXE3_uc010cnr.2_Silent_p.V527V|ALOXE3_uc010vuo.1_Silent_p.V659V	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3 isoform 2	527	Lipoxygenase.				leukotriene biosynthetic process|oxidation-reduction process		iron ion binding|lipoxygenase activity			lung(1)|central_nervous_system(1)	2														0.115385	14.237638	29.37978	12	92	KEEP	---	---	---	---	capture		Silent	SNP	8011889	8011889	545	17	C	A	A	A	262	21	ALOXE3	2	2
ELAC1	55520	broad.mit.edu	37	18	48513137	48513137	+	Silent	SNP	G	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:48513137G>C	uc002lez.2	+	c.774G>C	c.(772-774)GTG>GTC	p.V258V	SMAD4_uc010xdo.1_Intron	NM_018696	NP_061166	Q9H777	RNZ1_HUMAN	elaC homolog 1	258					tRNA 3'-trailer cleavage	nucleus	endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)										0.176471	10.227409	13.584139	6	28	KEEP	---	---	---	---	capture		Silent	SNP	48513137	48513137	5237	18	G	C	C	C	600	47	ELAC1	3	3
NPHS1	4868	broad.mit.edu	37	19	36336398	36336398	+	Missense_Mutation	SNP	C	A	A	rs114615449	by1000genomes	TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36336398C>A	uc002oby.2	-	c.1802G>T	c.(1801-1803)GGC>GTC	p.G601V		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	601	Ig-like C2-type 6.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.285714	8.589821	9.170055	4	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36336398	36336398	10986	19	C	A	A	A	338	26	NPHS1	2	2
CEACAM7	1087	broad.mit.edu	37	19	42190824	42190824	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42190824C>A	uc002ori.1	-	c.393G>T	c.(391-393)GTG>GTT	p.V131V	CEACAM7_uc010ehx.2_Silent_p.V131V|CEACAM7_uc010ehy.1_Silent_p.V131V	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion	131	Ig-like V-type.					anchored to membrane|integral to membrane|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)										0.163462	25.179718	36.435171	17	87	KEEP	---	---	---	---	capture		Silent	SNP	42190824	42190824	3330	19	C	A	A	A	366	29	CEACAM7	2	2
CEACAM7	1087	broad.mit.edu	37	19	42190826	42190826	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42190826C>A	uc002ori.1	-	c.391G>T	c.(391-393)GTG>TTG	p.V131L	CEACAM7_uc010ehx.2_Missense_Mutation_p.V131L|CEACAM7_uc010ehy.1_Missense_Mutation_p.V131L	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion	131	Ig-like V-type.					anchored to membrane|integral to membrane|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)										0.173077	31.02071	41.519607	18	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42190826	42190826	3330	19	C	A	A	A	221	17	CEACAM7	2	2
ZNF470	388566	broad.mit.edu	37	19	57089313	57089313	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57089313G>A	uc002qnl.3	+	c.1516G>A	c.(1516-1518)GAG>AAG	p.E506K	ZNF470_uc010etn.2_Intron	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	506					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)										0.243243	46.118211	50.561607	18	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57089313	57089313	18523	19	G	A	A	A	429	33	ZNF470	2	2
ZNF835	90485	broad.mit.edu	37	19	57175469	57175469	+	Silent	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57175469G>A	uc010ygo.1	-	c.1164C>T	c.(1162-1164)GAC>GAT	p.D388D	ZNF835_uc010ygn.1_Silent_p.D366D	NM_001005850	NP_001005850	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	388	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(3)|skin(1)	4														0.115385	2.707287	6.495574	3	23	KEEP	---	---	---	---	capture		Silent	SNP	57175469	57175469	18785	19	G	A	A	A	464	36	ZNF835	2	2
KCND3	3752	broad.mit.edu	37	1	112525025	112525025	+	Silent	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:112525025G>A	uc001ebu.1	-	c.324C>T	c.(322-324)TAC>TAT	p.Y108Y	KCND3_uc001ebv.1_Silent_p.Y108Y	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related	108	Cytoplasmic (Potential).					sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)										0.2	35.335153	42.445265	17	68	KEEP	---	---	---	---	capture		Silent	SNP	112525025	112525025	8325	1	G	A	A	A	516	40	KCND3	1	1
LRIG2	9860	broad.mit.edu	37	1	113658959	113658959	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:113658959A>G	uc001edf.1	+	c.2581A>G	c.(2581-2583)ACG>GCG	p.T861A	LRIG2_uc009wgn.1_Missense_Mutation_p.T758A	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	861	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)										0.185185	12.663965	15.168628	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113658959	113658959	9318	1	A	G	G	G	26	2	LRIG2	4	4
ZNF687	57592	broad.mit.edu	37	1	151260766	151260766	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151260766A>T	uc001exq.2	+	c.1999A>T	c.(1999-2001)ACC>TCC	p.T667S	ZNF687_uc001exp.1_Missense_Mutation_p.T676S|ZNF687_uc009wmo.2_Missense_Mutation_p.T667S|ZNF687_uc009wmp.2_Missense_Mutation_p.T667S	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	667					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)											0.24	13.035447	14.586695	6	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151260766	151260766	18687	1	A	T	T	T	78	6	ZNF687	3	3
