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
NEURL	9148	broad.mit.edu	36	10	105321397	105321397	+	Missense_Mutation	SNP	G	T	T			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105321397G>T	uc001kxh.1	+	c.477G>T	c.(475-477)GAG>GAT	p.E159D		NM_004210	NP_004201	O76050	NEU1A_HUMAN	neuralized-like	159	NHR 1.				nervous system development	perinuclear region of cytoplasm	zinc ion binding				0														0.421053	22.897178	23.000368	8	11	GG		KEEP	---	---	---	---	capture		Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)	Missense_Mutation	SNP	105321397	105321397	10744	10	G	T	T	35	35	NEURL	T	3	3
CYP2C8	1558	broad.mit.edu	36	10	96817041	96817041	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:96817041C>T	uc001kkb.1	-	c.395G>A	c.(394-396)CGG>CAG	p.R132Q	CYP2C8_uc001kkc.1_Non-coding_Transcript	NM_000770	NP_000761	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C,	132					exogenous drug catabolic process|organic acid metabolic process|oxidative demethylation|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|electron carrier activity|heme binding|oxygen binding				0		Colorectal(252;0.0397)			Aminophenazone(DB01424)|Amiodarone(DB01118)|Amodiaquine(DB00613)|Benzphetamine(DB00865)|Carbamazepine(DB00564)|Cerivastatin(DB00439)|Diclofenac(DB00586)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lovastatin(DB00227)|Midazolam(DB00683)|Montelukast(DB00471)|Nicardipine(DB00622)|Paclitaxel(DB01229)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rifampin(DB01045)|Rosiglitazone(DB00412)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Tolbutamide(DB01124)|Torasemide(DB00214)|Tretinoin(DB00755)|Trimethoprim(DB00440)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zopiclone(DB01198)									0.814286	381.818745	394.779	114	26	CC		KEEP	---	---	---	---	capture		all cancers(201;6.21e-05)	Missense_Mutation	SNP	96817041	96817041	4332	10	C	T	T	23	23	CYP2C8	T	1	1
MUC2	4583	broad.mit.edu	36	11	1070301	1070301	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1070301G>A	uc001lsx.1	+	c.1021G>A	c.(1021-1023)GGG>AGG	p.G341R		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	341	TIL.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.222222	10.191532	11.468304	4	14	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1070301	1070301	10369	11	G	A	A	39	39	MUC2	A	1	1
OR5M11	219487	broad.mit.edu	36	11	56066906	56066906	+	Missense_Mutation	SNP	G	C	C			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56066906G>C	uc001niy.1	-	c.404C>G	c.(403-405)ACG>AGG	p.T135R		NM_001005245	NP_001005245	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M,	135	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.458333	69.12962	69.203535	22	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56066906	56066906	11584	11	G	C	C	40	40	OR5M11	C	3	3
UVRAG	7405	broad.mit.edu	36	11	75268614	75268614	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:75268614G>A	uc001oxc.1	+	c.314G>A	c.(313-315)CGT>CAT	p.R105H		NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	105	C2.				DNA repair	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6														0.391732	575.942698	581.176929	199	309	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75268614	75268614	17673	11	G	A	A	40	40	UVRAG	A	1	1
NOP2	4839	broad.mit.edu	36	12	6545562	6545562	+	Missense_Mutation	SNP	T	G	G			TCGA-02-2485-01	TCGA-02-2485-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6545562T>G	uc001qph.1	-	c.428A>C	c.(427-429)GAC>GCC	p.D143A	NOP2_uc009zeq.1_5'Flank|NOP2_uc001qpi.1_Missense_Mutation_p.D143A|NOP2_uc001qpj.1_Intron|NOP2_uc001qpk.1_Missense_Mutation_p.D147A|NOP2_uc001qpl.1_Missense_Mutation_p.D147A|NOP2_uc001qpm.1_Missense_Mutation_p.D147A	NM_001033714	NP_001028886	P46087	NOP2_HUMAN	nucleolar protein 1, 120kDa	147					positive regulation of cell proliferation|rRNA processing	nucleolus	protein binding|RNA binding|S-adenosylmethionine-dependent methyltransferase activity			ovary(2)	2														0.484848	56.803235	56.809593	16	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6545562	6545562	10941	12	T	G	G	58	58	NOP2	G	4	4
ACSM2B	348158	broad.mit.edu	36	16	20456137	20456137	+	Nonsense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20456137G>A	uc002dhj.2	-	c.1678C>T	c.(1678-1680)CGA>TGA	p.R560*	ACSM2B_uc002dhk.2_Nonsense_Mutation_p.R560*	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	560					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2														0.400901	518.108678	521.935015	178	266	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	20456137	20456137	185	16	G	A	A	40	40	ACSM2B	A	5	1
ITGAM	3684	broad.mit.edu	36	16	31194497	31194497	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31194497C>T	uc002ebr.1	+	c.985C>T	c.(985-987)CGG>TGG	p.R329W	ITGAM_uc002ebq.1_Missense_Mutation_p.R329W|ITGAM_uc010cam.1_5'UTR	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M precursor	329	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1														0.385542	93.582617	94.534857	32	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31194497	31194497	8191	16	C	T	T	31	31	ITGAM	T	1	1
