#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_type
ARID2	196528	hgsc.bcm.edu	37	12	46244202	46244202	+	Missense_Mutation	SNP	C	C	T			TCGA-25-1628-01	TCGA-25-1628-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr12:46244202C>T	ENST00000334344.6	+	15	2468	c.2296C>T	c.(2296-2298)Cca>Tca	p.P766S	ARID2_ENST00000422737.1_Missense_Mutation_p.P617S|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000444670.1_Missense_Mutation_p.P376S|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	766					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P766S(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GCTTCACCATCCATCTGTAAT	0.473			"""N, S, F"""		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	ovary(1)	12											85.0	73.0	77.0					12																	46244202		2203	4300	6503	44530469	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2296C>T	12.37:g.46244202C>T	ENSP00000335044:p.Pro766Ser	Somatic		Capture	SOLID	Phase_III	44530469	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705450	0.48412	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	T	0.34072	1.38	5.83	5.83	0.93111	.	0.106321	0.64402	N	0.000004	T	0.36248	0.0960	L	0.27053	0.805	0.80722	D	1	P;P;B	0.36633	0.562;0.562;0.376	B;B;B	0.41036	0.346;0.346;0.141	T	0.15780	-1.0425	10	0.62326	D	0.03	-9.6831	20.1152	0.97926	0.0:1.0:0.0:0.0	.	766;376;766	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	S	766;617;376	ENSP00000335044:P766S	ENSP00000335044:P766S	P	+	1	0	ARID2	44530469	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.193000	0.58385	2.750000	0.94351	0.655000	0.94253	CCA		0.473	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		Missense_Mutation
ATP13A5	344905	hgsc.bcm.edu	37	3	193052730	193052730	+	Missense_Mutation	SNP	C	C	T	rs370567338		TCGA-25-1628-01	TCGA-25-1628-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr3:193052730C>T	ENST00000342358.4	-	10	1219	c.1102G>A	c.(1102-1104)Gtt>Att	p.V368I		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	368						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.V368I(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GTTTGCAAAACGACTGCTCGT	0.433																																																1	Substitution - Missense(1)	ovary(1)	3							ILE/VAL	0,4406		0,0,2203	94.0	94.0	94.0		1102	5.9	1.0	3		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	ATP13A5	NM_198505.2	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	368/1219	193052730	2,13004	2203	4300	6503	194535424	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.1102G>A	3.37:g.193052730C>T	ENSP00000341942:p.Val368Ile	Somatic		Capture	SOLID	Phase_III	194535424	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	SNP	19	Baylor	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731273	0.89390	0.0	2.33E-4	ENSG00000187527	ENST00000342358	D	0.94828	-3.53	5.86	5.86	0.93980	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.198393	0.34676	N	0.003780	D	0.97854	0.9295	M	0.91196	3.185	0.54753	D	0.999988	D	0.76494	0.999	D	0.70935	0.971	D	0.98281	1.0508	10	0.72032	D	0.01	-16.4559	18.7576	0.91838	0.0:1.0:0.0:0.0	.	368	Q4VNC0	AT135_HUMAN	I	368	ENSP00000341942:V368I	ENSP00000341942:V368I	V	-	1	0	ATP13A5	194535424	1.000000	0.71417	0.992000	0.48379	0.831000	0.47069	7.001000	0.76297	2.788000	0.95919	0.651000	0.88453	GTT		0.433	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		Missense_Mutation
BMPR1B	658	hgsc.bcm.edu	37	4	96025705	96025705	+	Missense_Mutation	SNP	A	A	T			TCGA-25-1628-01	TCGA-25-1628-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr4:96025705A>T	ENST00000515059.1	+	4	413	c.130A>T	c.(130-132)Aac>Tac	p.N44Y	BMPR1B_ENST00000394931.1_Missense_Mutation_p.N44Y|BMPR1B_ENST00000502683.1_Missense_Mutation_p.N44Y|BMPR1B_ENST00000264568.4_Missense_Mutation_p.N44Y|BMPR1B_ENST00000440890.2_Missense_Mutation_p.N74Y	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	44					BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.N44Y(2)		breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		AGACTCAGTCAACAATATTTG	0.433																																																2	Substitution - Missense(2)	ovary(2)	4											111.0	107.0	109.0					4																	96025705		2203	4299	6502	96244728	SO:0001583	missense	658			D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"""CD molecules"""	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.130A>T	4.37:g.96025705A>T	ENSP00000426617:p.Asn44Tyr	Somatic		Capture	SOLID	Phase_III	96244728	B2R953|B4DSV1|P78366	Missense_Mutation	SNP	ENST00000515059.1	37	CCDS3642.1	SNP	5	Baylor	.	