Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
PTEN	5728	broad.mit.edu	36	10	89710659	89710659	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710659C>T	uc001kfb.1	+	c.830C>T	c.(829-831)ACA>ATA	p.T277I		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	277	C2 tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.D268_F279>VGQNVSLLGKYI(2)|p.T277I(1)|p.G165_*404del(1)|p.W274_F341del(1)|p.G165_K342del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.703704	55.329884	56.330258	19	8	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89710659	89710659	13192	10	C	T	T	17	17	PTEN	T	2	2
OR4D5	219875	broad.mit.edu	36	11	123316221	123316221	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123316221C>T	uc001pzk.1	+	c.688C>T	c.(688-690)CGG>TGG	p.R230W		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	230	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)												0.353293	280.873719	287.243647	118	216	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)	Missense_Mutation	SNP	123316221	123316221	11464	11	C	T	T	19	19	OR4D5	T	1	1
ADAMTS15	170689	broad.mit.edu	36	11	129848805	129848805	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:129848805G>A	uc001qgh.1	+	c.2732G>A	c.(2731-2733)CGG>CAG	p.R911Q		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	911	TSP type-1 3.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|lung(1)|pancreas(1)	4	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)												0.452381	50.617662	50.70068	19	23	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)	Missense_Mutation	SNP	129848805	129848805	261	11	G	A	A	39	39	ADAMTS15	A	1	1
PELI3	246330	broad.mit.edu	36	11	65999999	65999999	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65999999G>T	uc001oic.2	+	c.1195G>T	c.(1195-1197)GGC>TGC	p.G399C	PELI3_uc001oid.2_Missense_Mutation_p.G375C|PELI3_uc001oie.2_Missense_Mutation_p.G250C	NM_145065	NP_659502	Q8N2H9	PELI3_HUMAN	pellino 3 alpha isoform 1	399						cytosol	protein binding			ovary(1)	1														0.333333	7.285932	7.586247	4	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65999999	65999999	12144	11	G	T	T	47	47	PELI3	T	3	3
GLTP	51228	broad.mit.edu	36	12	108774895	108774895	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:108774895C>T	uc001tpm.1	-	c.478G>A	c.(478-480)GAC>AAC	p.D160N		NM_016433	NP_057517	Q9NZD2	GLTP_HUMAN	glycolipid transfer protein	160						cytoplasm|membrane	glycolipid binding|glycolipid transporter activity				0		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)										OREG0022112	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.391192	378.278662	382.328071	151	235	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.0025)	Missense_Mutation	SNP	108774895	108774895	6739	12	C	T	T	29	29	GLTP	T	2	2
TUBA1A	7846	broad.mit.edu	36	12	47865181	47865181	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:47865181C>T	uc009zlf.1	-	c.1235G>A	c.(1234-1236)GGG>GAG	p.G412E	TUBA1B_uc001rto.1_Intron|TUBA1A_uc001rtp.1_Missense_Mutation_p.G412E|TUBA1A_uc001rtq.1_Missense_Mutation_p.G259E|TUBA1A_uc001rtr.1_Missense_Mutation_p.G259E|TUBA1A_uc009zlg.1_Missense_Mutation_p.G259E	NM_006009	NP_006000	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a	412					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|structural molecule activity				0						Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451)								0.436681	261.996628	262.802072	100	129	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47865181	47865181	17298	12	C	T	T	22	22	TUBA1A	T	2	2
CLSTN3	9746	broad.mit.edu	36	12	7193486	7193486	+	Silent	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7193486C>T	uc001qss.1	+	c.2211C>T	c.(2209-2211)CTC>CTT	p.L737L	CLSTN3_uc001qsr.1_Silent_p.L725L	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	725	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1														0.277778	36.501287	38.90126	15	39	CC		KEEP	---	---	---	---	capture			Silent	SNP	7193486	7193486	3701	12	C	T	T	30	30	CLSTN3	T	2	2