HYDIN	54768	broad.mit.edu	36	16	69460111	69460111	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69460111G>A	uc002ezr.1	-	c.11170C>T	c.(11170-11172)CGG>TGG	p.R3724W	HYDIN_uc010cfy.1_5'Flank	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	3725										ovary(1)	1		Ovarian(137;0.0654)												0.196203	63.540849	77.128127	31	127	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69460111	69460111	7767	16	G	A	A	38	38	HYDIN	A	1	1
HYDIN	54768	broad.mit.edu	36	16	69562096	69562096	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69562096C>T	uc002ezr.1	-	c.5444G>A	c.(5443-5445)CGT>CAT	p.R1815H	HYDIN_uc002ezt.1_Non-coding_Transcript|HYDIN_uc002ezu.1_Missense_Mutation_p.R118H	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1816										ovary(1)	1		Ovarian(137;0.0654)												0.236967	118.453944	131.78929	50	161	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69562096	69562096	7767	16	C	T	T	19	19	HYDIN	T	1	1
WNT3	7473	broad.mit.edu	36	17	42206338	42206338	+	Missense_Mutation	SNP	T	C	C			TCGA-02-2485-01	TCGA-02-2485-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:42206338T>C	uc002ikv.1	-	c.181A>G	c.(181-183)AAT>GAT	p.N61D		NM_030753	NP_110380	P56703	WNT3_HUMAN	wingless-type MMTV integration site family,	61					canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|cellular response to retinoic acid|dorsal/ventral axis specification|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic pattern specification|head morphogenesis|hemopoietic stem cell proliferation|inner ear morphogenesis|limb bud formation|mammary gland epithelium development|mesoderm formation|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|Spemann organizer formation at the anterior end of the primitive streak|Wnt receptor signaling pathway, calcium modulating pathway	early endosome|extracellular space|late endosome|membrane fraction|membrane raft|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|signal transducer activity				0														0.419355	71.830087	72.183647	26	36	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(9;0.0257)		Missense_Mutation	SNP	42206338	42206338	17962	17	T	C	C	63	63	WNT3	C	4	4
C17orf47	284083	broad.mit.edu	36	17	53976052	53976052	+	Missense_Mutation	SNP	C	A	A			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53976052C>A	uc002iwq.1	-	c.495G>T	c.(493-495)AAG>AAT	p.K165N		NM_001038704	NP_001033793	Q8NEP4	CQ047_HUMAN	hypothetical protein LOC284083	165										breast(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.148789	69.220622	103.441217	43	246	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53976052	53976052	1914	17	C	A	A	32	32	C17orf47	A	3	3
CD300A	11314	broad.mit.edu	36	17	69981495	69981495	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:69981495C>T	uc002jkv.1	+	c.266C>T	c.(265-267)ACC>ATC	p.T89I	CD300A_uc002jkw.1_Intron|CD300A_uc010dfr.1_Intron|CD300A_uc010dfs.1_Intron	NM_007261	NP_009192	Q9UGN4	CLM8_HUMAN	leukocyte membrane antigen	89	Extracellular (Potential).|Ig-like V-type.				cell adhesion	integral to membrane|plasma membrane	receptor activity			ovary(1)	1														0.417391	138.901273	139.579221	48	67	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69981495	69981495	3124	17	C	T	T	18	18	CD300A	T	2	2
TP53	7157	broad.mit.edu	36	17	7518263	7518263	+	Missense_Mutation	SNP	C	T	T	rs11540652	by-hapmap	TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518263C>T	uc002gim.2	-	c.743G>A	c.(742-744)CGG>CAG	p.R248Q	TP53_uc002gig.1_Missense_Mutation_p.R248Q|TP53_uc002gih.1_Missense_Mutation_p.R248Q|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116Q|TP53_uc010cng.1_Missense_Mutation_p.R116Q|TP53_uc002gii.1_Missense_Mutation_p.R116Q|TP53_uc010cnh.1_Missense_Mutation_p.R248Q|TP53_uc010cni.1_Missense_Mutation_p.R248Q|TP53_uc002gij.2_Missense_Mutation_p.R248Q|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R155Q|TP53_uc002gio.2_Missense_Mutation_p.R116Q	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; 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.R248Q(503)|p.R248L(63)|p.R248P(11)|p.0?(6)|p.N247_R248delNR(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(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)				Pancreas(47;798 1329 9957 10801)	R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIN87_STOMACH)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NIHOVCAR3_OVARY)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(HCC70_BREAST)|R248Q(KYSE150_OESOPHAGUS)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PC14_LUNG)	111	p.R248L(NCIH211-Tumor)|p.R248L(NB4-Tumor)|p.R248L(PC14-Tumor)|p.R248L(KYO1-Tumor)|p.R248L(PCM6-Tumor)|p.R248L(NUDHL1-Tumor)|p.R248L(BL41-Tumor)|p.R248Q(FADU-Tumor)|p.R248L(CI1-Tumor)|p.R248L(SW1463-Tumor)|p.R248L(COLO699-Tumor)|p.R248L(HS683-Tumor)|p.R248*(DB-Tumor)|p.R248L(HCC1143-Tumor)|p.R248L(NCIN87-Tumor)|p.R248A(SF126-Tumor)|p.R248L(PANC02.03-Tumor)|p.R248L(HEC1B-Tumor)|p.R248L(PECAPJ15-Tumor)|p.R248L(LNCAPCLONEFGC-Tumor)|p.R248L(NIHOVCAR3-Tumor)|p.R248L(NUDUL1-Tumor)|p.R248L(ONCODG1-Tumor)|p.R248L(RT112-Tumor)|p.R248L(SF295-Tumor)|p.R248L(P12ICHIKAWA-Tumor)|p.R248L(DND41-Tumor)|p.R248Q(SBC5-Tumor)|p.R248L(KOPN8-Tumor)|p.R248L(KASUMI1-Tumor)|p.R248L(EM2-Tumor)|p.R248L(SKUT1-Tumor)|p.R248L(NCCSTCK140-Tumor)|p.R248L(TE6-Tumor)|p.R248L(MOLM6-Tumor)|p.R248L(SEM-Tumor)|p.R248L(NAMALWA-Tumor)|p.R248L(CA46-Tumor)|p.R248L(639V-Tumor)|p.R248L(SKM1-Tumor)|p.R248Q(NCIH1573-Tumor)|p.R248Q(NCIH1618-Tumor)|p.R248L(HCC70-Tumor)|p.R248L(WSUDLCL2-Tumor)|p.R248L(HEC1A-Tumor)|p.R248L(KYSE150-Tumor)|p.R248L(HSC4-Tumor)|p.R248L(CL40-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.342857	67.875287	69.403996	24	46	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518263	7518263	16923	17	C	T	T	23	23	TP53	T	1	1