.	.	.	.	.	.	.	.	.	A	19.40	3.821063	0.71028	.	.	ENSG00000138696	ENST00000515059;ENST00000506363;ENST00000512312;ENST00000509540;ENST00000440890;ENST00000502683;ENST00000264568;ENST00000394931	D;D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	5.68	5.68	0.88126	TGF-beta receptor/activin receptor, type I/II (1);	0.000000	0.85682	D	0.000000	D	0.96346	0.8808	M	0.92923	3.36	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97234	0.9886	10	0.87932	D	0	.	14.9072	0.70730	1.0:0.0:0.0:0.0	.	44	O00238	BMR1B_HUMAN	Y	44;44;44;44;74;44;44;44	ENSP00000426617:N44Y;ENSP00000421144:N44Y;ENSP00000425444:N44Y;ENSP00000421671:N44Y;ENSP00000401907:N74Y;ENSP00000424693:N44Y;ENSP00000264568:N44Y;ENSP00000378389:N44Y	ENSP00000264568:N44Y	N	+	1	0	BMPR1B	96244728	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	4.504000	0.60414	2.161000	0.67846	0.482000	0.46254	AAC		0.433	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		Missense_Mutation
VRTN	55237	hgsc.bcm.edu	37	14	74824462	74824463	+	Frame_Shift_Ins	INS	-	-	G	rs533419765|rs201579420		TCGA-25-1628-01	TCGA-25-1628-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr14:74824462_74824463insG	ENST00000256362.4	+	2	1217_1218	c.976_977insG	c.(976-978)cggfs	p.R326fs		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	326					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)	p.V329fs*25(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						CAGCTTCCACCGGGGGGGCGTC	0.644																																																1	Insertion - Frameshift(1)	ovary(1)	14																																								73894216	SO:0001589	frameshift_variant	55237			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.983dupG	14.37:g.74824469_74824469dupG	ENSP00000256362:p.Arg326fs	Somatic		Capture	SOLID	Phase_III	73894215	Q9NVC7	Frame_Shift_Ins	INS	ENST00000256362.4	37	CCDS9830.1	INS	23	Baylor																																																																																				0.644	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		Frame_Shift_Ins
CAMKK1	84254	hgsc.bcm.edu	37	17	3787704	3787704	+	Silent	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr17:3787704G>A	ENST00000348335.2	-	3	526	c.378C>T	c.(376-378)aaC>aaT	p.N126N	CAMKK1_ENST00000381771.2_Silent_p.N126N|CAMKK1_ENST00000158166.5_Silent_p.N126N|CAMKK1_ENST00000381769.2_Silent_p.N153N	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	126					synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.N126N(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		GCTTGTACTGGTTCAGCTGCA	0.612																																																1	Substitution - coding silent(1)	ovary(1)	17											178.0	169.0	172.0					17																	3787704		2203	4300	6503	3734453	SO:0001819	synonymous_variant	84254			AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.378C>T	17.37:g.3787704G>A		Somatic		Capture	SOLID	Phase_III	3734453	Q9BQH3	Silent	SNP	ENST00000348335.2	37	CCDS11038.1	SNP	44	Baylor																																																																																				0.612	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207		Silent
SMG8	55181	hgsc.bcm.edu	37	17	57290517	57290517	+	Missense_Mutation	SNP	A	A	C			TCGA-25-1628-01	TCGA-25-1628-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr17:57290517A>C	ENST00000543872.2	+	4	2597	c.2333A>C	c.(2332-2334)aAc>aCc	p.N778T	CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.N778T			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	778					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)		p.N778T(1)		NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						AAGTCTTATAACTTTCATACA	0.438																																																1	Substitution - Missense(1)	ovary(1)	17											104.0	107.0	106.0					17																	57290517		2203	4300	6503	54645299	SO:0001583	missense	55181			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2333A>C	17.37:g.57290517A>C	ENSP00000438748:p.Asn778Thr	Somatic		Capture	SOLID	Phase_III	54645299	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	SNP	2	Baylor	.	