FLG	2312	broad.mit.edu	37	1	152283735	152283735	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152283735C>A	uc001ezu.1	-	c.3627G>T	c.(3625-3627)GGG>GGT	p.G1209G		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1209	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.147826	48.573841	76.052227	34	196	KEEP	---	---	---	---	capture		Silent	SNP	152283735	152283735	6160	1	C	A	A	A	327	26	FLG	2	2
S100A7L2	645922	broad.mit.edu	37	1	153410770	153410770	+	Silent	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153410770G>A	uc010pdx.1	-	c.69C>T	c.(67-69)GAC>GAT	p.D23D		NM_001045479	NP_001038944			S100 calcium binding protein A7-like 2											ovary(1)	1	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.164835	27.092957	36.777289	15	76	KEEP	---	---	---	---	capture		Silent	SNP	153410770	153410770	14265	1	G	A	A	A	620	48	S100A7L2	2	2
POU2F1	5451	broad.mit.edu	37	1	167341161	167341161	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167341161C>T	uc001gef.2	+	c.257C>T	c.(256-258)TCT>TTT	p.S86F	POU2F1_uc010plg.1_Non-coding_Transcript|POU2F1_uc001gec.2_Missense_Mutation_p.S74F|POU2F1_uc001ged.2_Missense_Mutation_p.S72F|POU2F1_uc001gee.2_Missense_Mutation_p.S74F|POU2F1_uc010plh.1_Missense_Mutation_p.S74F|POU2F1_uc001geg.2_5'UTR	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	74					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			central_nervous_system(2)|breast(1)	3														0.091787	8.563219	43.311898	19	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167341161	167341161	12701	1	C	T	T	T	416	32	POU2F1	2	2
BLZF1	8548	broad.mit.edu	37	1	169338766	169338766	+	Silent	SNP	T	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:169338766T>C	uc001gfx.1	+	c.6T>C	c.(4-6)ACT>ACC	p.T2T	NME7_uc001gfu.2_5'Flank|NME7_uc010plq.1_5'Flank|NME7_uc001gft.2_5'Flank|BLZF1_uc001gfw.2_Silent_p.T2T|BLZF1_uc001gfy.2_Silent_p.T2T|NME7_uc001gfv.1_5'Flank	NM_003666	NP_003657	Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	2					cell proliferation|Golgi organization|Golgi to plasma membrane protein transport|regulation of cell growth|regulation of transcription from RNA polymerase II promoter	Golgi lumen|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0	all_hematologic(923;0.208)													0.344828	62.183282	63.416239	20	38	KEEP	---	---	---	---	capture		Silent	SNP	169338766	169338766	1478	1	T	C	C	C	678	53	BLZF1	4	4
HMCN1	83872	broad.mit.edu	37	1	185976334	185976334	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:185976334G>T	uc001grq.1	+	c.4550G>T	c.(4549-4551)AGA>ATA	p.R1517I		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1517	Ig-like C2-type 12.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.111111	4.035869	14.850134	8	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185976334	185976334	7511	1	G	T	T	T	429	33	HMCN1	2	2
DDOST	1650	broad.mit.edu	37	1	20981967	20981967	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:20981967A>G	uc009vpw.1	-	c.568T>C	c.(568-570)TCA>CCA	p.S190P	DDOST_uc001bdo.1_Missense_Mutation_p.S190P|DDOST_uc010odd.1_5'UTR|DDOST_uc010ode.1_Missense_Mutation_p.S153P	NM_005216	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide-protein	190	Lumenal (Potential).				innate immune response|post-translational protein modification|protein N-linked glycosylation via asparagine|response to cytokine stimulus|T cell activation	integral to membrane|microsome|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)										0.112903	5.584621	14.765079	7	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20981967	20981967	4506	1	A	G	G	G	156	12	DDOST	4	4
USH2A	7399	broad.mit.edu	37	1	215914876	215914876	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215914876C>A	uc001hku.1	-	c.11552G>T	c.(11551-11553)AGT>ATT	p.S3851I		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3851	Fibronectin type-III 23.|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)										0.162162	20.555704	28.585927	12	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215914876	215914876	17598	1	C	A	A	A	260	20	USH2A	2	2
HSPG2	3339	broad.mit.edu	37	1	22213794	22213794	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:22213794G>A	uc009vqd.2	-	c.992C>T	c.(991-993)CCC>CTC	p.P331L	HSPG2_uc001bfj.2_Missense_Mutation_p.P331L|HSPG2_uc009vqe.1_3'UTR	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	331	LDL-receptor class A 3.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)	8		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)									0.107143	3.023813	7.294656	3	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22213794	22213794	7730	1	G	A	A	A	559	43	HSPG2	2	2