TP53	7157	broad.mit.edu	36	17	7519275	7519275	+	Missense_Mutation	SNP	G	T	T			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519275G>T	uc002gim.2	-	c.380C>A	c.(379-381)TCC>TAC	p.S127Y	TP53_uc002gig.1_Missense_Mutation_p.S127Y|TP53_uc002gih.1_Missense_Mutation_p.S127Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Missense_Mutation_p.S127Y|TP53_uc010cni.1_Missense_Mutation_p.S127Y|TP53_uc002gij.2_Missense_Mutation_p.S127Y|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.S34Y|TP53_uc002gio.2_5'UTR	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	127	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (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.S127F(18)|p.S127Y(8)|p.0?(6)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.P128fs*42(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.Y126fs*11(1)|p.S127C(1)|p.S127_Q136del10(1)|p.P13fs*18(1)|p.?(1)|p.S127fs*42(1)|p.Y126fs*18(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)				Pancreas(47;798 1329 9957 10801)		111	(CORL279-Tumor)|p.S127F(SNU410-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.47619	57.407374	57.427064	20	22	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519275	7519275	16923	17	G	T	T	41	41	TP53	T	3	3
CILP2	148113	broad.mit.edu	36	19	19516884	19516884	+	Missense_Mutation	SNP	T	G	G			TCGA-02-2485-01	TCGA-02-2485-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19516884T>G	uc002nmw.2	+	c.2548T>G	c.(2548-2550)TAC>GAC	p.Y850D	CILP2_uc002nmv.2_Missense_Mutation_p.Y844D	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	844						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1														0.285714	12.201703	14.072184	12	30	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19516884	19516884	3564	19	T	G	G	57	57	CILP2	G	4	4
ATP13A1	57130	broad.mit.edu	36	19	19617294	19617294	+	Silent	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19617294C>T	uc002nnh.2	-	c.3552G>A	c.(3550-3552)GCG>GCA	p.A1184A	GMIP_uc002nnd.1_5'Flank|ATP13A1_uc002nne.1_Silent_p.A324A|ATP13A1_uc002nnf.2_Silent_p.A552A|ATP13A1_uc002nng.1_Silent_p.A1066A	NM_020410	NP_065143	Q9HD20	AT131_HUMAN	ATPase type 13A1	1184	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(3)|large_intestine(2)|central_nervous_system(1)	6						Esophageal Squamous(142;920 1789 9047 14684 24777)								0.227273	12.266559	13.766211	5	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	19617294	19617294	1142	19	C	T	T	27	27	ATP13A1	T	1	1
ZNF681	148213	broad.mit.edu	36	19	23719334	23719334	+	Silent	SNP	T	C	C			TCGA-02-2485-01	TCGA-02-2485-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:23719334T>C	uc002nrk.2	-	c.858A>G	c.(856-858)GAA>GAG	p.E286E	ZNF681_uc002nrl.2_Silent_p.E217E|ZNF681_uc002nrj.2_Silent_p.E217E	NM_138286	NP_612143	Q96N22	ZN681_HUMAN	zinc finger protein 681	286	C2H2-type 5; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)												0.334711	253.405338	259.253643	81	161	TT		KEEP	---	---	---	---	capture			Silent	SNP	23719334	23719334	18683	19	T	C	C	52	52	ZNF681	C	4	4
THEG	51298	broad.mit.edu	36	19	326850	326850	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:326850G>A	uc002lol.1	-	c.121C>T	c.(121-123)CGG>TGG	p.R41W	THEG_uc002lom.1_Missense_Mutation_p.R41W	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	41					cell differentiation|chaperone-mediated protein complex assembly|multicellular organismal development|spermatogenesis	nucleus	protein binding			ovary(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)												0.367742	147.849967	150.225962	57	98	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	326850	326850	16385	19	G	A	A	38	38	THEG	A	1	1
EEF2	1938	broad.mit.edu	36	19	3931665	3931665	+	Missense_Mutation	SNP	A	C	C			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3931665A>C	uc002lze.1	-	c.1193T>G	c.(1192-1194)ATT>AGT	p.I398S		NM_001961	NP_001952	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	398						cytosol|ribonucleoprotein complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0		Hepatocellular(1079;0.137)				Colon(165;1804 1908 4071 6587 18799)								0.281481	115.380127	121.184226	38	97	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3931665	3931665	5116	19	A	C	C	4	4	EEF2	C	4	4
IRGC	56269	broad.mit.edu	36	19	48914815	48914815	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48914815G>A	uc002oxh.1	+	c.265G>A	c.(265-267)GTC>ATC	p.V89I	IRGC_uc010eix.1_Missense_Mutation_p.V89I	NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	89	GTP.					membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)	1		Prostate(69;0.0435)				Colon(189;350 2037 11447 13433 38914)								0.304878	63.948141	66.731214	25	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48914815	48914815	8141	19	G	A	A	40	40	IRGC	A	1	1