ACSM4	341392	broad.mit.edu	36	12	7368453	7368453	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7368453C>T	uc001qsx.1	+	c.1528C>T	c.(1528-1530)CGC>TGC	p.R510C		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member	510					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0														0.439394	75.863199	76.074424	29	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7368453	7368453	187	12	C	T	T	23	23	ACSM4	T	1	1
COL4A2	1284	broad.mit.edu	36	13	109956830	109956830	+	Nonsense_Mutation	SNP	C	A	A			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:109956830C>A	uc001vqx.1	+	c.4470C>A	c.(4468-4470)TAC>TAA	p.Y1490*		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	1490	Collagen IV NC1.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)												0.285714	8.179644	8.767541	4	10	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)		Nonsense_Mutation	SNP	109956830	109956830	3828	13	C	A	A	18	18	COL4A2	A	5	3
IQCH	64799	broad.mit.edu	36	15	65451865	65451865	+	Silent	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:65451865C>T	uc002aqo.1	+	c.1116C>T	c.(1114-1116)GCC>GCT	p.A372A	IQCH_uc002aqn.1_Silent_p.A199A|IQCH_uc002aqq.1_Silent_p.A120A|IQCH_uc002aqp.1_Silent_p.A124A	NM_001031715	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H isoform 1	372	IQ.									ovary(1)	1														0.356061	129.091784	131.499284	47	85	CC		KEEP	---	---	---	---	capture		Colorectal(3;0.0856)	Silent	SNP	65451865	65451865	8114	15	C	T	T	23	23	IQCH	T	1	1
MAN2C1	4123	broad.mit.edu	36	15	73447563	73447563	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73447563A>C	uc002baf.1	-	c.131T>G	c.(130-132)GTG>GGG	p.V44G	MAN2C1_uc002bag.1_Missense_Mutation_p.V44G|MAN2C1_uc002bah.1_Missense_Mutation_p.V44G|MAN2C1_uc010bkk.1_Missense_Mutation_p.V44G	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	44					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0														0.444444	8.390659	8.415742	4	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73447563	73447563	9601	15	A	C	C	6	6	MAN2C1	C	4	4
EARS2	124454	broad.mit.edu	36	16	23453914	23453914	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23453914C>G	uc002dlu.2	-	c.754G>C	c.(754-756)GTC>CTC	p.V252L	EARS2_uc002dlr.2_Non-coding_Transcript|EARS2_uc002dls.2_Non-coding_Transcript|EARS2_uc002dlt.2_Missense_Mutation_p.V252L	NM_001083614	NP_001077083	Q5JPH6	SYEM_HUMAN	glutamyl tRNA synthetase 2	252					glutamyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|glutamate-tRNA ligase activity|RNA binding				0					L-Glutamic Acid(DB00142)									0.1875	6.416386	7.878858	3	13	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0353)	Missense_Mutation	SNP	23453914	23453914	5064	16	C	G	G	19	19	EARS2	G	3	3
ZKSCAN2	342357	broad.mit.edu	36	16	25158830	25158830	+	Silent	SNP	T	C	C			TCGA-27-1837-01	TCGA-27-1837-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:25158830T>C	uc002dod.2	-	c.2712A>G	c.(2710-2712)GAA>GAG	p.E904E		NM_001012981	NP_001012999	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	904	C2H2-type 5.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|breast(1)	4														0.395349	165.102797	166.337616	51	78	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0378)	Silent	SNP	25158830	25158830	18278	16	T	C	C	60	60	ZKSCAN2	C	4	4
ZNF48	197407	broad.mit.edu	36	16	30317012	30317012	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30317012C>T	uc002dya.1	+	c.940C>T	c.(940-942)CGG>TGG	p.R314W	ZNF48_uc002dxz.1_Missense_Mutation_p.R191W	NM_152652	NP_689865	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	314	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.416667	83.144723	83.57865	30	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30317012	30317012	18528	16	C	T	T	23	23	ZNF48	T	1	1
NCOR1	9611	broad.mit.edu	36	17	16002873	16002873	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:16002873C>T	uc002gpo.1	-	c.658G>A	c.(658-660)GAG>AAG	p.E220K	NCOR1_uc002gpn.1_Missense_Mutation_p.E220K|NCOR1_uc002gpp.1_Missense_Mutation_p.E111K|NCOR1_uc002gpr.2_Missense_Mutation_p.E111K|NCOR1_uc002gps.1_Missense_Mutation_p.E220K|NCOR1_uc010coz.1_Missense_Mutation_p.E36K|NCOR1_uc010cpa.1_Missense_Mutation_p.E220K|NCOR1_uc010cpb.1_Missense_Mutation_p.E220K	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	220	Interaction with ZBTB33 and HEXIM1.				cellular lipid metabolic process|chromatin modification|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of JNK cascade|regulation of fatty acid transport|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	spindle microtubule|transcriptional repressor complex	histone deacetylase binding|promoter binding|transcription corepressor activity			ovary(1)|kidney(1)	2														0.353846	110.29259	112.748672	46	84	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)	Missense_Mutation	SNP	16002873	16002873	10634	17	C	T	T	29	29	NCOR1	T	2	2
