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
GPR120	338557	broad.mit.edu	36	10	95316580	95316580	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0241-01	TCGA-06-0241-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:95316580T>G	uc001kir.1	+	c.113T>G	c.(112-114)GTG>GGG	p.V38G	GPR120_uc001kis.1_Missense_Mutation_p.V38G	NM_181745	NP_859529	Q5NUL3	O3FA1_HUMAN	G protein-coupled receptor 120	38	Extracellular (Potential).				negative regulation of cytokine secretion|negative regulation of inflammatory response|regulation of glucose transport	integral to membrane|plasma membrane	fatty acid binding				0		Colorectal(252;0.122)												0.6	8.624817	8.668368	3	2	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95316580	95316580	6910	10	T	G	G	59	59	GPR120	G	4	4
MUC5B	727897	broad.mit.edu	36	11	1207864	1207864	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1207864G>A	uc001ltb.2	+	c.1283G>A	c.(1282-1284)TGC>TAC	p.C428Y	MUC5B_uc009yct.1_Missense_Mutation_p.C425Y	NM_002458	NP_002449	Q9HC84	MUC5B_HUMAN	mucin 5, subtype B, tracheobronchial	425	VWFD 2.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)												0.44	173.68645	174.161445	66	84	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	Missense_Mutation	SNP	1207864	1207864	10373	11	G	A	A	46	46	MUC5B	A	2	2
NAV2	89797	broad.mit.edu	36	11	20056169	20056169	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:20056169G>A	uc009yhw.1	+	c.5290G>A	c.(5290-5292)GCA>ACA	p.A1764T	NAV2_uc001mpp.1_Missense_Mutation_p.A1644T|NAV2_uc001mpr.2_Missense_Mutation_p.A1708T|NAV2_uc009yhx.1_Missense_Mutation_p.A772T|NAV2_uc009yhy.1_Missense_Mutation_p.A670T|NAV2_uc009yhz.1_Missense_Mutation_p.A353T|NAV2_uc001mpu.1_Missense_Mutation_p.A146T	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	1764	Potential.					nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.513514	53.720461	53.726256	19	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20056169	20056169	10580	11	G	A	A	38	38	NAV2	A	1	1
LRP1	4035	broad.mit.edu	36	12	55867450	55867450	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55867450C>T	uc001snd.1	+	c.6975C>T	c.(6973-6975)GTC>GTT	p.V2325V		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2325	LDL-receptor class B 22.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.438095	125.923448	126.275944	46	59	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0103)	Silent	SNP	55867450	55867450	9324	12	C	T	T	29	29	LRP1	T	2	2
MBIP	51562	broad.mit.edu	36	14	35859479	35859479	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:35859479G>T	uc001wtm.1	-	c.67C>A	c.(67-69)CCC>ACC	p.P23T	MBIP_uc001wtn.1_Missense_Mutation_p.P23T|MBIP_uc001wto.1_Missense_Mutation_p.P23T	NM_016586	NP_057670	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1 isoform 1	23					histone H3 acetylation|inactivation of MAPK activity involved in osmosensory signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm|nucleolus	identical protein binding|protein kinase inhibitor activity				0	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)									91				0.822581	154.848238	160.919295	51	11	GG		KEEP	---	---	---	---	capture	Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)	Missense_Mutation	SNP	35859479	35859479	9737	14	G	T	T	44	44	MBIP	T	3	3
FBN1	2200	broad.mit.edu	36	15	46575026	46575026	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:46575026C>T	uc001zwx.1	-	c.2471G>A	c.(2470-2472)AGC>AAC	p.S824N		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	824	EGF-like 13; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)								2933				0.435294	562.376225	563.933614	185	240	CC		KEEP	---	---	---	---	capture		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)	Missense_Mutation	SNP	46575026	46575026	5938	15	C	T	T	28	28	FBN1	T	2	2
AKAP13	11214	broad.mit.edu	36	15	83924976	83924976	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:83924976C>T	uc002blu.1	+	c.2673C>T	c.(2671-2673)GAC>GAT	p.D891D	AKAP13_uc002blt.1_Silent_p.D891D|AKAP13_uc002blv.1_Silent_p.D891D|AKAP13_uc010bne.1_5'Flank	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	891					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|ovary(1)|liver(1)	8						Melanoma(94;603 1453 3280 32295 32951)								0.447853	221.151699	221.538235	73	90	CC		KEEP	---	---	---	---	capture			Silent	SNP	83924976	83924976	452	15	C	T	T	20	20	AKAP13	T	2	2
FANCI	55215	broad.mit.edu	36	15	87660635	87660635	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:87660635A>G	uc010bnp.1	+	c.3928A>G	c.(3928-3930)ACT>GCT	p.T1310A	FANCI_uc002bnm.1_Missense_Mutation_p.T1250A|FANCI_uc002bnn.1_Non-coding_Transcript|FANCI_uc002bnp.1_Missense_Mutation_p.T1070A|FANCI_uc002bnq.1_Missense_Mutation_p.T723A|POLG_uc002bns.2_3'UTR|POLG_uc002bnr.2_3'UTR	NM_001113378	NP_001106849	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I isoform	1310					cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)									1164				0.276596	35.756465	37.866783	13	34	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87660635	87660635	5905	15	A	G	G	6	6	FANCI	G	4	4