CEACAM16	388551	broad.mit.edu	36	19	49898711	49898711	+	Missense_Mutation	SNP	G	C	C			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49898711G>C	uc002ozq.1	+	c.467G>C	c.(466-468)GGC>GCC	p.G156A		NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion	97										ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)												0.222222	8.591487	9.86944	4	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49898711	49898711	3321	19	G	C	C	42	42	CEACAM16	C	3	3
EXOC3L2	90332	broad.mit.edu	36	19	50419998	50419998	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50419998G>A	uc002pay.1	-	c.418C>T	c.(418-420)CGC>TGC	p.R140C		NM_138568	NP_612635	Q2M3D2	EX3L2_HUMAN	protein 7 transactivated by hepatitis B virus X	140											0		all_neural(266;0.224)|Ovarian(192;0.231)												0.208333	9.760943	11.653174	5	19	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00883)	Missense_Mutation	SNP	50419998	50419998	5498	19	G	A	A	38	38	EXOC3L2	A	1	1
LILRB2	10288	broad.mit.edu	36	19	59475503	59475503	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59475503C>T	uc002qfb.1	-	c.310G>A	c.(310-312)GCT>ACT	p.A104T	LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.1_Missense_Mutation_p.A104T|LILRB2_uc010erj.1_Non-coding_Transcript|LILRB2_uc002qfc.1_Missense_Mutation_p.A104T	NM_005874	NP_005865	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor,	104	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity				0	Ovarian(34;0.19)													0.331984	210.710825	216.866194	82	165	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.105)	Missense_Mutation	SNP	59475503	59475503	9117	19	C	T	T	27	27	LILRB2	T	1	1
MUC16	94025	broad.mit.edu	36	19	8907871	8907871	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8907871G>A	uc002mkp.1	-	c.34760C>T	c.(34759-34761)ACG>ATG	p.T11587M		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11589	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.319728	126.177507	130.420023	47	100	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8907871	8907871	10367	19	G	A	A	40	40	MUC16	A	1	1
OR7E24	26648	broad.mit.edu	36	19	9222873	9222873	+	Missense_Mutation	SNP	A	G	G			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9222873A>G	uc002mlb.1	+	c.154A>G	c.(154-156)ATG>GTG	p.M52V		NM_001079935	NP_001073404	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E,	52	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.406897	168.592033	169.69145	59	86	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9222873	9222873	11632	19	A	G	G	8	8	OR7E24	G	4	4
FLG	2312	broad.mit.edu	36	1	150546388	150546388	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150546388C>T	uc001ezu.1	-	c.7598G>A	c.(7597-7599)CGT>CAT	p.R2533H		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2533	Ser-rich.|Filaggrin 15.				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)													0.323246	594.145755	614.326044	235	492	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150546388	150546388	6160	1	C	T	T	19	19	FLG	T	1	1
EPHB2	2048	broad.mit.edu	36	1	22983566	22983566	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:22983566G>A	uc009vqj.1	+	c.221G>A	c.(220-222)CGG>CAG	p.R74Q	EPHB2_uc001bge.1_Missense_Mutation_p.R74Q|EPHB2_uc001bgf.1_Missense_Mutation_p.R74Q	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	74	Extracellular (Potential).				axon guidance|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)								437				0.5	58.725395	58.725395	19	19	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)	Missense_Mutation	SNP	22983566	22983566	5368	1	G	A	A	39	39	EPHB2	A	1	1
SLCO4A1	28231	broad.mit.edu	36	20	60769698	60769698	+	Silent	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60769698C>T	uc002ydb.1	+	c.1629C>T	c.(1627-1629)GAC>GAT	p.D543D	SLCO4A1_uc002ydc.1_Non-coding_Transcript|LOC100127888_uc002ydd.1_5'Flank|SLCO4A1_uc002yde.1_Missense_Mutation_p.T3M	NM_016354	NP_057438	Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family	543	Extracellular (Potential).|Kazal-like.				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)					Pancreas(168;741 2006 10379 40139 45334)				402				0.178571	26.779872	34.946891	15	69	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Silent	SNP	60769698	60769698	15226	20	C	T	T	19	19	SLCO4A1	T	1	1
DNMT3L	29947	broad.mit.edu	36	21	44493352	44493352	+	Missense_Mutation	SNP	A	G	G			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44493352A>G	uc002zeh.1	-	c.980T>C	c.(979-981)ATC>ACC	p.I327T	DNMT3L_uc002zeg.1_Missense_Mutation_p.I327T	NM_013369	NP_037501	Q9UJW3	DNM3L_HUMAN	cytosine-5-methyltransferase 3-like protein	327					DNA methylation|regulation of gene expression by genetic imprinting|spermatogenesis	cytosol	enzyme activator activity|enzyme binding|transcription repressor activity|zinc ion binding				0														0.571429	8.984755	9.013879	4	3	AA		KEEP	---	---	---	---	capture		Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)	Missense_Mutation	SNP	44493352	44493352	4861	21	A	G	G	12	12	DNMT3L	G	4	4