MAPK7	5598	broad.mit.edu	36	17	19224730	19224730	+	Silent	SNP	T	C	C			TCGA-27-1837-01	TCGA-27-1837-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19224730T>C	uc002gvn.1	+	c.615T>C	c.(613-615)CGT>CGC	p.R205R	B9D1_uc010cqm.1_5'Flank|B9D1_uc002gvl.2_5'Flank|MAPK7_uc002gvo.1_Silent_p.R66R|MAPK7_uc002gvp.1_Silent_p.R205R|MAPK7_uc002gvq.1_Silent_p.R205R	NM_139033	NP_620601	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	205	Necessary for oligomerization (By similarity).|Protein kinase.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(3)|lung(1)|skin(1)	5	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)								p.R205R(ONS76-Tumor)	176				0.222222	9.392294	10.668685	4	14	TT		KEEP	---	---	---	---	capture			Silent	SNP	19224730	19224730	9665	17	T	C	C	59	59	MAPK7	C	4	4
SLC4A1	6521	broad.mit.edu	36	17	39691002	39691002	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39691002C>T	uc002igf.2	-	c.1160G>A	c.(1159-1161)CGG>CAG	p.R387Q	SLC4A1_uc002igg.2_Missense_Mutation_p.R387Q	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	387	Cytoplasmic.				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)												0.388889	131.832391	133.198158	49	77	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.115)	Missense_Mutation	SNP	39691002	39691002	15147	17	C	T	T	23	23	SLC4A1	T	1	1
ABCA5	23461	broad.mit.edu	36	17	64802432	64802432	+	Missense_Mutation	SNP	T	G	G			TCGA-27-1837-01	TCGA-27-1837-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64802432T>G	uc002jif.1	-	c.1454A>C	c.(1453-1455)AAG>ACG	p.K485T	ABCA5_uc002jie.1_Non-coding_Transcript|ABCA5_uc002jig.1_Missense_Mutation_p.K485T|ABCA5_uc002jih.1_Missense_Mutation_p.K485T|ABCA5_uc010dfe.1_Missense_Mutation_p.K485T	NM_018672	NP_758424	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	485	ABC transporter 1.				cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation|reverse cholesterol transport	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)	3	Breast(10;3.72e-11)													0.383648	184.83402	186.722338	61	98	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64802432	64802432	36	17	T	G	G	56	56	ABCA5	G	4	4
FDPS	2224	broad.mit.edu	36	1	153554657	153554657	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153554657A>G	uc001fkc.1	+	c.635A>G	c.(634-636)TAT>TGT	p.Y212C	FDPS_uc001fkd.1_Missense_Mutation_p.Y146C|FDPS_uc001fke.1_Missense_Mutation_p.Y212C|FDPS_uc001fkf.1_Missense_Mutation_p.Y146C|FDPS_uc001fkg.1_Missense_Mutation_p.Y212C|C1orf104_uc001fkh.1_Intron|RUSC1_uc001fkj.2_5'Flank|RUSC1_uc001fkk.2_5'Flank	NM_002004	NP_001995	P14324	FPPS_HUMAN	farnesyl diphosphate synthase isoform a	212					cholesterol biosynthetic process|interspecies interaction between organisms|isoprenoid biosynthetic process	cytosol|nucleus	dimethylallyltranstransferase activity|geranyltranstransferase activity|metal ion binding				0	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)				Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)									0.385135	175.854386	177.560829	57	91	AA		KEEP	---	---	---	---	capture	Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Missense_Mutation	SNP	153554657	153554657	6040	1	A	G	G	16	16	FDPS	G	4	4
TPR	7175	broad.mit.edu	36	1	184577083	184577083	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184577083A>G	uc001grv.1	-	c.3812T>C	c.(3811-3813)GTA>GCA	p.V1271A		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1271	Potential.				carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)								1949				0.42	207.115479	207.949199	63	87	AA		KEEP	---	---	---	---	capture		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)	Missense_Mutation	SNP	184577083	184577083	16960	1	A	G	G	14	14	TPR	G	4	4