ITGAM	3684	broad.mit.edu	36	16	31216386	31216386	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31216386C>T	uc002ebr.1	+	c.1407C>T	c.(1405-1407)AAC>AAT	p.N469N	ITGAM_uc002ebq.1_Silent_p.N469N|ITGAM_uc010cam.1_Missense_Mutation_p.R73W|ITGAM_uc010can.1_De_novo_Start_OutOfFrame	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M precursor	469	FG-GAP 5.|Extracellular (Potential).|Potential.				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1														0.436782	431.429382	432.643879	152	196	CC		KEEP	---	---	---	---	capture			Silent	SNP	31216386	31216386	8191	16	C	T	T	19	19	ITGAM	T	1	1
NOL3	8996	broad.mit.edu	36	16	65766279	65766279	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65766279G>A	uc002erp.1	+	c.550G>A	c.(550-552)GAG>AAG	p.E184K	NOL3_uc002erq.1_Silent_p.Q180Q	NM_003946	NP_003937	O60936	NOL3_HUMAN	nucleolar protein 3	Error:Variant_position_missing_in_O60936_after_alignment					anti-apoptosis|apoptosis|mRNA processing|RNA splicing	cytosol|nucleolus	identical protein binding|RNA binding				0		Ovarian(137;0.192)												0.484848	47.649906	47.658104	16	17	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)	Missense_Mutation	SNP	65766279	65766279	10926	16	G	A	A	33	33	NOL3	A	2	2
KCTD19	146212	broad.mit.edu	36	16	65894680	65894680	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65894680C>T	uc002esu.2	-	c.513G>A	c.(511-513)GAG>GAA	p.E171E	KCTD19_uc002est.2_5'UTR	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain	171						voltage-gated potassium channel complex	voltage-gated potassium channel activity				0		Ovarian(137;0.192)												0.4125	100.579857	101.108984	33	47	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)	Silent	SNP	65894680	65894680	8412	16	C	T	T	24	24	KCTD19	T	2	2
MTSS1L	92154	broad.mit.edu	36	16	69271437	69271437	+	Silent	SNP	C	G	G			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69271437C>G	uc002ezj.1	-	c.228G>C	c.(226-228)TCG>TCC	p.S76S	MTSS1L_uc002ezk.1_5'UTR	NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	76	IMD.				filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1														0.3	7.467102	7.798833	3	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	69271437	69271437	10356	16	C	G	G	23	23	MTSS1L	G	3	3
TP53	7157	broad.mit.edu	36	17	7518263	7518263	+	Missense_Mutation	SNP	C	T	T	rs11540652	by-hapmap	TCGA-06-0241-01	TCGA-06-0241-01	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)			0.66	109.789395	110.920732	33	17	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
THEG	51298	broad.mit.edu	36	19	318156	318156	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:318156C>T	uc002lol.1	-	c.822G>A	c.(820-822)CCG>CCA	p.P274P	THEG_uc002lom.1_Silent_p.P250P	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	274	THEG 4.				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)												0.422727	261.562465	262.701314	93	127	CC		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)	Silent	SNP	318156	318156	16385	19	C	T	T	31	31	THEG	T	1	1
ELSPBP1	64100	broad.mit.edu	36	19	53203753	53203753	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53203753G>C	uc002pht.1	+	c.17G>C	c.(16-18)AGT>ACT	p.S6T		NM_022142	NP_071425	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	6					single fertilization	extracellular region					0		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)												0.361111	84.027801	85.251297	26	46	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)	Missense_Mutation	SNP	53203753	53203753	5275	19	G	C	C	36	36	ELSPBP1	C	3	3
TNNT1	7138	broad.mit.edu	36	19	60340283	60340283	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60340283C>T	uc002qjb.2	-	c.611G>A	c.(610-612)CGG>CAG	p.R204Q	TNNT1_uc002qiz.2_Missense_Mutation_p.R134Q|TNNT1_uc002qja.2_Missense_Mutation_p.R134Q|TNNT1_uc002qjc.2_Missense_Mutation_p.R204Q|TNNT1_uc002qje.2_Missense_Mutation_p.R193Q|TNNT1_uc002qjd.2_Missense_Mutation_p.R193Q	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a	204					muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1														0.61194	129.27802	130.011277	41	26	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)	Missense_Mutation	SNP	60340283	60340283	16871	19	C	T	T	23	23	TNNT1	T	1	1