LBR	3930	broad.mit.edu	37	1	225594529	225594529	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:225594529C>A	uc001hoy.2	-	c.1320G>T	c.(1318-1320)GCG>GCT	p.A440A	LBR_uc001hoz.2_Silent_p.A440A|LBR_uc001hpa.1_Silent_p.A440A	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	440					cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)	1	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)										0.190476	26.069761	31.707749	12	51	KEEP	---	---	---	---	capture		Silent	SNP	225594529	225594529	8975	1	C	A	A	A	236	19	LBR	1	1
OBSCN	84033	broad.mit.edu	37	1	228466462	228466462	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228466462G>T	uc009xez.1	+	c.6932G>T	c.(6931-6933)TGT>TTT	p.C2311F	OBSCN_uc001hsn.2_Missense_Mutation_p.C2311F|OBSCN_uc001hsp.1_Missense_Mutation_p.C10F|OBSCN_uc001hsq.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2311	Ig-like 23.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.222222	9.39006	10.66805	4	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228466462	228466462	11217	1	G	T	T	T	624	48	OBSCN	2	2
TRIM58	25893	broad.mit.edu	37	1	248039392	248039392	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248039392A>T	uc001ido.2	+	c.1062A>T	c.(1060-1062)GAA>GAT	p.E354D	OR2W3_uc001idp.1_Intron	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	354	B30.2/SPRY.					intracellular	zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)											0.143791	28.002956	46.818342	22	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248039392	248039392	17077	1	A	T	T	T	37	3	TRIM58	3	3
ROR1	4919	broad.mit.edu	37	1	64644284	64644284	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:64644284C>G	uc001dbj.2	+	c.2560C>G	c.(2560-2562)CGG>GGG	p.R854G		NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	854	Cytoplasmic (Potential).|Ser/Thr-rich.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|stomach(1)|breast(1)|skin(1)|kidney(1)	13										216				0.098039	4.344863	12.584239	5	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64644284	64644284	14005	1	C	G	G	G	399	31	ROR1	3	3
CST9	128822	broad.mit.edu	37	20	23584335	23584335	+	Silent	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23584335G>A	uc002wtl.2	-	c.292C>T	c.(292-294)CTG>TTG	p.L98L		NM_001008693	NP_001008693	Q5W186	CST9_HUMAN	cystatin 9 precursor	98						extracellular region	cysteine-type endopeptidase inhibitor activity			ovary(1)	1	Colorectal(13;0.0993)													0.153846	26.23819	38.152701	16	88	KEEP	---	---	---	---	capture		Silent	SNP	23584335	23584335	4120	20	G	A	A	A	464	36	CST9	2	2
MOCS3	27304	broad.mit.edu	37	20	49575867	49575867	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49575867C>T	uc002xvy.1	+	c.488C>T	c.(487-489)CCA>CTA	p.P163L	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	163					enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			ovary(1)|skin(1)	2														0.078431	-0.632152	8.625789	4	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49575867	49575867	10083	20	C	T	T	T	273	21	MOCS3	2	2
TMPRSS2	7113	broad.mit.edu	37	21	42866376	42866376	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:42866376C>T	uc010gor.2	-	c.256G>A	c.(256-258)GTG>ATG	p.V86M	TMPRSS2_uc002yzj.2_Missense_Mutation_p.V49M|TMPRSS2_uc010gos.1_Missense_Mutation_p.V49M	NM_001135099	NP_001128571	O15393	TMPS2_HUMAN	transmembrane protease, serine 2 isoform 1	49	Cytoplasmic (Potential).				proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2058)|TMPRSS2/ETV1(24)	prostate(2082)|central_nervous_system(1)	2083		Prostate(19;4.48e-07)|all_epithelial(19;0.031)								848				0.153846	18.456579	27.390283	12	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42866376	42866376	16788	21	C	T	T	T	247	19	TMPRSS2	1	1
RASD2	23551	broad.mit.edu	37	22	35947786	35947786	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:35947786G>T	uc003anx.2	+	c.508G>T	c.(508-510)GAG>TAG	p.E170*	RASD2_uc003any.2_Nonsense_Mutation_p.E170*	NM_014310	NP_055125	Q96D21	RHES_HUMAN	RASD family, member 2 precursor	170					locomotory behavior|positive regulation of protein kinase B signaling cascade|positive regulation of protein sumoylation|regulation of cAMP-mediated signaling|small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity			skin(1)	1														0.294118	26.44343	27.729296	10	24	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	35947786	35947786	13528	22	G	T	T	T	481	37	RASD2	5	1
LRP1B	53353	broad.mit.edu	37	2	141027872	141027873	+	Missense_Mutation	DNP	CA	AT	AT			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141027872_141027873CA>AT	uc002tvj.1	-	c.13185_13186TG>AT	c.(13183-13188)GATGGC>GAATGC	p.4395_4396DG>EC		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4395_4396	Extracellular (Potential).|EGF-like 14.				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)			0.176471	22.154726	28.867588	12	56	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	141027872	141027873	9328	2	CA	AT	AT	AT	273	21	LRP1B	2	2