CYP4X1	260293	broad.mit.edu	36	1	47274158	47274158	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:47274158G>A	uc001cqt.1	+	c.586G>A	c.(586-588)GCT>ACT	p.A196T	CYP4X1_uc001cqr.1_Missense_Mutation_p.A195T|CYP4X1_uc001cqs.1_Missense_Mutation_p.A131T	NM_178033	NP_828847	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X,	196					oxidation-reduction process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)	1														0.348485	109.40504	112.081301	46	86	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47274158	47274158	4358	1	G	A	A	38	38	CYP4X1	A	1	1
CLDN14	23562	broad.mit.edu	36	21	36755264	36755264	+	Silent	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:36755264G>A	uc002yvk.1	-	c.600C>T	c.(598-600)GCC>GCT	p.A200A	CLDN14_uc002yvn.1_Silent_p.A200A|CLDN14_uc002yvo.1_Silent_p.A200A|CLDN14_uc002yvl.1_Silent_p.A200A|CLDN14_uc002yvm.1_Silent_p.A200A|CLDN14_uc010gna.1_Silent_p.A200A	NM_012130	NP_652763	O95500	CLD14_HUMAN	claudin 14	200	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0														0.4375	81.489782	81.707725	28	36	GG		KEEP	---	---	---	---	capture			Silent	SNP	36755264	36755264	3611	21	G	A	A	47	47	CLDN14	A	2	2
DIP2A	23181	broad.mit.edu	36	21	46802670	46802670	+	Missense_Mutation	SNP	G	C	C	rs35987285	unknown	TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:46802670G>C	uc002zjo.1	+	c.3905G>C	c.(3904-3906)GGC>GCC	p.G1302A	DIP2A_uc002zjr.2_Missense_Mutation_p.G269A|DIP2A_uc002zjs.1_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	DIP2-like protein isoform a	1302					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)													0.75	11.740522	12.153304	6	2	GG		KEEP	---	---	---	---	capture		Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)	Missense_Mutation	SNP	46802670	46802670	4706	21	G	C	C	42	42	DIP2A	C	3	3
RFPL1	5988	broad.mit.edu	36	22	28164818	28164818	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:28164818C>T	uc003afn.1	+	c.38C>T	c.(37-39)TCA>TTA	p.S13L	RFPL1S_uc003afm.1_Non-coding_Transcript	NM_021026	NP_066306	O75677	RFPL1_HUMAN	ret finger protein-like 1	13							zinc ion binding				0														0.331461	145.35006	149.837557	59	119	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28164818	28164818	13724	22	C	T	T	29	29	RFPL1	T	2	2
ALPPL2	251	broad.mit.edu	36	2	232982714	232982714	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:232982714C>T	uc002vss.2	+	c.1487C>T	c.(1486-1488)GCG>GTG	p.A496V		NM_031313	NP_112603	P10696	PPBN_HUMAN	placental-like alkaline phosphatase	496					phosphorylation	anchored to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)			Amifostine(DB01143)|Levamisole(DB00848)									0.47619	25.845307	25.855797	10	11	CC		KEEP	---	---	---	---	capture		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Missense_Mutation	SNP	232982714	232982714	552	2	C	T	T	27	27	ALPPL2	T	1	1
DPYSL5	56896	broad.mit.edu	36	2	27004643	27004643	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1837-01	TCGA-27-1837-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27004643T>C	uc002rhu.2	+	c.617T>C	c.(616-618)CTG>CCG	p.L206P	DPYSL5_uc002rhv.2_Missense_Mutation_p.L206P	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	206					axon guidance|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.257576	41.841577	45.36059	17	49	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27004643	27004643	4934	2	T	C	C	55	55	DPYSL5	C	4	4
TTC15	51112	broad.mit.edu	36	2	3404746	3404746	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:3404746A>C	uc002qxm.1	+	c.1252A>C	c.(1252-1254)ACC>CCC	p.T418P	TTC15_uc002qxn.1_Missense_Mutation_p.T418P|TTC15_uc010ewm.1_Missense_Mutation_p.T418P	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15	418							binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)												0.384615	6.774757	6.957021	5	8	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)	Missense_Mutation	SNP	3404746	3404746	17236	2	A	C	C	6	6	TTC15	C	4	4
SLC9A10	285335	broad.mit.edu	36	3	113480343	113480343	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:113480343G>A	uc003dyu.1	-	c.241C>T	c.(241-243)CGT>TGT	p.R81C	SLC9A10_uc010hqc.1_Missense_Mutation_p.R81C	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	81	Helical; (Potential).				cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5														0.324176	142.464928	147.457452	59	123	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113480343	113480343	15207	3	G	A	A	37	37	SLC9A10	A	1	1