RHBDD3	25807	broad.mit.edu	36	22	27991524	27991524	+	Missense_Mutation	SNP	A	C	C			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:27991524A>C	uc003aeq.1	-	c.92T>G	c.(91-93)GTG>GGG	p.V31G	RHBDD3_uc003aer.1_Non-coding_Transcript|EWSR1_uc003aes.2_5'Flank|EWSR1_uc003aet.1_5'Flank|EWSR1_uc003aeu.1_5'Flank|EWSR1_uc003aev.1_5'Flank|EWSR1_uc003aew.1_5'Flank|EWSR1_uc003aex.1_5'Flank	NM_012265	NP_036397	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	31	Helical; (Potential).					integral to membrane	serine-type endopeptidase activity				0														0.285714	7.186789	7.769287	4	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27991524	27991524	13793	22	A	C	C	6	6	RHBDD3	C	4	4
KIAA1644	85352	broad.mit.edu	36	22	43023950	43023950	+	Silent	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:43023950G>A	uc003bet.2	-	c.216C>T	c.(214-216)AAC>AAT	p.N72N		NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352	72	Extracellular (Potential).					integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)												0.47351	422.10045	422.284014	143	159	GG		KEEP	---	---	---	---	capture			Silent	SNP	43023950	43023950	8559	22	G	A	A	40	40	KIAA1644	A	1	1
SCN3A	6328	broad.mit.edu	36	2	165727573	165727573	+	Missense_Mutation	SNP	T	C	C			TCGA-02-2485-01	TCGA-02-2485-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:165727573T>C	uc002ucx.1	-	c.706A>G	c.(706-708)ATT>GTT	p.I236V	SCN3A_uc002ucy.1_Missense_Mutation_p.I236V|SCN3A_uc002ucz.1_Missense_Mutation_p.I236V|SCN3A_uc002uda.1_Missense_Mutation_p.I105V|SCN3A_uc002udb.1_Missense_Mutation_p.I105V	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	236						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.451087	252.904926	253.287863	83	101	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165727573	165727573	14400	2	T	C	C	51	51	SCN3A	C	4	4
HOXD3	3232	broad.mit.edu	36	2	176744981	176744981	+	Silent	SNP	C	G	G			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:176744981C>G	uc002ukt.1	+	c.1032C>G	c.(1030-1032)GGC>GGG	p.G344G		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	344					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|regulation of transcription, DNA-dependent|thyroid gland development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.307692	8.895873	9.324239	4	9	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)	Silent	SNP	176744981	176744981	7615	2	C	G	G	27	27	HOXD3	G	3	3
ZNF804A	91752	broad.mit.edu	36	2	185510758	185510758	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:185510758G>A	uc002uph.1	+	c.2390G>A	c.(2389-2391)AGG>AAG	p.R797K		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	797						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.417476	135.713597	136.323767	43	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	185510758	185510758	18768	2	G	A	A	35	35	ZNF804A	A	2	2
COL6A3	1293	broad.mit.edu	36	2	237913940	237913940	+	Silent	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237913940G>A	uc002vwl.2	-	c.8358C>T	c.(8356-8358)TTC>TTT	p.F2786F	COL6A3_uc002vwj.2_Silent_p.F167F|COL6A3_uc002vwk.2_Silent_p.F2619F|COL6A3_uc002vwm.2_Silent_p.F2585F|COL6A3_uc002vwn.2_Silent_p.F2586F|COL6A3_uc002vwo.2_Silent_p.F2580F	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2786	VWFA 12.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.452991	157.964423	158.188916	53	64	GG		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Silent	SNP	237913940	237913940	3839	2	G	A	A	37	37	COL6A3	A	1	1
COLQ	8292	broad.mit.edu	36	3	15487058	15487058	+	Nonsense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:15487058G>A	uc003bzx.1	-	c.706C>T	c.(706-708)CGA>TGA	p.R236*	COLQ_uc003bzv.1_Nonsense_Mutation_p.R226*|COLQ_uc003bzz.1_Nonsense_Mutation_p.R227*|COLQ_uc010heo.1_Nonsense_Mutation_p.R202*|COLQ_uc003cab.1_Nonsense_Mutation_p.R236*|COLQ_uc003cac.1_Non-coding_Transcript|COLQ_uc003cae.1_Nonsense_Mutation_p.R95*|COLQ_uc003cad.1_Non-coding_Transcript	NM_005677	NP_005668	Q9Y215	COLQ_HUMAN	acetylcholinesterase collagen-like tail subunit	236	Heparan sulfate proteoglycan binding (Potential).|Collagen-like 1.				acetylcholine catabolic process in synaptic cleft|asymmetric protein localization	basal lamina|cell junction|collagen|extracellular space|synapse					0														0.414474	180.701256	181.670263	63	89	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	15487058	15487058	3851	3	G	A	A	40	40	COLQ	A	5	1
PIK3CA	5290	broad.mit.edu	36	3	180399615	180399615	+	Missense_Mutation	SNP	A	G	G			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180399615A>G	uc003fjk.1	+	c.308A>G	c.(307-309)GAA>GGA	p.E103G		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	103					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.460432	223.193656	223.38219	64	75	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180399615	180399615	12337	3	A	G	G	9	9	PIK3CA	G	4	4
CNTN4	152330	broad.mit.edu	36	3	3051350	3051350	+	Silent	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:3051350C>T	uc003bpc.1	+	c.1818C>T	c.(1816-1818)GAC>GAT	p.D606D	CNTN4_uc003bpb.1_Silent_p.D277D|CNTN4_uc003bpd.1_Silent_p.D606D|CNTN4_uc003bpe.1_Silent_p.D278D|CNTN4_uc003bpf.1_Silent_p.D277D	NM_175607	NP_783302	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	606	Fibronectin type-III 1.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)												0.438776	119.702963	120.023766	43	55	CC		KEEP	---	---	---	---	capture		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)	Silent	SNP	3051350	3051350	3781	3	C	T	T	19	19	CNTN4	T	1	1