PEG3	5178	broad.mit.edu	36	19	62019811	62019811	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:62019811C>T	uc002qnu.1	-	c.1811G>A	c.(1810-1812)CGC>CAC	p.R604H	ZIM2_uc010etp.1_Intron|ZIM2_uc002qnq.1_Intron|ZIM2_uc002qnr.1_Intron|PEG3_uc010etq.1_5'Flank|PEG3_uc002qnt.1_Missense_Mutation_p.R575H|PEG3_uc002qnv.1_Missense_Mutation_p.R604H|PEG3_uc010etr.1_Missense_Mutation_p.R604H|PEG3_uc002qnw.1_Missense_Mutation_p.R480H|PEG3_uc002qnx.1_Missense_Mutation_p.R478H	NM_006210	NP_006201	Q9GZU2	PEG3_HUMAN	paternally expressed 3	604					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.R604H(1)		ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)												0.457831	106.132212	106.261575	38	45	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0269)	Missense_Mutation	SNP	62019811	62019811	12141	19	C	T	T	27	27	PEG3	T	1	1
FAM46C	54855	broad.mit.edu	36	1	117967167	117967167	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:117967167G>A	uc001ehe.1	+	c.154G>A	c.(154-156)GTC>ATC	p.V52I	FAM46C_uc009whh.1_Missense_Mutation_p.V52I	NM_017709	NP_060179	Q5VWP2	FA46C_HUMAN	hypothetical protein LOC54855	52											0	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)									Multiple Myeloma(3;1.13e-06)			0.410256	132.868429	133.693536	48	69	GG		KEEP	---	---	---	---	capture		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)	Missense_Mutation	SNP	117967167	117967167	5788	1	G	A	A	40	40	FAM46C	A	1	1
ZNF697	90874	broad.mit.edu	36	1	119967273	119967273	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:119967273C>A	uc001ehy.1	-	c.1216G>T	c.(1216-1218)GAG>TAG	p.E406*		NM_001080470	NP_001073939	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	406					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)												0.428571	16.847126	16.909503	6	8	CC		KEEP	---	---	---	---	capture		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)	Nonsense_Mutation	SNP	119967273	119967273	18695	1	C	A	A	31	31	ZNF697	A	5	3
AQP10	89872	broad.mit.edu	36	1	152561153	152561153	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152561153G>A	uc001feu.1	+	c.226G>A	c.(226-228)GTC>ATC	p.V76I	AQP10_uc001fev.2_Missense_Mutation_p.V76I	NM_080429	NP_536354	Q96PS8	AQP10_HUMAN	aquaporin 10	76	Cytoplasmic (Potential).				response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)													0.489796	66.38165	66.386459	24	25	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.185)		Missense_Mutation	SNP	152561153	152561153	833	1	G	A	A	40	40	AQP10	A	1	1
TMEM79	84283	broad.mit.edu	36	1	154521672	154521672	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154521672G>A	uc001foe.1	+	c.31G>A	c.(31-33)GAA>AAA	p.E11K	SMG5_uc001foc.2_5'Flank|TMEM79_uc001fod.1_5'UTR|TMEM79_uc009wrw.1_Missense_Mutation_p.E11K	NM_032323	NP_115699	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	11						integral to membrane					0	Hepatocellular(266;0.158)													0.380165	132.416595	133.942437	46	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154521672	154521672	16742	1	G	A	A	41	41	TMEM79	A	2	2
HSPA6	3310	broad.mit.edu	36	1	159761230	159761230	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0241-01	TCGA-06-0241-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159761230T>G	uc001gap.1	+	c.158T>G	c.(157-159)GTC>GGC	p.V53G	HSPA6_uc001gaq.1_Missense_Mutation_p.V53G	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	53					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)													0.666667	12.319709	12.532938	6	3	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00376)		Missense_Mutation	SNP	159761230	159761230	7714	1	T	G	G	58	58	HSPA6	G	4	4
PLCH2	9651	broad.mit.edu	36	1	2397999	2397999	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:2397999C>G	uc001aji.1	+	c.112C>G	c.(112-114)CTC>GTC	p.L38V		NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	38	Necessary for plasma membrane localization (By similarity).				intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)												0.2	6.786873	8.463477	4	16	CC		KEEP	---	---	---	---	capture		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)	Missense_Mutation	SNP	2397999	2397999	12464	1	C	G	G	28	28	PLCH2	G	3	3
CSF3R	1441	broad.mit.edu	36	1	36704987	36704987	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36704987G>A	uc001cax.1	-	c.2150C>T	c.(2149-2151)ACG>ATG	p.T717M	MRPS15_uc001cas.2_5'Flank|CSF3R_uc001cat.1_Missense_Mutation_p.T252M|CSF3R_uc009vvc.1_Missense_Mutation_p.T219M|CSF3R_uc001cau.1_Missense_Mutation_p.T90M|CSF3R_uc001cav.1_Missense_Mutation_p.T690M|CSF3R_uc001caw.1_Missense_Mutation_p.T690M|CSF3R_uc001cay.1_Missense_Mutation_p.R659C	NM_156039	NP_724781	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor isoform c	690	Cytoplasmic (Potential).				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity	p.T717M(1)		central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)					322				0.48	308.672971	308.751828	108	117	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36704987	36704987	4078	1	G	A	A	40	40	CSF3R	A	1	1