XIRP2	129446	broad.mit.edu	37	2	168100767	168100767	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168100767C>A	uc002udx.2	+	c.2865C>A	c.(2863-2865)AAC>AAA	p.N955K	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.N780K|XIRP2_uc010fpq.2_Missense_Mutation_p.N733K|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	780	Xin 12.				actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.190476	22.761356	28.419406	12	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168100767	168100767	18011	2	C	A	A	A	220	17	XIRP2	2	2
SP3	6670	broad.mit.edu	37	2	174783494	174783494	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:174783494T>A	uc002uig.2	-	c.1659A>T	c.(1657-1659)GAA>GAT	p.E553D	SP3_uc002uie.2_Missense_Mutation_p.E485D|SP3_uc002uif.2_Missense_Mutation_p.E500D|SP3_uc010zel.1_Missense_Mutation_p.E550D	NM_003111	NP_003102	Q02447	SP3_HUMAN	Sp3 transcription factor isoform 1	553	Repressor domain.			KEE->AAA: Increases transcriptional activity.|KEE->RED: 200-fold increase in transcriptional activation.|KEE->REA: 200-fold increase in transcriptional activation.	negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	protein binding|transcription activator activity|transcription repressor activity|zinc ion binding		EWSR1/SP3(3)	soft_tissue(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.185)											0.242424	17.579974	19.580337	8	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	174783494	174783494	15465	2	T	A	A	A	725	56	SP3	3	3
TTN	7273	broad.mit.edu	37	2	179458092	179458092	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179458092G>T	uc010zfg.1	-	c.51139C>A	c.(51139-51141)CTG>ATG	p.L17047M	TTN_uc010zfh.1_Missense_Mutation_p.L10742M|TTN_uc010zfi.1_Missense_Mutation_p.L10675M|TTN_uc010zfj.1_Missense_Mutation_p.L10550M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	Error:Variant_position_missing_in_Q4ZG20_after_alignment										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				0.052632	-10.200088	9.887508	5	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179458092	179458092	17290	2	G	T	T	T	451	35	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179578798	179578798	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179578798A>T	uc010zfg.1	-	c.22855T>A	c.(22855-22857)TGG>AGG	p.W7619R	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.W4280R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3537										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				0.179104	24.448868	30.962959	12	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179578798	179578798	17290	2	A	T	T	T	78	6	TTN	3	3
COL3A1	1281	broad.mit.edu	37	2	189850488	189850488	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:189850488G>T	uc002uqj.1	+	c.431G>T	c.(430-432)TGC>TTC	p.C144F		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	144					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				0.166667	8.08847	10.613831	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	189850488	189850488	3826	2	G	T	T	T	598	46	COL3A1	2	2
SLC19A3	80704	broad.mit.edu	37	2	228560708	228560708	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228560708C>A	uc002vpi.2	-	c.1069G>T	c.(1069-1071)GCC>TCC	p.A357S	SLC19A3_uc002vpj.2_Non-coding_Transcript|SLC19A3_uc010zlv.1_Missense_Mutation_p.A353S	NM_025243	NP_079519	Q9BZV2	S19A3_HUMAN	solute carrier family 19, member 3	357	Helical; (Potential).				thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|reduced folate carrier activity|thiamine uptake transmembrane transporter activity			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)									0.152174	11.832292	17.129569	7	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228560708	228560708	14926	2	C	A	A	A	325	25	SLC19A3	2	2
SPHKAP	80309	broad.mit.edu	37	2	228855814	228855814	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228855814C>A	uc002vpq.2	-	c.4861G>T	c.(4861-4863)GAT>TAT	p.D1621Y	SPHKAP_uc002vpp.2_Missense_Mutation_p.D1592Y|SPHKAP_uc010zlx.1_Intron	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1621						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.195122	15.975372	19.530594	8	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228855814	228855814	15560	2	C	A	A	A	416	32	SPHKAP	2	2
SP140	11262	broad.mit.edu	37	2	231090581	231090581	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231090581G>T	uc002vql.2	+	c.22G>T	c.(22-24)GGG>TGG	p.G8W	SP140_uc010zma.1_Non-coding_Transcript|SP140_uc002vqj.2_Missense_Mutation_p.G8W|SP140_uc002vqk.2_Missense_Mutation_p.G8W|SP140_uc002vqn.2_Missense_Mutation_p.G8W|SP140_uc002vqm.2_Missense_Mutation_p.G8W|SP140_uc010fxl.2_Missense_Mutation_p.G8W	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1	8					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)						802				0.213483	38.86116	45.632225	19	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231090581	231090581	15462	2	G	T	T	T	559	43	SP140	2	2