SOX14	8403	broad.mit.edu	36	3	138966728	138966728	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:138966728C>G	uc003erm.1	+	c.412C>G	c.(412-414)CTG>GTG	p.L138V		NM_004189	NP_004180	O95416	SOX14_HUMAN	SRY-box 14	138					negative regulation of transcription from RNA polymerase II promoter|nervous system development|transcription, DNA-dependent	nucleus	sequence-specific DNA binding|transcription repressor activity				0														0.4	26.83927	27.059387	10	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	138966728	138966728	15445	3	C	G	G	24	24	SOX14	G	3	3
GRIP2	80852	broad.mit.edu	36	3	14536644	14536644	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14536644C>T	uc003byt.1	-	c.1298G>A	c.(1297-1299)CGG>CAG	p.R433Q	GRIP2_uc003bys.1_5'UTR	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2	336					synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1														0.230769	7.718187	8.581689	3	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14536644	14536644	7067	3	C	T	T	23	23	GRIP2	T	1	1
CCDC12	151903	broad.mit.edu	36	3	46940121	46940121	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:46940121C>T	uc003cqo.1	-	c.286G>A	c.(286-288)GAG>AAG	p.E96K		NM_144716	NP_653317	Q8WUD4	CCD12_HUMAN	coiled-coil domain containing 12	96											0		Prostate(884;0.0143)|Ovarian(412;0.0448)|Acute lymphoblastic leukemia(5;0.143)										OREG0015545	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.428571	24.77157	24.864935	9	12	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(275;2.2e-56)|BRCA - Breast invasive adenocarcinoma(193;0.00136)|KIRC - Kidney renal clear cell carcinoma(197;0.00703)|Kidney(197;0.00809)	Missense_Mutation	SNP	46940121	46940121	2875	3	C	T	T	31	31	CCDC12	T	1	1
OR5H1	26341	broad.mit.edu	36	3	99334540	99334540	+	Silent	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99334540G>A	uc003dsf.1	+	c.309G>A	c.(307-309)TCG>TCA	p.S103S		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	103	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2														0.377907	331.899877	336.384789	130	214	GG		KEEP	---	---	---	---	capture			Silent	SNP	99334540	99334540	11569	3	G	A	A	40	40	OR5H1	A	1	1
ENPEP	2028	broad.mit.edu	36	4	111617492	111617492	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:111617492G>A	uc003iab.2	+	c.473G>A	c.(472-474)CGG>CAG	p.R158Q		NM_001977	NP_001968	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	158	Extracellular (Potential).				cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(203;0.217)			L-Glutamic Acid(DB00142)									0.351695	220.35137	224.930363	83	153	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	Missense_Mutation	SNP	111617492	111617492	5321	4	G	A	A	39	39	ENPEP	A	1	1
UGT2B28	54490	broad.mit.edu	36	4	70182965	70182965	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70182965C>A	uc003hej.1	+	c.866C>A	c.(865-867)CCT>CAT	p.P289H	UGT2B28_uc010ihr.1_Missense_Mutation_p.P289H	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	289					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0					Flunitrazepam(DB01544)									0.388298	189.913188	191.974254	73	115	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70182965	70182965	17518	4	C	A	A	24	24	UGT2B28	A	3	3
PCDHB15	56121	broad.mit.edu	36	5	140606989	140606989	+	Silent	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140606989C>T	uc003lje.1	+	c.1659C>T	c.(1657-1659)GAC>GAT	p.D553D		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	553	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)	4														0.402985	66.335301	66.878164	27	40	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Silent	SNP	140606989	140606989	11960	5	C	T	T	19	19	PCDHB15	T	1	1