BAP1	8314	broad.mit.edu	36	3	52413619	52413619	+	Silent	SNP	A	C	C			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52413619A>C	uc003ddx.1	-	c.1140T>G	c.(1138-1140)GGT>GGG	p.G380G	BAP1_uc003ddw.1_5'Flank|BAP1_uc010hmg.1_5'Flank|BAP1_uc010hmh.1_Non-coding_Transcript	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	380					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			eye(28)|lung(2)|ovary(1)|breast(1)	32						GBM(101;493 1458 7992 21037 25532)				294				0.428571	6.483879	6.574957	6	8	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	Silent	SNP	52413619	52413619	1332	3	A	C	C	6	6	BAP1	C	4	4
SLCO6A1	133482	broad.mit.edu	36	5	101763161	101763161	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:101763161G>A	uc003knn.2	-	c.1811C>T	c.(1810-1812)ACG>ATG	p.T604M	SLCO6A1_uc003kno.2_Missense_Mutation_p.T351M|SLCO6A1_uc003knp.1_Missense_Mutation_p.T604M|SLCO6A1_uc003knq.1_Missense_Mutation_p.T542M	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	604	Helical; Name=10; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|central_nervous_system(1)	4		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)												0.341463	38.53808	39.44844	14	27	GG		KEEP	---	---	---	---	capture		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)	Missense_Mutation	SNP	101763161	101763161	15229	5	G	A	A	40	40	SLCO6A1	A	1	1
REEP2	51308	broad.mit.edu	36	5	137809174	137809174	+	Silent	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137809174G>A	uc003lda.1	+	c.684G>A	c.(682-684)GCG>GCA	p.A228A	REEP2_uc003lcz.1_Silent_p.A226A	NM_016606	NP_057690	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	226						integral to membrane					0														0.461538	84.456702	84.538204	30	35	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)		Silent	SNP	137809174	137809174	13674	5	G	A	A	38	38	REEP2	A	1	1
PCDHA12	56137	broad.mit.edu	36	5	140237443	140237443	+	Silent	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140237443G>A	uc003lic.1	+	c.2202G>A	c.(2200-2202)CCG>CCA	p.P734P	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhs.1_Intron|PCDHA9_uc003lhu.1_Intron|PCDHA10_uc003lhx.1_Intron|PCDHA10_uc003lhw.1_Intron|PCDHA11_uc003lia.1_Intron|PCDHA12_uc003lib.1_Silent_p.P734P	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	734	5 X 4 AA repeats of P-X-X-P.|Cytoplasmic (Potential).|PXXP 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0						Pancreas(113;759 1672 13322 24104 50104)								0.238095	25.566513	28.172464	10	32	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140237443	140237443	11942	5	G	A	A	39	39	PCDHA12	A	1	1
MAML1	9794	broad.mit.edu	36	5	179125072	179125072	+	Missense_Mutation	SNP	C	A	A			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:179125072C>A	uc003mkm.1	+	c.455C>A	c.(454-456)TCC>TAC	p.S152Y	MAML1_uc003mkn.1_Missense_Mutation_p.S152Y	NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1	152					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(3)|ovary(2)	5	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)								189				0.440367	134.188184	134.524655	48	61	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	179125072	179125072	9588	5	C	A	A	30	30	MAML1	A	3	3
HECA	51696	broad.mit.edu	36	6	139529464	139529464	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:139529464G>A	uc003qin.1	+	c.622G>A	c.(622-624)GAG>AAG	p.E208K		NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase	208					respiratory tube development						0														0.443182	116.912322	117.15952	39	49	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)	Missense_Mutation	SNP	139529464	139529464	7321	6	G	A	A	37	37	HECA	A	1	1
JARID2	3720	broad.mit.edu	36	6	15628407	15628407	+	Silent	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:15628407C>T	uc003nbj.1	+	c.3687C>T	c.(3685-3687)CCC>CCT	p.P1229P		NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	1229					central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)								694				0.359649	113.264418	115.231544	41	73	CC		KEEP	---	---	---	---	capture			Silent	SNP	15628407	15628407	8249	6	C	T	T	22	22	JARID2	T	2	2
LGSN	51557	broad.mit.edu	36	6	64062806	64062806	+	Missense_Mutation	SNP	A	C	C			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:64062806A>C	uc003peh.1	-	c.134T>G	c.(133-135)GTG>GGG	p.V45G	LGSN_uc003pei.1_Missense_Mutation_p.V45G|LGSN_uc003pej.1_Missense_Mutation_p.V45G	NM_016571	NP_057655	Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase	45					glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(1)	1					L-Glutamic Acid(DB00142)									0.173184	68.115737	86.184271	31	148	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64062806	64062806	9085	6	A	C	C	6	6	LGSN	C	4	4
DSP	1832	broad.mit.edu	36	6	7528890	7528890	+	Silent	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7528890G>A	uc003mxp.1	+	c.6396G>A	c.(6394-6396)GGG>GGA	p.G2132G	DSP_uc003mxq.1_Silent_p.G1533G	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	2132	Plectin 4.|Globular 2.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)												0.422857	230.119998	231.028581	74	101	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.000508)	Silent	SNP	7528890	7528890	4965	6	G	A	A	43	43	DSP	A	2	2