DCLK3	85443	broad.mit.edu	37	3	36779132	36779132	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36779132C>T	uc003cgi.2	-	c.1019G>A	c.(1018-1020)CGG>CAG	p.R340Q		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	340					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|ovary(1)|breast(1)|kidney(1)	8										128				0.068966	-8.250776	19.617806	10	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36779132	36779132	4464	3	C	T	T	T	299	23	DCLK3	1	1
BSN	8927	broad.mit.edu	37	3	49689125	49689125	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49689125G>T	uc003cxe.3	+	c.2136G>T	c.(2134-2136)GGG>GGT	p.G712G		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	712					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	zinc ion binding			ovary(5)|central_nervous_system(1)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)										0.294118	32.529641	34.455612	15	36	KEEP	---	---	---	---	capture		Silent	SNP	49689125	49689125	1561	3	G	T	T	T	548	43	BSN	2	2
ROBO2	6092	broad.mit.edu	37	3	77626672	77626672	+	Silent	SNP	A	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:77626672A>C	uc003dpz.2	+	c.2247A>C	c.(2245-2247)GTA>GTC	p.V749V	ROBO2_uc003dpy.3_Silent_p.V745V|ROBO2_uc011bgj.1_Non-coding_Transcript|ROBO2_uc011bgk.1_Silent_p.V749V	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	745	Fibronectin type-III 3.|Extracellular (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|ovary(1)|large_intestine(1)|liver(1)	8				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)						1049				0.333333	63.825283	65.56291	23	46	KEEP	---	---	---	---	capture		Silent	SNP	77626672	77626672	13993	3	A	C	C	C	171	14	ROBO2	4	4
FAT4	79633	broad.mit.edu	37	4	126411871	126411871	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126411871G>T	uc003ifj.3	+	c.13894G>T	c.(13894-13896)GAT>TAT	p.D4632Y	FAT4_uc011cgp.1_Missense_Mutation_p.D2873Y|FAT4_uc003ifi.1_Missense_Mutation_p.D2109Y	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4632	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.2375	42.380921	47.42168	19	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126411871	126411871	5928	4	G	T	T	T	533	41	FAT4	2	2
WDFY3	23001	broad.mit.edu	37	4	85752722	85752722	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:85752722C>A	uc003hpd.2	-	c.613G>T	c.(613-615)GAG>TAG	p.E205*	WDFY3_uc003hpf.2_Nonsense_Mutation_p.E205*	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	205						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)										0.166667	21.824442	30.045938	13	65	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	85752722	85752722	17842	4	C	A	A	A	390	30	WDFY3	5	2
EGR1	1958	broad.mit.edu	37	5	137802964	137802964	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137802964G>A	uc003ldb.1	+	c.826G>A	c.(826-828)GGC>AGC	p.G276S	EGR1_uc011cyu.1_Intron	NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	276					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of glomerular metanephric mesangial cell proliferation|regulation of protein sumoylation|type I interferon-mediated signaling pathway	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|specific RNA polymerase II transcription factor activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)											0.132075	9.420943	16.380071	7	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137802964	137802964	5160	5	G	A	A	A	559	43	EGR1	2	2
PCDHB2	56133	broad.mit.edu	37	5	140474884	140474884	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140474884A>C	uc003lil.2	+	c.510A>C	c.(508-510)CAA>CAC	p.Q170H	PCDHB2_uc003lim.1_5'UTR	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	170	Extracellular (Potential).|Cadherin 2.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.170213	17.271085	22.106387	8	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140474884	140474884	11962	5	A	C	C	C	11	1	PCDHB2	4	4
C5orf40	408263	broad.mit.edu	37	5	156769987	156769987	+	Silent	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156769987C>T	uc003lwu.2	-	c.558G>A	c.(556-558)AAG>AAA	p.K186K	CYFIP2_uc003lwq.2_Intron|CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001001343	NP_001001343	Q8TBE3	FNDC9_HUMAN	hypothetical protein LOC408263	186						integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)									OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.107143	14.813104	40.582928	18	150	KEEP	---	---	---	---	capture		Silent	SNP	156769987	156769987	2397	5	C	T	T	T	415	32	C5orf40	2	2
CDHR2	54825	broad.mit.edu	37	5	176017474	176017474	+	Silent	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176017474G>A	uc003mem.1	+	c.3402G>A	c.(3400-3402)GGG>GGA	p.G1134G	CDHR2_uc003men.1_Silent_p.G1134G	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor	1134	Extracellular (Potential).				homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2														0.333333	25.641816	26.378932	10	20	KEEP	---	---	---	---	capture		Silent	SNP	176017474	176017474	3248	5	G	A	A	A	535	42	CDHR2	2	2