PCDHGB2	56103	broad.mit.edu	36	5	140720911	140720911	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140720911A>C	uc003ljs.1	+	c.1025A>C	c.(1024-1026)GAT>GCT	p.D342A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljr.1_Missense_Mutation_p.D342A	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	342	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.43617	134.368236	134.700726	41	53	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140720911	140720911	11983	5	A	C	C	12	12	PCDHGB2	C	4	4
PCDHGA11	56105	broad.mit.edu	36	5	140782869	140782869	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140782869C>T	uc003lkq.1	+	c.1891C>T	c.(1891-1893)CGG>TGG	p.R631W	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.R631W|PCDHGA11_uc003lkp.1_Intron	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	631	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.539683	89.341813	89.427544	34	29	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140782869	140782869	11972	5	C	T	T	27	27	PCDHGA11	T	1	1
RNF145	153830	broad.mit.edu	36	5	158536336	158536336	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:158536336A>G	uc010jiq.1	-	c.593T>C	c.(592-594)ATT>ACT	p.I198T	RNF145_uc003lxo.1_Missense_Mutation_p.I196T|RNF145_uc003lxp.2_Missense_Mutation_p.I168T|RNF145_uc010jir.1_Missense_Mutation_p.I184T	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145	168	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(2)	2	Renal(175;0.00196)	Medulloblastoma(196;0.0523)												0.159091	15.20513	20.069908	7	37	AA		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	158536336	158536336	13924	5	A	G	G	4	4	RNF145	G	4	4
EMID2	136227	broad.mit.edu	36	7	100850070	100850070	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100850070G>A	uc010lhy.1	+	c.251G>A	c.(250-252)CGG>CAG	p.R84Q	EMID2_uc003uyo.1_Missense_Mutation_p.R84Q	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2	84	EMI.					collagen				ovary(1)	1	Lung NSC(181;0.215)													0.313725	37.673604	39.2532	16	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100850070	100850070	5284	7	G	A	A	39	39	EMID2	A	1	1
FBXL13	222235	broad.mit.edu	36	7	102391266	102391266	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102391266C>T	uc003vaq.2	-	c.674G>A	c.(673-675)CGT>CAT	p.R225H	FBXL13_uc010liq.1_Missense_Mutation_p.R40H|FBXL13_uc010lir.1_Missense_Mutation_p.R225H|FBXL13_uc003var.2_Non-coding_Transcript|FBXL13_uc003vas.2_Missense_Mutation_p.R225H|FBXL13_uc003vav.2_Non-coding_Transcript	NM_145032	NP_659469	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13 isoform	225											0														0.254438	93.043058	102.295045	43	126	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102391266	102391266	5946	7	C	T	T	19	19	FBXL13	T	1	1
RELN	5649	broad.mit.edu	36	7	103155802	103155802	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:103155802G>A	uc003vca.1	-	c.745C>T	c.(745-747)CGA>TGA	p.R249*	RELN_uc010liz.1_Nonsense_Mutation_p.R249*	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	249					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.275	95.129411	102.42827	44	116	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Nonsense_Mutation	SNP	103155802	103155802	13689	7	G	A	A	40	40	RELN	A	5	1
ABCA13	154664	broad.mit.edu	36	7	48382556	48382556	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:48382556C>A	uc003toq.1	+	c.10884C>A	c.(10882-10884)AGC>AGA	p.S3628R	ABCA13_uc010kys.1_Missense_Mutation_p.S757R|ABCA13_uc003tos.1_Missense_Mutation_p.S509R	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3683	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10														0.45	313.220461	313.788737	117	143	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48382556	48382556	32	7	C	A	A	26	26	ABCA13	A	3	3
SEMA3C	10512	broad.mit.edu	36	7	80294679	80294679	+	Missense_Mutation	SNP	T	G	G	rs13310887	by-hapmap	TCGA-27-1837-01	TCGA-27-1837-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:80294679T>G	uc003uhj.1	-	c.325A>C	c.(325-327)ACA>CCA	p.T109P		NM_006379	NP_006370	Q99985	SEM3C_HUMAN	semaphorin 3C	109	Sema.				immune response|response to drug	membrane	receptor activity			ovary(1)	1														0.235294	32.60906	35.852815	12	39	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	80294679	80294679	14512	7	T	G	G	59	59	SEMA3C	G	4	4