LRWD1	222229	broad.mit.edu	36	7	101893376	101893376	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:101893376C>T	uc003uzn.1	+	c.188C>T	c.(187-189)CCG>CTG	p.P63L	ALKBH4_uc003uzl.1_5'Flank|ALKBH4_uc003uzm.1_5'Flank|LRWD1_uc003uzo.1_5'UTR	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain	63	LRR 2.				chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding				0														0.333333	61.577184	63.299593	24	48	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101893376	101893376	9423	7	C	T	T	23	23	LRWD1	T	1	1
CHRM2	1129	broad.mit.edu	36	7	136351278	136351278	+	Missense_Mutation	SNP	A	G	G			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:136351278A>G	uc003vtf.1	+	c.1126A>G	c.(1126-1128)AAG>GAG	p.K376E	CHRM2_uc003vtg.1_Missense_Mutation_p.K376E|CHRM2_uc003vtm.1_Missense_Mutation_p.K376E|CHRM2_uc003vtj.1_Missense_Mutation_p.K376E|CHRM2_uc003vtk.1_Missense_Mutation_p.K376E|CHRM2_uc003vtl.1_Missense_Mutation_p.K376E|CHRM2_uc003vti.1_Missense_Mutation_p.K376E|CHRM2_uc003vto.1_Missense_Mutation_p.K376E|CHRM2_uc003vtn.1_Missense_Mutation_p.K376E|CHRM2_uc010lmw.1_Missense_Mutation_p.K376E	NM_001006630	NP_001006633	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	376	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)									0.320574	205.738502	211.724008	67	142	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	136351278	136351278	3511	7	A	G	G	9	9	CHRM2	G	4	4
NOD1	10392	broad.mit.edu	36	7	30458883	30458883	+	Silent	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:30458883G>A	uc003tav.1	-	c.675C>T	c.(673-675)GAC>GAT	p.D225D	NOD1_uc010kvs.1_Intron	NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain	225	NACHT.				activation of caspase activity|activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|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	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)	1														0.381679	133.130474	134.733107	50	81	GG		KEEP	---	---	---	---	capture			Silent	SNP	30458883	30458883	10919	7	G	A	A	40	40	NOD1	A	1	1
VPS41	27072	broad.mit.edu	36	7	38801619	38801619	+	Missense_Mutation	SNP	G	C	C			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:38801619G>C	uc003tgy.1	-	c.688C>G	c.(688-690)CTG>GTG	p.L230V	VPS41_uc003tgz.1_Missense_Mutation_p.L205V|VPS41_uc010kxn.1_Intron	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	230					Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			central_nervous_system(1)	1														0.199074	108.097205	126.301429	43	173	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38801619	38801619	17777	7	G	C	C	36	36	VPS41	C	3	3
POM121L12	285877	broad.mit.edu	36	7	53071354	53071354	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:53071354G>A	uc003tpz.1	+	c.496G>A	c.(496-498)GCC>ACC	p.A166T		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	hypothetical protein LOC285877	166											0														0.765306	216.29282	222.595571	75	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53071354	53071354	12669	7	G	A	A	38	38	POM121L12	A	1	1
POM121L12	285877	broad.mit.edu	36	7	53071645	53071645	+	Missense_Mutation	SNP	G	A	A			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:53071645G>A	uc003tpz.1	+	c.787G>A	c.(787-789)GCC>ACC	p.A263T		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	hypothetical protein LOC285877	263											0														0.128205	51.688865	98.944564	45	306	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53071645	53071645	12669	7	G	A	A	38	38	POM121L12	A	1	1
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	A	A			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>A	uc003tqk.1	+	c.866C>A	c.(865-867)GCC>GAC	p.A289D	EGFR_uc003tqh.1_Missense_Mutation_p.A289D|EGFR_uc003tqi.1_Missense_Mutation_p.A289D|EGFR_uc003tqj.1_Missense_Mutation_p.A289D|EGFR_uc010kzg.1_Missense_Mutation_p.A244D	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.A289V(20)|p.V30_R297>G(10)|p.A289D(3)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.945946	3028.880566	3156.905509	910	52	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55189316	55189316	5156	7	C	A	A	26	26	EGFR	A	3	3
RP1	6101	broad.mit.edu	36	8	55704382	55704382	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:55704382C>T	uc003xsd.1	+	c.5387C>T	c.(5386-5388)ACG>ATG	p.T1796M	RP1_uc003xse.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1796					cell projection organization|intracellular signal transduction|phototransduction, visible light|visual perception	cilium axoneme|cytoplasm|microtubule|photoreceptor connecting cilium|photoreceptor outer segment				ovary(4)|pancreas(1)	5		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)				Colon(91;1014 1389 7634 14542 40420)								0.348485	65.407509	66.743558	23	43	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		Missense_Mutation	SNP	55704382	55704382	14011	8	C	T	T	19	19	RP1	T	1	1
SVEP1	79987	broad.mit.edu	36	9	112283342	112283342	+	Splice_Site_SNP	SNP	C	G	G			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:112283342C>G	uc010mtz.1	-	c.2365_splice	c.e12+1	p.K789_splice	SVEP1_uc010mua.1_Splice_Site_SNP_p.K789_splice|SVEP1_uc004beu.2_Splice_Site_SNP_p.K789_splice	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.285714	12.194222	12.771038	4	10	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	112283342	112283342	15940	9	C	G	G	20	20	SVEP1	G	5	3