RTEL1	51750	broad.mit.edu	36	20	61796573	61796573	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61796573G>T	uc002yft.1	+	c.3145G>T	c.(3145-3147)GTG>TTG	p.V1049L	RTEL1_uc002yfu.1_Missense_Mutation_p.V1049L|RTEL1_uc002yfw.1_Non-coding_Transcript|RTEL1_uc002yfx.1_Missense_Mutation_p.V294L|TNFRSF6B_uc002yfy.1_5'Flank|TNFRSF6B_uc002yfz.1_5'Flank	NM_032957	NP_116575	Q9NZ71	RTEL1_HUMAN	regulator of telomere elongation helicase 1	1049					DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)													0.418605	47.635121	47.88529	18	25	GG		KEEP	---	---	---	---	capture	Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)		Missense_Mutation	SNP	61796573	61796573	14200	20	G	T	T	36	36	RTEL1	T	3	3
ZC3H7B	23264	broad.mit.edu	36	22	40081727	40081727	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0241-01	TCGA-06-0241-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40081727T>G	uc003azw.1	+	c.2189T>G	c.(2188-2190)GTC>GGC	p.V730G	ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	746					interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1														0.235294	6.952155	8.085719	4	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40081727	40081727	18161	22	T	G	G	58	58	ZC3H7B	G	4	4
TBC1D8	11138	broad.mit.edu	36	2	101021487	101021487	+	Silent	SNP	G	T	T			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:101021487G>T	uc010fiv.1	-	c.1098C>A	c.(1096-1098)ATC>ATA	p.I366I	TBC1D8_uc002tau.2_Silent_p.I123I	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	366					blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3														0.469965	373.093844	373.319878	133	150	GG		KEEP	---	---	---	---	capture			Silent	SNP	101021487	101021487	16151	2	G	T	T	45	45	TBC1D8	T	3	3
LRP1B	53353	broad.mit.edu	36	2	141314117	141314117	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:141314117A>T	uc002tvj.1	-	c.5122T>A	c.(5122-5124)TAC>AAC	p.Y1708N		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1708	Extracellular (Potential).|LDL-receptor class B 16.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)				Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.425926	63.606072	63.866227	23	31	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	Missense_Mutation	SNP	141314117	141314117	9328	2	A	T	T	15	15	LRP1B	T	4	4
CD207	50489	broad.mit.edu	36	2	70914335	70914335	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:70914335C>T	uc002shg.1	-	c.515G>A	c.(514-516)CGG>CAG	p.R172Q		NM_015717	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 antigen, langerin	172	Potential.|Extracellular (Potential).				defense response to virus	endocytic vesicle|integral to membrane	mannose binding			ovary(1)|lung(1)	2														0.475	123.648137	123.691388	38	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70914335	70914335	3110	2	C	T	T	23	23	CD207	T	1	1
YEATS2	55689	broad.mit.edu	36	3	184937246	184937246	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:184937246G>A	uc003fly.1	+	c.859G>A	c.(859-861)GTC>ATC	p.V287I		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	287	YEATS.				histone H3 acetylation|negative regulation of gene-specific transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	specific transcriptional repressor activity|TBP-class protein binding			ovary(2)|large_intestine(1)	3	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)													0.416667	249.676146	251.028916	95	133	GG		KEEP	---	---	---	---	capture	all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Missense_Mutation	SNP	184937246	184937246	18055	3	G	A	A	40	40	YEATS2	A	1	1
ITGA9	3680	broad.mit.edu	36	3	37522529	37522529	+	Silent	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:37522529G>A	uc003chd.1	+	c.777G>A	c.(775-777)CCG>CCA	p.P259P	ITGA9_uc003chc.2_Silent_p.P259P	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	259	Extracellular (Potential).|FG-GAP 4.				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|lung(1)|pancreas(1)	5														0.25	23.039063	25.306703	10	30	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)	Silent	SNP	37522529	37522529	8187	3	G	A	A	40	40	ITGA9	A	1	1
ARL8B	55207	broad.mit.edu	36	3	5189343	5189343	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:5189343A>G	uc003bqg.1	+	c.290A>G	c.(289-291)GAT>GGT	p.D97G		NM_018184	NP_060654	Q9NVJ2	ARL8B_HUMAN	ADP-ribosylation factor-like 10C	97					cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0														0.446809	219.711482	220.0584	63	78	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)	Missense_Mutation	SNP	5189343	5189343	965	3	A	G	G	12	12	ARL8B	G	4	4
MAGI1	9223	broad.mit.edu	36	3	65351908	65351908	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:65351908G>T	uc003dmn.1	-	c.2365C>A	c.(2365-2367)CCA>ACA	p.P789T	MAGI1_uc003dmm.1_Missense_Mutation_p.P789T|MAGI1_uc003dmo.1_Missense_Mutation_p.P789T|MAGI1_uc003dmp.1_Missense_Mutation_p.P789T|MAGI1_uc010hnx.1_Missense_Mutation_p.P72T	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	789					cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			kidney(1)|pancreas(1)	2		Lung NSC(201;0.0016)												0.392405	183.2118	184.814502	62	96	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)	Missense_Mutation	SNP	65351908	65351908	9573	3	G	T	T	44	44	MAGI1	T	3	3