CDH10	1008	broad.mit.edu	37	5	24509847	24509847	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:24509847G>T	uc003jgr.1	-	c.1084C>A	c.(1084-1086)CTA>ATA	p.L362I	CDH10_uc011cnu.1_Non-coding_Transcript	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	362	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)										0.209302	20.351778	23.715059	9	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24509847	24509847	3225	5	G	T	T	T	451	35	CDH10	2	2
IRX2	153572	broad.mit.edu	37	5	2748735	2748735	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:2748735T>G	uc003jda.2	-	c.1087A>C	c.(1087-1089)ACC>CCC	p.T363P	IRX2_uc003jdb.2_Missense_Mutation_p.T363P	NM_001134222	NP_001127694	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	363					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			skin(1)	1				GBM - Glioblastoma multiforme(108;0.204)										0.4	9.449725	9.549758	4	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2748735	2748735	8148	5	T	G	G	G	780	60	IRX2	4	4
ITGA2	3673	broad.mit.edu	37	5	52386429	52386429	+	Nonstop_Mutation	SNP	A	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:52386429A>C	uc003joy.2	+	c.3546A>C	c.(3544-3546)TGA>TGC	p.*1182C	ITGA2_uc011cqa.1_Non-coding_Transcript|ITGA2_uc011cqb.1_Non-coding_Transcript|ITGA2_uc011cqc.1_Nonstop_Mutation_p.*1106C|ITGA2_uc011cqd.1_Non-coding_Transcript|ITGA2_uc011cqe.1_Non-coding_Transcript	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor	1182					axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)												0.246154	43.770264	47.58198	16	49	KEEP	---	---	---	---	capture		Nonstop_Mutation	SNP	52386429	52386429	8179	5	A	C	C	C	117	9	ITGA2	5	4
SOBP	55084	broad.mit.edu	37	6	107955722	107955722	+	Silent	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:107955722C>T	uc003prx.2	+	c.1674C>T	c.(1672-1674)AAC>AAT	p.N558N		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	558							metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)										0.272727	8.121756	8.632865	3	8	KEEP	---	---	---	---	capture		Silent	SNP	107955722	107955722	15412	6	C	T	T	T	246	19	SOBP	1	1
GOPC	57120	broad.mit.edu	37	6	117884489	117884489	+	Silent	SNP	A	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117884489A>G	uc003pxu.2	-	c.1317T>C	c.(1315-1317)AGT>AGC	p.S439S	GOPC_uc003pxq.1_Intron|DCBLD1_uc003pxs.2_Intron|GOPC_uc003pxv.2_Silent_p.S431S	NM_020399	NP_065132	Q9HD26	GOPC_HUMAN	golgi associated PDZ and coiled-coil motif	439					apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding				0		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)						74				0.14	9.89189	16.153735	7	43	KEEP	---	---	---	---	capture		Silent	SNP	117884489	117884489	6846	6	A	G	G	G	76	6	GOPC	4	4
SYNE1	23345	broad.mit.edu	37	6	152792777	152792777	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:152792777C>A	uc010kiw.2	-	c.1587G>T	c.(1585-1587)AAG>AAT	p.K529N	SYNE1_uc003qot.3_Missense_Mutation_p.K536N|SYNE1_uc003qou.3_Missense_Mutation_p.K529N|SYNE1_uc010kjb.1_Missense_Mutation_p.K512N|SYNE1_uc003qpa.1_Missense_Mutation_p.K529N|SYNE1_uc003qox.1_Missense_Mutation_p.K45N|SYNE1_uc003qoz.2_5'UTR|SYNE1_uc003qoy.2_Missense_Mutation_p.K96N	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	529	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.157895	41.399515	58.367652	24	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152792777	152792777	15966	6	C	A	A	A	259	20	SYNE1	2	2
CLPS	1208	broad.mit.edu	37	6	35763532	35763532	+	Silent	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:35763532G>A	uc003ole.1	-	c.183C>T	c.(181-183)AGC>AGT	p.S61S	CLPS_uc003olf.1_Intron	NM_001832	NP_001823	P04118	COL_HUMAN	colipase preproprotein	61					lipid catabolic process|lipid digestion|retinoid metabolic process|steroid metabolic process	extracellular region					0						Melanoma(167;2962 3494 37796)								0.07	-3.754557	15.238871	7	93	KEEP	---	---	---	---	capture		Silent	SNP	35763532	35763532	3691	6	G	A	A	A	490	38	CLPS	1	1
HYAL4	23553	broad.mit.edu	37	7	123517127	123517127	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123517127G>T	uc003vlc.2	+	c.1364G>T	c.(1363-1365)TGC>TTC	p.C455F	HYAL4_uc011knz.1_3'UTR	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	455	Helical; (Potential).				fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity				0														0.082353	-0.516247	14.550953	7	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123517127	123517127	7766	7	G	T	T	T	598	46	HYAL4	2	2
CHRM2	1129	broad.mit.edu	37	7	136700551	136700551	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:136700551C>A	uc003vtf.1	+	c.939C>A	c.(937-939)GGC>GGA	p.G313G	CHRM2_uc003vtg.1_Silent_p.G313G|CHRM2_uc003vtj.1_Silent_p.G313G|CHRM2_uc003vtk.1_Silent_p.G313G|CHRM2_uc003vtl.1_Silent_p.G313G|CHRM2_uc003vtm.1_Silent_p.G313G|CHRM2_uc003vti.1_Silent_p.G313G|CHRM2_uc003vto.1_Silent_p.G313G|CHRM2_uc003vtn.1_Silent_p.G313G	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	313	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)									0.192547	66.458142	80.656653	31	130	KEEP	---	---	---	---	capture		Silent	SNP	136700551	136700551	3511	7	C	A	A	A	327	26	CHRM2	2	2