GRM3	2913	broad.mit.edu	36	7	86253887	86253887	+	Silent	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86253887G>A	uc003uid.1	+	c.843G>A	c.(841-843)TCG>TCA	p.S281S	GRM3_uc010lef.1_Silent_p.S279S|GRM3_uc010leg.1_Silent_p.S153S|GRM3_uc010leh.1_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	281	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				ovary(3)|central_nervous_system(2)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GBM(52;969 1098 3139 52280)								0.282051	48.381777	51.673266	22	56	GG		KEEP	---	---	---	---	capture			Silent	SNP	86253887	86253887	7077	7	G	A	A	38	38	GRM3	A	1	1
ZNF706	51123	broad.mit.edu	36	8	102283137	102283137	+	Silent	SNP	A	G	G			TCGA-27-1837-01	TCGA-27-1837-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:102283137A>G	uc003yka.1	-	c.9T>C	c.(7-9)CGT>CGC	p.R3R	ZNF706_uc003ykb.1_Silent_p.R3R	NM_001042510	NP_057180	Q9Y5V0	ZN706_HUMAN	HSPC038 protein	3						intracellular	zinc ion binding			ovary(2)	2	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)													0.2	13.461557	17.359068	9	36	AA		KEEP	---	---	---	---	capture	Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)		Silent	SNP	102283137	102283137	18706	8	A	G	G	6	6	ZNF706	G	4	4
CSMD1	64478	broad.mit.edu	36	8	3204181	3204181	+	Silent	SNP	C	T	T			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:3204181C>T	uc010lrh.1	-	c.3207G>A	c.(3205-3207)ACG>ACA	p.T1069T	CSMD1_uc003wqc.2_Silent_p.T534T|CSMD1_uc003wqe.2_Silent_p.T225T	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1069	Sushi 6.|Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)												0.4125	83.45625	83.991449	33	47	CC		KEEP	---	---	---	---	capture		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)	Silent	SNP	3204181	3204181	4085	8	C	T	T	19	19	CSMD1	T	1	1
C9orf80	58493	broad.mit.edu	36	9	114491704	114491704	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1837-01	TCGA-27-1837-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:114491704C>A	uc004bgg.1	-	c.143G>T	c.(142-144)AGA>ATA	p.R48I	C9orf80_uc010muk.1_Intron	NM_021218	NP_067041	Q9NRY2	SOSSC_HUMAN	hypothetical protein LOC58493	48					DNA repair|response to ionizing radiation	SOSS complex	protein binding				0														0.384615	102.568225	103.784142	40	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114491704	114491704	2614	9	C	A	A	32	32	C9orf80	A	3	3
SPIN2B	474343	broad.mit.edu	36	X	57163422	57163422	+	Silent	SNP	G	A	A			TCGA-27-1837-01	TCGA-27-1837-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:57163422G>A	uc004duy.1	-	c.366C>T	c.(364-366)GCC>GCT	p.A122A	SPIN2B_uc004duz.1_Silent_p.A122A|SPIN2B_uc004dva.1_Silent_p.A122A|SPIN2B_uc010nkk.1_Silent_p.A122A	NM_001006682	NP_001006684	Q9BPZ2	SPI2B_HUMAN	spindlin-like protein 2	122					apoptosis|cell cycle|gamete generation	nucleus					0														0.8	307.054788	317.092293	96	24	GG		KEEP	---	---	---	---	capture			Silent	SNP	57163422	57163422	15566	23	G	A	A	47	47	SPIN2B	A	2	2
HCRT	3060	broad.mit.edu	36	17	37590027	37590029	+	In_Frame_Del	DEL	GCA	-	-			TCGA-27-1837-01	TCGA-27-1837-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37590027_37590029delGCA	uc002hzc.1	-	c.65_67delTGC	c.(64-69)CTGCCG>CCG	p.L22del		NM_001524	NP_001515	O43612	OREX_HUMAN	orexin precursor	22					neuropeptide signaling pathway	cell junction|extracellular region|rough endoplasmic reticulum|synaptic vesicle					0		all_cancers(22;1.39e-06)|all_epithelial(22;9.98e-06)|Breast(137;0.000143)|Ovarian(249;0.0221)|Myeloproliferative disorder(1115;0.0255)|Colorectal(1115;0.069)		BRCA - Breast invasive adenocarcinoma(366;0.124)										0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	37590027	37590029	7283	17	GCA	-	-	42	42	HCRT	-	5	5
TYRP1	7306	broad.mit.edu	36	9	12692411	12692414	+	Frame_Shift_Del	DEL	ACAA	-	-			TCGA-27-1837-01	TCGA-27-1837-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:12692411_12692414delACAA	uc003zkv.2	+	c.1054_1057delACAA	c.(1054-1059)ACAAACfs	p.T352fs		NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	352_353	Lumenal, melanosome (Potential).				melanin biosynthetic process|oxidation-reduction process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)										0.40			34	50				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	12692411	12692414	17373	9	ACAA	-	-	14	14	TYRP1	-	5	5