KIAA1109	84162	broad.mit.edu	36	4	123326707	123326707	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:123326707C>T	uc003ieh.1	+	c.425C>T	c.(424-426)TCG>TTG	p.S142L	KIAA1109_uc003iei.1_5'UTR	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	hypothetical protein LOC84162	142					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(7)|central_nervous_system(1)|pancreas(1)	9														0.416667	131.555076	132.209966	45	63	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123326707	123326707	8516	4	C	T	T	31	31	KIAA1109	T	1	1
ANKRD50	57182	broad.mit.edu	36	4	125812542	125812542	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:125812542A>G	uc003ifg.2	-	c.1340T>C	c.(1339-1341)TTA>TCA	p.L447S	ANKRD50_uc010inw.1_Missense_Mutation_p.L447S	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	447										central_nervous_system(1)	1														0.414545	403.424172	405.17188	114	161	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125812542	125812542	685	4	A	G	G	13	13	ANKRD50	G	4	4
SH3D19	152503	broad.mit.edu	36	4	152315646	152315646	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:152315646G>C	uc010ipl.1	-	c.311C>G	c.(310-312)CCA>CGA	p.P104R	SH3D19_uc003imc.2_Missense_Mutation_p.P107R|SH3D19_uc003ime.2_Missense_Mutation_p.P107R|SH3D19_uc010ipm.1_Missense_Mutation_p.P107R	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a	107	Pro-rich.				cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)	1	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)												0.437768	320.07121	320.879204	102	131	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152315646	152315646	14740	4	G	C	C	47	47	SH3D19	C	3	3
PCDHA2	56146	broad.mit.edu	36	5	140156404	140156404	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140156404C>T	uc003lhd.1	+	c.1671C>T	c.(1669-1671)GAC>GAT	p.D557D	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhc.1_Silent_p.D557D	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	557	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4														0.397163	154.704501	155.997319	56	85	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140156404	140156404	11944	5	C	T	T	19	19	PCDHA2	T	1	1
RBM27	54439	broad.mit.edu	36	5	145578751	145578751	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:145578751G>A	uc003lnz.2	+	c.70G>A	c.(70-72)GAT>AAT	p.D24N	RBM27_uc003lny.2_Missense_Mutation_p.D24N	NM_018989	NP_061862	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	24					mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3														0.47549	279.065242	279.171096	97	107	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	145578751	145578751	13589	5	G	A	A	45	45	RBM27	A	2	2
NDST1	3340	broad.mit.edu	36	5	149902715	149902715	+	Silent	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149902715A>G	uc003lsk.2	+	c.1959A>G	c.(1957-1959)AAA>AAG	p.K653K	NDST1_uc003lsm.1_Silent_p.K653K	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	653	Heparan sulfate N-sulfotransferase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)	1		all_hematologic(541;0.224)												0.415042	494.122206	496.381787	149	210	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Silent	SNP	149902715	149902715	10654	5	A	G	G	3	3	NDST1	G	4	4
HIVEP2	3097	broad.mit.edu	36	6	143116384	143116384	+	Silent	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:143116384A>G	uc003qjd.1	-	c.6894T>C	c.(6892-6894)ACT>ACC	p.T2298T		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	2298					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						Esophageal Squamous(107;843 1510 13293 16805 42198)								0.36	173.625721	176.206675	54	96	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)	Silent	SNP	143116384	143116384	7478	6	A	G	G	11	11	HIVEP2	G	4	4
T	6862	broad.mit.edu	36	6	166491982	166491982	+	Silent	SNP	G	T	T			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:166491982G>T	uc003qut.1	-	c.1122C>A	c.(1120-1122)GCC>GCA	p.A374A	T_uc003quu.1_Silent_p.A373A|T_uc003quv.1_Silent_p.A315A	NM_003181	NP_003172	O15178	BRAC_HUMAN	transcription factor T	373					anterior/posterior axis specification, embryo|mesoderm development|primitive streak formation	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)												0.423077	60.437404	60.706618	22	30	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)	Silent	SNP	166491982	166491982	16009	6	G	T	T	43	43	T	T	3	3