.	.	.	.	.	.	.	.	.	A	8.674	0.903640	0.17760	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.42131	0.98;0.98	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.49406	0.1555	N	0.25144	0.715	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.40098	-0.9581	10	0.20519	T	0.43	-21.996	15.8218	0.78654	1.0:0.0:0.0:0.0	.	778	Q8ND04	SMG8_HUMAN	T	778	ENSP00000300917:N778T;ENSP00000438748:N778T	ENSP00000300917:N778T	N	+	2	0	SMG8	54645299	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	7.142000	0.77339	2.326000	0.78906	0.533000	0.62120	AAC		0.438	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		Missense_Mutation
DSEL	92126	hgsc.bcm.edu	37	18	65181474	65181474	+	Silent	SNP	A	A	G			TCGA-25-1628-01	TCGA-25-1628-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr18:65181474A>G	ENST00000310045.7	-	2	1875	c.402T>C	c.(400-402)aaT>aaC	p.N134N	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA|RP11-638L3.1_ENST00000583687.1_lincRNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	124					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.N134N(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				AAGGAGGCAGATTGTTACCAT	0.418																																																1	Substitution - coding silent(1)	ovary(1)	18											114.0	101.0	106.0					18																	65181474		2203	4300	6503	63332454	SO:0001819	synonymous_variant	92126			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.402T>C	18.37:g.65181474A>G		Somatic		Capture	SOLID	Phase_III	63332454	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1	SNP	12	Baylor																																																																																				0.418	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		Silent
GRIN2C	2905	hgsc.bcm.edu	37	17	72846013	72846013	+	Silent	SNP	G	G	A	rs201943001		TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr17:72846013G>A	ENST00000293190.5	-	7	1697	c.1551C>T	c.(1549-1551)tcC>tcT	p.S517S	GRIN2C_ENST00000347612.4_Silent_p.S517S|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	517					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.S517S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTACGATCTCGGAGCGTTCCT	0.607																																																1	Substitution - coding silent(1)	ovary(1)	17											108.0	98.0	102.0					17																	72846013		2203	4300	6503	70357608	SO:0001819	synonymous_variant	2905				CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1551C>T	17.37:g.72846013G>A		Somatic		Capture	SOLID	Phase_III	70357608	B2RTT1	Silent	SNP	ENST00000293190.5	37	CCDS32724.1	SNP	39	Baylor																																																																																				0.607	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			Silent
GRB2	2885	hgsc.bcm.edu	37	17	73389683	73389683	+	Missense_Mutation	SNP	G	G	T			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr17:73389683G>T	ENST00000392562.1	-	2	809	c.27C>A	c.(25-27)ttC>ttA	p.F9L	GRB2_ENST00000578961.1_Missense_Mutation_p.F9L|GRB2_ENST00000316615.5_Missense_Mutation_p.F9L|GRB2_ENST00000392564.1_Missense_Mutation_p.F9L|GRB2_ENST00000392563.1_Missense_Mutation_p.F9L|GRB2_ENST00000316804.5_Missense_Mutation_p.F9L|RP11-16C1.1_ENST00000578226.1_RNA			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	9	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				aging (GO:0007568)|anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to ionizing radiation (GO:0071479)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of MAPK cascade (GO:0043408)|signal transduction in response to DNA damage (GO:0042770)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Grb2-EGFR complex (GO:0070436)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|identical protein binding (GO:0042802)|insulin receptor substrate binding (GO:0043560)|neurotrophin TRKA receptor binding (GO:0005168)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.F9L(1)		breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	17	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)	CAGTAGCTTTGAAGTCATATT	0.557																																																1	Substitution - Missense(1)	ovary(1)	17											301.0	240.0	260.0					17																	73389683		2203	4300	6503	70901278	SO:0001583	missense	2885				CCDS11721.1, CCDS11722.1	17q24-q25	2013-02-14			ENSG00000177885	ENSG00000177885		"""SH2 domain containing"""	4566	protein-coding gene	gene with protein product		108355					Standard	NM_002086		Approved	NCKAP2	uc002jnx.4	P62993	OTTHUMG00000134332	ENST00000392562.1:c.27C>A	17.37:g.73389683G>T	ENSP00000376345:p.Phe9Leu	Somatic		Capture	SOLID	Phase_III	70901278	P29354|Q14450|Q63057|Q63059	Missense_Mutation	SNP	ENST00000392562.1	37	CCDS11721.1	SNP	45	Baylor	.	