HOXA2	3199	broad.mit.edu	37	7	27140509	27140509	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27140509G>T	uc003syh.2	-	c.967C>A	c.(967-969)CAG>AAG	p.Q323K		NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2	323						nucleus	sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.297872	74.964085	78.397186	28	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27140509	27140509	7584	7	G	T	T	T	598	46	HOXA2	2	2
DTX2	113878	broad.mit.edu	37	7	76112337	76112337	+	Silent	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:76112337C>T	uc011kgk.1	+	c.508C>T	c.(508-510)CTG>TTG	p.L170L	DTX2_uc003uff.3_Silent_p.L261L|DTX2_uc003ufg.3_Silent_p.L261L|DTX2_uc003ufh.3_Silent_p.L261L|DTX2_uc003ufj.3_Silent_p.L261L	NM_020892	NP_065943	Q86UW9	DTX2_HUMAN	deltex 2 isoform a	261					Notch signaling pathway	cytoplasm|nucleus	protein binding|zinc ion binding			ovary(1)	1														0.082474	-0.862545	16.351815	8	89	KEEP	---	---	---	---	capture		Silent	SNP	76112337	76112337	4979	7	C	T	T	T	363	28	DTX2	2	2
ABCB4	5244	broad.mit.edu	37	7	87081014	87081014	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:87081014G>T	uc003uiv.1	-	c.633C>A	c.(631-633)ATC>ATA	p.I211I	ABCB4_uc003uiw.1_Silent_p.I211I|ABCB4_uc003uix.1_Silent_p.I211I	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	211	ABC transmembrane type-1 1.|Extracellular (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.211111	44.47391	51.421365	19	71	KEEP	---	---	---	---	capture		Silent	SNP	87081014	87081014	44	7	G	T	T	T	577	45	ABCB4	2	2
COL22A1	169044	broad.mit.edu	37	8	139715564	139715564	+	Silent	SNP	G	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139715564G>C	uc003yvd.2	-	c.2544C>G	c.(2542-2544)CCC>CCG	p.P848P	COL22A1_uc011ljo.1_Silent_p.P148P	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	848	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.109091	6.011958	14.336373	6	49	KEEP	---	---	---	---	capture		Silent	SNP	139715564	139715564	3819	8	G	C	C	C	496	39	COL22A1	3	3
HGSNAT	138050	broad.mit.edu	37	8	43033258	43033258	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:43033258C>T	uc003xpx.3	+	c.893C>T	c.(892-894)ACT>ATT	p.T298I		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	326	Cytoplasmic (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)											0.15	26.657477	38.40277	15	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43033258	43033258	7372	8	C	T	T	T	260	20	HGSNAT	2	2
LYPLA1	10434	broad.mit.edu	37	8	54967647	54967647	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:54967647G>T	uc003xry.2	-	c.333C>A	c.(331-333)AAC>AAA	p.N111K	LYPLA1_uc011ldx.1_Missense_Mutation_p.N106K|LYPLA1_uc003xrz.2_Missense_Mutation_p.N90K	NM_006330	NP_006321	O75608	LYPA1_HUMAN	lysophospholipase 1	111					fatty acid metabolic process|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytosol	lysophospholipase activity|palmitoyl-(protein) hydrolase activity			central_nervous_system(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)											0.081081	0.195403	6.81172	3	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54967647	54967647	9493	8	G	T	T	T	620	48	LYPLA1	2	2
CHD7	55636	broad.mit.edu	37	8	61768603	61768603	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:61768603A>G	uc003xue.2	+	c.7006A>G	c.(7006-7008)AGG>GGG	p.R2336G		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2336					central nervous system development|chromatin assembly or disassembly|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	chromatin|nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|lung(1)|breast(1)|pancreas(1)	8		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)											0.142857	7.481637	10.922435	4	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61768603	61768603	3464	8	A	G	G	G	192	15	CHD7	4	4
SULF1	23213	broad.mit.edu	37	8	70488255	70488255	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:70488255G>T	uc010lza.1	+	c.223G>T	c.(223-225)GCC>TCC	p.A75S	SULF1_uc003xyd.2_Missense_Mutation_p.A75S|SULF1_uc003xye.2_Missense_Mutation_p.A75S|SULF1_uc003xyf.2_Missense_Mutation_p.A75S|SULF1_uc003xyg.2_Missense_Mutation_p.A75S	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	75					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)						p.A75T(JVM2-Tumor)	473				0.210526	15.742499	18.643957	8	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70488255	70488255	15890	8	G	T	T	T	546	42	SULF1	2	2