TRIM40	135644	broad.mit.edu	36	6	30222839	30222839	+	Silent	SNP	C	G	G			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30222839C>G	uc003npk.2	+	c.540C>G	c.(538-540)GGC>GGG	p.G180G	TRIM40_uc003npm.2_Silent_p.G151G	NM_138700	NP_619645	Q6P9F5	TRI40_HUMAN	tripartite motif-containing 40	180						intracellular	zinc ion binding			ovary(1)	1														0.28	12.791178	13.897346	7	18	CC		KEEP	---	---	---	---	capture			Silent	SNP	30222839	30222839	17059	6	C	G	G	26	26	TRIM40	G	3	3
POU5F1	5460	broad.mit.edu	36	6	31241392	31241392	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31241392A>G	uc003nsv.1	-	c.592T>C	c.(592-594)TGT>CGT	p.C198R	POU5F1_uc003nsu.1_Missense_Mutation_p.C103R	NM_002701	NP_002692	Q01860	PO5F1_HUMAN	POU domain, class 5, transcription factor 1	198	POU-specific.				anatomical structure morphogenesis|blastocyst development|BMP signaling pathway involved in heart induction|cardiac cell fate determination|cell fate commitment involved in formation of primary germ layers|gene-specific transcription from RNA polymerase II promoter|mRNA transcription from RNA polymerase II promoter|negative regulation of gene silencing by miRNA|positive regulation of catenin import into nucleus|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of SMAD protein import into nucleus|regulation of asymmetric cell division|regulation of heart induction by regulation of canonical Wnt receptor signaling pathway|regulation of methylation-dependent chromatin silencing|regulation of transcription, DNA-dependent|response to wounding|somatic stem cell maintenance|somatic stem cell maintenance	cytosol|nucleoplasm|transcription factor complex	miRNA binding|promoter binding|sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulator activity|ubiquitin protein ligase binding		EWSR1/POU5F1(10)	skin(7)|salivary_gland(2)|bone(2)	11										210				0.444444	90.097366	90.265713	28	35	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31241392	31241392	12711	6	A	G	G	6	6	POU5F1	G	4	4
NEU1	4758	broad.mit.edu	36	6	31937029	31937029	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0241-01	TCGA-06-0241-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31937029T>C	uc003nxq.2	-	c.530A>G	c.(529-531)GAT>GGT	p.D177G	NEU1_uc010jtg.1_Non-coding_Transcript|NEU1_uc003nxr.2_Non-coding_Transcript|NEU1_uc010jth.1_Missense_Mutation_p.D8G|NEU1_uc003nxs.2_Missense_Mutation_p.D177G	NM_000434	NP_000425	Q99519	NEUR1_HUMAN	neuraminidase precursor	177	BNR 2.					cytoplasmic membrane-bounded vesicle|lysosomal lumen|lysosomal membrane|plasma membrane	exo-alpha-sialidase activity|protein binding			ovary(1)	1					Oseltamivir(DB00198)|Zanamivir(DB00558)									0.484375	322.375206	322.415534	93	99	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31937029	31937029	10740	6	T	C	C	50	50	NEU1	C	4	4
DNAJC2	27000	broad.mit.edu	36	7	102740762	102740762	+	Silent	SNP	A	G	G			TCGA-06-0241-01	TCGA-06-0241-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102740762A>G	uc003vbo.1	-	c.1659T>C	c.(1657-1659)CCT>CCC	p.P553P	DNAJC2_uc003vbn.1_Silent_p.P178P|DNAJC2_uc010lix.1_Silent_p.P500P|DNAJC2_uc003vbp.1_Silent_p.P178P|PMPCB_uc003vbl.1_3'UTR|PMPCB_uc003vbm.1_3'UTR|PMPCB_uc010liv.1_3'UTR|PMPCB_uc010liw.1_3'UTR	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	553	SANT 2.				'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1														0.276549	393.787	414.095043	125	327	AA		KEEP	---	---	---	---	capture			Silent	SNP	102740762	102740762	4822	7	A	G	G	3	3	DNAJC2	G	4	4
RELN	5649	broad.mit.edu	36	7	103068279	103068279	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:103068279C>T	uc003vca.1	-	c.2016G>A	c.(2014-2016)CCG>CCA	p.P672P	RELN_uc010liz.1_Silent_p.P672P	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	672	EGF-like 1.				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)								0.283333	84.902134	89.960333	34	86	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Silent	SNP	103068279	103068279	13689	7	C	T	T	19	19	RELN	T	1	1
MAGI2	9863	broad.mit.edu	36	7	77811089	77811089	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:77811089C>T	uc003ugx.1	-	c.1350G>A	c.(1348-1350)CTG>CTA	p.L450L	MAGI2_uc003ugy.1_Silent_p.L450L|MAGI2_uc010ldx.1_Silent_p.L59L|MAGI2_uc010ldy.1_Silent_p.L59L	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	450	PDZ 2.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)	5		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)												0.309091	128.251933	133.617501	51	114	CC		KEEP	---	---	---	---	capture			Silent	SNP	77811089	77811089	9574	7	C	T	T	25	25	MAGI2	T	2	2
FAM83H	286077	broad.mit.edu	36	8	144880117	144880117	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144880117C>T	uc003yzk.1	-	c.3502G>A	c.(3502-3504)GTG>ATG	p.V1168M	FAM83H_uc010mfk.1_Non-coding_Transcript	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	hypothetical protein LOC286077	1168					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.392857	62.435473	62.999027	22	34	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)		Missense_Mutation	SNP	144880117	144880117	5866	8	C	T	T	19	19	FAM83H	T	1	1