DOCK8	81704	broad.mit.edu	36	9	276571	276571	+	Silent	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:276571C>T	uc003zgf.1	+	c.267C>T	c.(265-267)GAC>GAT	p.D89D	DOCK8_uc003zgi.1_Silent_p.D21D|DOCK8_uc010mgu.1_De_novo_Start_OutOfFrame|DOCK8_uc010mgv.1_Silent_p.D21D|DOCK8_uc010mgt.1_Silent_p.D21D|DOCK8_uc003zgg.1_Silent_p.D21D|DOCK8_uc003zgh.1_Non-coding_Transcript	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	89					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)												0.477064	155.795234	155.844836	52	57	CC		KEEP	---	---	---	---	capture		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)	Silent	SNP	276571	276571	4877	9	C	T	T	19	19	DOCK8	T	1	1
DCAF12L2	340578	broad.mit.edu	36	X	125127572	125127572	+	Missense_Mutation	SNP	G	T	T			TCGA-02-2485-01	TCGA-02-2485-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:125127572G>T	uc004euk.1	-	c.17C>A	c.(16-18)ACA>AAA	p.T6K		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	WD repeat domain 40C	6										lung(2)|large_intestine(1)|ovary(1)|pancreas(1)	5														0.631579	36.989126	37.274827	12	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125127572	125127572	4436	23	G	T	T	48	48	DCAF12L2	T	3	3
PRPS2	5634	broad.mit.edu	36	X	12738161	12738161	+	Missense_Mutation	SNP	T	A	A			TCGA-02-2485-01	TCGA-02-2485-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:12738161T>A	uc004cva.1	+	c.514T>A	c.(514-516)TCA>ACA	p.S172T	PRPS2_uc004cvb.1_Missense_Mutation_p.S169T|PRPS2_uc010nec.1_Missense_Mutation_p.S105T	NM_001039091	NP_001034180	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	169					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity				0														0.896907	264.710297	279.891401	87	10	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12738161	12738161	13023	23	T	A	A	62	62	PRPS2	A	4	4
PLXNB3	5365	broad.mit.edu	36	X	152695969	152695969	+	Silent	SNP	C	G	G			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152695969C>G	uc004fii.1	+	c.5040C>G	c.(5038-5040)CGC>CGG	p.R1680R	SRPK3_uc004fik.1_5'UTR|PLXNB3_uc010nuk.1_Silent_p.R1703R	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3	1680	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)													0.210526	7.387494	8.862858	4	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	152695969	152695969	12551	23	C	G	G	27	27	PLXNB3	G	3	3
MAP3K15	389840	broad.mit.edu	36	X	19297154	19297154	+	Missense_Mutation	SNP	C	G	G			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:19297154C>G	uc004czk.1	-	c.1930G>C	c.(1930-1932)GCC>CCC	p.A644P	MAP3K15_uc004czi.1_Missense_Mutation_p.A103P|MAP3K15_uc004czj.1_Missense_Mutation_p.A604P	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase	1169					protein phosphorylation		ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|skin(1)	6	Hepatocellular(33;0.183)													0.2	9.094643	11.57269	6	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19297154	19297154	9632	23	C	G	G	26	26	MAP3K15	G	3	3
MSN	4478	broad.mit.edu	36	X	64866257	64866257	+	Missense_Mutation	SNP	A	G	G			TCGA-02-2485-01	TCGA-02-2485-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:64866257A>G	uc004dwf.1	+	c.425A>G	c.(424-426)CAT>CGT	p.H142R		NM_002444	NP_002435	P26038	MOES_HUMAN	moesin	142	FERM.				leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(2)	8										172				0.894737	114.172878	120.055704	34	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64866257	64866257	10278	23	A	G	G	8	8	MSN	G	4	4
HEPH	9843	broad.mit.edu	36	X	65403183	65403183	+	Missense_Mutation	SNP	C	T	T			TCGA-02-2485-01	TCGA-02-2485-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:65403183C>T	uc004dwn.1	+	c.3427C>T	c.(3427-3429)CGC>TGC	p.R1143C	HEPH_uc004dwm.1_Missense_Mutation_p.R1141C|HEPH_uc004dwo.1_Missense_Mutation_p.R874C|HEPH_uc010nkr.1_Missense_Mutation_p.R952C|HEPH_uc004dwp.1_Missense_Mutation_p.R1141C	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	1141	Cytoplasmic (Potential).				cellular iron ion homeostasis|copper ion transport|oxidation-reduction process|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9										386				0.169492	18.214281	24.314233	10	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65403183	65403183	7337	23	C	T	T	19	19	HEPH	T	1	1
WNT2B	7482	broad.mit.edu	36	1	112861347	112861348	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-02-2485-01	TCGA-02-2485-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:112861347_112861348delCT	uc001ecb.1	+	c.763_764delCT	c.(763-765)CTCfs	p.L255fs	WNT2B_uc001eca.1_Frame_Shift_Del_p.L236fs|WNT2B_uc009wgg.1_Frame_Shift_Del_p.L163fs	NM_024494	NP_078613	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family,	255					chondrocyte differentiation|cornea development in camera-type eye|dorsal/ventral axis specification|forebrain regionalization|hemopoietic stem cell proliferation|iris morphogenesis|lens development in camera-type eye|lung induction|male gonad development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding|signal transducer activity			ovary(1)	1	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.45			51	62				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	112861347	112861348	17961	1	CT	-	-	20	20	WNT2B	-	5	5