.	.	.	.	.	.	.	.	.	G	34	5.380633	0.95945	.	.	ENSG00000177885	ENST00000316804;ENST00000392562;ENST00000392564;ENST00000392563;ENST00000316615	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15	5.87	5.87	0.94306	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.81711	0.4880	M	0.91717	3.235	0.80722	D	1	B;P	0.40909	0.321;0.732	B;P	0.59056	0.164;0.851	D	0.83547	0.0099	10	0.87932	D	0	-16.5535	19.8132	0.96556	0.0:0.0:1.0:0.0	.	9;9	P62993-2;P62993	.;GRB2_HUMAN	L	9	ENSP00000339007:F9L;ENSP00000376345:F9L;ENSP00000376347:F9L;ENSP00000376346:F9L;ENSP00000317360:F9L	ENSP00000317360:F9L	F	-	3	2	GRB2	70901278	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.709000	0.68384	2.785000	0.95823	0.655000	0.94253	TTC		0.557	GRB2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259476.1			Missense_Mutation
GRM1	2911	hgsc.bcm.edu	37	6	146351124	146351124	+	Silent	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr6:146351124G>A	ENST00000282753.1	+	1	706	c.471G>A	c.(469-471)gcG>gcA	p.A157A	GRM1_ENST00000355289.4_Silent_p.A157A|GRM1_ENST00000392299.2_Silent_p.A157A|GRM1_ENST00000361719.2_Silent_p.A157A|GRM1_ENST00000507907.1_Silent_p.A157A|GRM1_ENST00000492807.2_Silent_p.A157A			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	157					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.A157A(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		AGCCCATTGCGGGAGTGATCG	0.577																																																1	Substitution - coding silent(1)	ovary(1)	6											68.0	72.0	71.0					6																	146351124		2203	4300	6503	146392817	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.471G>A	6.37:g.146351124G>A		Somatic		Capture	SOLID	Phase_III	146392817	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1	SNP	39	Baylor																																																																																				0.577	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		Silent
KLHL42	57542	hgsc.bcm.edu	37	12	27944691	27944691	+	Missense_Mutation	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr12:27944691G>A	ENST00000381271.2	+	2	1234	c.923G>A	c.(922-924)gGg>gAg	p.G308E		NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	308					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G308E(1)									GCCATCGGAGGGCAGGCCGTT	0.483																																																1	Substitution - Missense(1)	ovary(1)	12											216.0	206.0	210.0					12																	27944691		2203	4300	6503	27835958	SO:0001583	missense	57542			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"""Kelch-like"""	29252	protein-coding gene	gene with protein product			"""kelch domain containing 5"""	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.923G>A	12.37:g.27944691G>A	ENSP00000370671:p.Gly308Glu	Somatic		Capture	SOLID	Phase_III	27835958	Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	37	CCDS31763.1	SNP	43	Baylor	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888575	0.91814	.	.	ENSG00000087448	ENST00000381271	D	0.99494	-6.01	4.86	4.86	0.63082	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.99535	4.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96586	0.9434	10	0.87932	D	0	.	17.1803	0.86853	0.0:0.0:1.0:0.0	.	308	Q9P2K6	KLDC5_HUMAN	E	308	ENSP00000370671:G308E	ENSP00000370671:G308E	G	+	2	0	KLHDC5	27835958	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	9.069000	0.93967	2.505000	0.84491	0.650000	0.86243	GGG		0.483	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		Missense_Mutation