EYA1	2138	broad.mit.edu	36	8	72290418	72290418	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:72290418G>A	uc003xys.2	-	c.1460C>T	c.(1459-1461)TCG>TTG	p.S487L	EYA1_uc003xyt.2_Missense_Mutation_p.S454L|EYA1_uc003xyr.2_Missense_Mutation_p.S452L|EYA1_uc010lzf.1_Missense_Mutation_p.S414L|EYA1_uc003xyu.1_Missense_Mutation_p.S487L|EYA1_uc003xyv.1_Missense_Mutation_p.S365L	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	487			S -> P (in BOR1).		double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity	p.S487L(1)		ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)													0.404878	241.188201	242.808245	83	122	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.0837)|all cancers(69;0.247)		Missense_Mutation	SNP	72290418	72290418	5522	8	G	A	A	37	37	EYA1	A	1	1
TESK1	7016	broad.mit.edu	36	9	35598190	35598190	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35598190C>G	uc003zxa.1	+	c.829C>G	c.(829-831)CTG>GTG	p.L277V	TESK1_uc003zwz.1_Non-coding_Transcript|TESK1_uc010mks.1_Missense_Mutation_p.L117V	NM_006285	NP_006276	Q15569	TESK1_HUMAN	testis-specific protein kinase 1	277	Protein kinase.				cell junction assembly|protein phosphorylation|spermatogenesis	cytosol	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5										56				0.238938	79.268177	86.299721	27	86	CC		KEEP	---	---	---	---	capture	Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Missense_Mutation	SNP	35598190	35598190	16294	9	C	G	G	32	32	TESK1	G	3	3
KIAA1432	57589	broad.mit.edu	36	9	5755489	5755489	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:5755489G>A	uc003zji.1	+	c.2680G>A	c.(2680-2682)GAC>AAC	p.D894N	KIAA1432_uc003zjh.2_Missense_Mutation_p.D894N|KIAA1432_uc003zjj.1_Missense_Mutation_p.D436N	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	973						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)												0.389513	298.864755	301.710381	104	163	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)	Missense_Mutation	SNP	5755489	5755489	8542	9	G	A	A	41	41	KIAA1432	A	2	2
COL4A6	1288	broad.mit.edu	36	X	107299427	107299427	+	Silent	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:107299427G>A	uc004enw.2	-	c.3648C>T	c.(3646-3648)ATC>ATT	p.I1216I	COL4A6_uc004env.2_Silent_p.I1215I|COL4A6_uc010npk.1_Silent_p.I1191I	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	1216	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.437956	170.973748	171.434164	60	77	GG		KEEP	---	---	---	---	capture			Silent	SNP	107299427	107299427	3833	23	G	A	A	37	37	COL4A6	A	1	1
SLC9A6	10479	broad.mit.edu	36	X	134908724	134908724	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:134908724C>T	uc004ezk.1	+	c.724C>T	c.(724-726)CAA>TAA	p.Q242*	SLC9A6_uc004ezj.1_Nonsense_Mutation_p.Q210*	NM_001042537	NP_001036002	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen	210					regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.392308	268.979864	271.622737	102	158	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	134908724	134908724	15215	23	C	T	T	17	17	SLC9A6	T	5	2
PLXNB3	5365	broad.mit.edu	36	X	152686924	152686924	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152686924C>T	uc004fii.1	+	c.1113C>T	c.(1111-1113)GGC>GGT	p.G371G	PLXNB3_uc010nuk.1_Silent_p.G394G	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3	371	Extracellular (Potential).|Sema.				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)													0.429577	165.140081	165.75604	61	81	CC		KEEP	---	---	---	---	capture			Silent	SNP	152686924	152686924	12551	23	C	T	T	27	27	PLXNB3	T	1	1
MAGEB4	4115	broad.mit.edu	36	X	30170897	30170897	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30170897C>T	uc004dcb.1	+	c.724C>T	c.(724-726)CGA>TGA	p.R242*	MAGEB1_uc004dcc.1_5'Flank|MAGEB1_uc004dcd.1_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	242	MAGE.									ovary(1)	1														0.442623	163.635518	163.985014	54	68	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	30170897	30170897	9559	23	C	T	T	23	23	MAGEB4	T	5	1
TAB3	257397	broad.mit.edu	36	X	30782276	30782276	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30782276C>T	uc004dcj.1	-	c.1427G>A	c.(1426-1428)CGC>CAC	p.R476H	TAB3_uc004dck.1_Missense_Mutation_p.R476H|TAB3_uc010ngl.1_Missense_Mutation_p.R476H	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	476					activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1						Pancreas(164;1598 1985 29022 43301 49529)								0.428571	209.985679	210.766315	75	100	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30782276	30782276	16018	23	C	T	T	27	27	TAB3	T	1	1