ZFHX4	79776	broad.mit.edu	37	8	77767551	77767551	+	Silent	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77767551C>A	uc003yav.2	+	c.8259C>A	c.(8257-8259)ACC>ACA	p.T2753T	ZFHX4_uc003yau.1_Silent_p.T2798T|ZFHX4_uc003yaw.1_Silent_p.T2753T	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2753					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)											0.144928	16.908179	25.276026	10	59	KEEP	---	---	---	---	capture		Silent	SNP	77767551	77767551	18223	8	C	A	A	A	288	23	ZFHX4	1	1
RECK	8434	broad.mit.edu	37	9	36087705	36087705	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:36087705G>A	uc003zyv.2	+	c.652G>A	c.(652-654)GAC>AAC	p.D218N	RECK_uc003zyw.2_Missense_Mutation_p.D90N|RECK_uc003zyx.2_Non-coding_Transcript	NM_021111	NP_066934	O95980	RECK_HUMAN	RECK protein precursor	218	Knot 4.|5 X Knot repeats.					anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)											0.101266	5.758851	18.275718	8	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36087705	36087705	13669	9	G	A	A	A	585	45	RECK	2	2
TPD52L3	89882	broad.mit.edu	37	9	6328730	6328730	+	Silent	SNP	C	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:6328730C>G	uc003zjw.2	+	c.135C>G	c.(133-135)ACC>ACG	p.T45T	TPD52L3_uc003zjv.2_Silent_p.T45T|TPD52L3_uc003zjx.1_Silent_p.T45T	NM_033516	NP_277051	Q96J77	TPD55_HUMAN	protein kinase NYD-SP25 isoform 1	45	Potential.						protein binding				0		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0198)|Lung(218;0.1)										0.283784	48.913785	52.043226	21	53	KEEP	---	---	---	---	capture		Silent	SNP	6328730	6328730	16944	9	C	G	G	G	275	22	TPD52L3	3	3
PRUNE2	158471	broad.mit.edu	37	9	79320649	79320649	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:79320649A>C	uc010mpk.2	-	c.6541T>G	c.(6541-6543)TCT>GCT	p.S2181A	PRUNE2_uc004akj.3_5'Flank|PRUNE2_uc010mpl.1_5'Flank	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	2181					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0														0.176471	20.951903	27.672416	12	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79320649	79320649	13092	9	A	C	C	C	143	11	PRUNE2	4	4
DCAF12L2	340578	broad.mit.edu	37	X	125299692	125299692	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:125299692C>A	uc004euk.1	-	c.216G>T	c.(214-216)GAG>GAT	p.E72D		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	72										lung(2)|large_intestine(1)|ovary(1)|pancreas(1)	5														0.291667	17.006308	17.945799	7	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125299692	125299692	4436	23	C	A	A	A	311	24	DCAF12L2	2	2
MAGEB18	286514	broad.mit.edu	37	X	26157197	26157197	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:26157197T>A	uc004dbq.1	+	c.95T>A	c.(94-96)GTG>GAG	p.V32E		NM_173699	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	32							protein binding			central_nervous_system(1)	1														0.190476	15.377002	19.138259	8	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26157197	26157197	9556	23	T	A	A	A	767	59	MAGEB18	3	3
MXRA5	25878	broad.mit.edu	37	X	3228090	3228090	+	Silent	SNP	G	T	T			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3228090G>T	uc004crg.3	-	c.8154C>A	c.(8152-8154)GGC>GGA	p.G2718G		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2718	Ig-like C2-type 11.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.222222	16.180477	18.738085	8	28	KEEP	---	---	---	---	capture		Silent	SNP	3228090	3228090	10397	23	G	T	T	T	535	42	MXRA5	2	2
ZCCHC5	203430	broad.mit.edu	37	X	77912915	77912915	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77912915C>A	uc004edc.1	-	c.1003G>T	c.(1003-1005)GGG>TGG	p.G335W		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	335							nucleic acid binding|zinc ion binding			ovary(1)	1														0.162162	9.924581	13.943715	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77912915	77912915	18179	23	C	A	A	A	312	24	ZCCHC5	2	2
FOXN4	121643	broad.mit.edu	37	12	109725661	109725662	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:109725661_109725662insG	uc001toe.3	-	c.455_456insC	c.(454-456)CCGfs	p.P152fs	FOXN4_uc009zvg.2_5'UTR|FOXN4_uc001tof.3_Intron	NM_213596	NP_998761	Q96NZ1	FOXN4_HUMAN	forkhead box N4	152	Pro-rich.				axon extension|embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|pattern specification process|positive regulation of gene-specific transcription|regulation of heart contraction|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)	2														0.50			3	3		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	109725661	109725662	6268	12	-	G	G	G	288	23	FOXN4	5	5
PRSS12	8492	broad.mit.edu	37	4	119273504	119273505	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z005-01	TCGA-17-Z005-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:119273504_119273505insG	uc003ica.1	-	c.371_372insC	c.(370-372)CCAfs	p.P124fs		NM_003619	NP_003610	P56730	NETR_HUMAN	neurotrypsin precursor	124	Kringle.					membrane	scavenger receptor activity				0														0.43			3	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	119273504	119273505	13065	4	-	G	G	G	704	55	PRSS12	5	5