RGN	9104	broad.mit.edu	36	X	46836495	46836495	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46836495C>G	uc004dgz.1	+	c.786C>G	c.(784-786)TGC>TGG	p.C262W	RGN_uc004dha.1_Missense_Mutation_p.C262W|RGN_uc010nho.1_Missense_Mutation_p.C209W|RGN_uc010nhp.1_Missense_Mutation_p.C190W	NM_152869	NP_690608	Q15493	RGN_HUMAN	regucalcin	262					cellular calcium ion homeostasis|positive regulation of ATPase activity|regulation of calcium-mediated signaling	cytoplasm|nucleus	calcium ion binding|enzyme regulator activity|gluconolactonase activity|zinc ion binding				0														0.358974	46.441468	47.123501	14	25	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46836495	46836495	13755	23	C	G	G	27	27	RGN	G	3	3
USP11	8237	broad.mit.edu	36	X	46983466	46983466	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46983466G>A	uc004dhp.1	+	c.359G>A	c.(358-360)GGG>GAG	p.G120E	USP11_uc004dhq.1_5'UTR	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific protease 11	120	DUSP.				protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|central_nervous_system(1)	2														0.353846	68.004902	69.229395	23	42	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46983466	46983466	17604	23	G	A	A	43	43	USP11	A	2	2
KLF8	11279	broad.mit.edu	36	X	56308627	56308627	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:56308627C>A	uc004dur.1	+	c.371C>A	c.(370-372)ACG>AAG	p.T124K	KLF8_uc010nkg.1_Missense_Mutation_p.T119K|KLF8_uc010nkh.1_Non-coding_Transcript	NM_007250	NP_009181	O95600	KLF8_HUMAN	Kruppel-like factor 8	124					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.401709	146.596447	147.586207	47	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56308627	56308627	8664	23	C	A	A	19	19	KLF8	A	3	3
UBQLN2	29978	broad.mit.edu	36	X	56608771	56608771	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:56608771C>T	uc004dus.1	+	c.1740C>T	c.(1738-1740)GTC>GTT	p.V580V		NM_013444	NP_038472	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	580						cytoplasm|nucleus|plasma membrane	binding			ovary(1)|skin(1)	2						Esophageal Squamous(104;218 1492 6022 10838 28884)								0.452055	91.157191	91.304421	33	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	56608771	56608771	17455	23	C	T	T	29	29	UBQLN2	T	2	2
ASB12	142689	broad.mit.edu	36	X	63361933	63361933	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:63361933G>A	uc004dvq.1	-	c.323C>T	c.(322-324)ACG>ATG	p.T108M	ASB12_uc004dvp.1_Missense_Mutation_p.T99M|ASB12_uc004dvr.1_Missense_Mutation_p.T99M	NM_130388	NP_569059	Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box-containing protein	99	ANK 2.				intracellular signal transduction					ovary(2)	2														0.461538	65.584795	65.65261	24	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63361933	63361933	1034	23	G	A	A	40	40	ASB12	A	1	1
KIF4A	24137	broad.mit.edu	36	X	69511892	69511892	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0241-01	TCGA-06-0241-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:69511892G>A	uc004dyg.1	+	c.1892G>A	c.(1891-1893)CGT>CAT	p.R631H	KIF4A_uc004dyf.1_Missense_Mutation_p.R631H|KIF4A_uc010nkw.1_Missense_Mutation_p.R631H	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	631	Potential.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4														0.396341	180.436499	181.9794	65	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69511892	69511892	8614	23	G	A	A	40	40	KIF4A	A	1	1
GPR174	84636	broad.mit.edu	36	X	78314036	78314036	+	Silent	SNP	C	T	T			TCGA-06-0241-01	TCGA-06-0241-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:78314036C>T	uc004edg.1	+	c.876C>T	c.(874-876)TAC>TAT	p.Y292Y		NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79	292	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2														0.396907	226.309225	228.120354	77	117	CC		KEEP	---	---	---	---	capture			Silent	SNP	78314036	78314036	6947	23	C	T	T	20	20	GPR174	T	2	2
MICALCL	84953	broad.mit.edu	36	11	12272963	12272965	+	In_Frame_Del	DEL	CTA	-	-			TCGA-06-0241-01	TCGA-06-0241-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272963_12272965delCTA	uc001mkg.1	+	c.1409_1411delCTA	c.(1408-1413)CCTACA>CCA	p.T471del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.64			9	5				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272963	12272965	9962	11	CTA	-	-	24	24	MICALCL	-	5	5
PCDH17	27253	broad.mit.edu	36	13	57105303	57105304	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-0241-01	TCGA-06-0241-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:57105303_57105304insA	uc001vhq.1	+	c.622_623insA	c.(622-624)CACfs	p.H208fs	PCDH17_uc010aec.1_Frame_Shift_Ins_p.H208fs	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	208	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(2)|pancreas(2)	4		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		Melanoma(72;952 1291 1619 12849 33676)								0.34			31	60				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	57105303	57105304	11932	13	-	A	A	29	29	PCDH17	A	5	5