LRSAM1	90678	hgsc.bcm.edu	37	9	130230081	130230081	+	Silent	SNP	T	T	G			TCGA-25-1628-01	TCGA-25-1628-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr9:130230081T>G	ENST00000323301.4	+	9	1195	c.591T>G	c.(589-591)acT>acG	p.T197T	LRSAM1_ENST00000373324.4_Silent_p.T197T|LRSAM1_ENST00000373322.1_Silent_p.T197T|LRSAM1_ENST00000300417.6_Silent_p.T197T	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	197					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T197T(2)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						GTGCCGGCACTGCGGCCATCT	0.622																																																2	Substitution - coding silent(2)	ovary(2)	9											67.0	51.0	56.0					9																	130230081		2203	4300	6503	129269902	SO:0001819	synonymous_variant	90678			AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"""Sterile alpha motif (SAM) domain containing"""	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.591T>G	9.37:g.130230081T>G		Somatic		Capture	SOLID	Phase_III	129269902	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Silent	SNP	ENST00000323301.4	37	CCDS6873.1	SNP	55	Baylor																																																																																				0.622	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361		Silent
MMEL1	79258	hgsc.bcm.edu	37	1	2528036	2528036	+	Silent	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr1:2528036G>A	ENST00000378412.3	-	14	1526	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y	MMEL1_ENST00000288709.6_Silent_p.Y446Y|MMEL1_ENST00000502556.1_Silent_p.Y298Y			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	455						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Y446Y(1)		cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		CCTCCCTGACGTAGAGGGAGC	0.652																																																1	Substitution - coding silent(1)	ovary(1)	1											110.0	88.0	95.0					1																	2528036		2203	4300	6503	2517896	SO:0001819	synonymous_variant	79258			AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.1365C>T	1.37:g.2528036G>A		Somatic		Capture	SOLID	Phase_III	2517896	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2	SNP	40	Baylor																																																																																				0.652	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		Silent
MTHFD1	4522	hgsc.bcm.edu	37	14	64886575	64886575	+	Missense_Mutation	SNP	A	A	G			TCGA-25-1628-01	TCGA-25-1628-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr14:64886575A>G	ENST00000545908.1	+	8	1056	c.827A>G	c.(826-828)gAa>gGa	p.E276G	MTHFD1_ENST00000216605.8_Missense_Mutation_p.E220G			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	220	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.|Substrate binding.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)	p.E220G(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	GGTCAGCCTGAAATGGTTAAA	0.443																																					Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)											1	Substitution - Missense(1)	ovary(1)	14											123.0	114.0	117.0					14																	64886575		2203	4300	6503	63956328	SO:0001583	missense	4522			J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.827A>G	14.37:g.64886575A>G	ENSP00000438588:p.Glu276Gly	Somatic		Capture	SOLID	Phase_III	63956328	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		SNP	9	Baylor	.	.	.	.	.	.	.	.	.	.	A	18.14	3.558735	0.65538	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605;ENST00000555252	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.74	5.74	0.90152	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.43612	0.1255	L	0.31065	0.9	0.80722	D	1	B;B;B	0.18610	0.029;0.029;0.006	B;B;B	0.20184	0.017;0.028;0.01	T	0.31308	-0.9948	10	0.49607	T	0.09	-26.7219	14.6068	0.68486	1.0:0.0:0.0:0.0	.	276;220;220	F5H2F4;P11586;G3V2B8	.;C1TC_HUMAN;.	G	276;220;276;200	ENSP00000438588:E276G;ENSP00000450560:E220G;ENSP00000216605:E276G;ENSP00000451309:E200G	ENSP00000216605:E220G	E	+	2	0	MTHFD1	63956328	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.339000	0.96797	2.192000	0.70111	0.528000	0.53228	GAA		0.443	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			Missense_Mutation
NWD1	284434	hgsc.bcm.edu	37	19	16870240	16870240	+	Splice_Site	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr19:16870240G>A	ENST00000552788.1	+	5	1973		c.e5+1		NWD1_ENST00000339803.6_Splice_Site|NWD1_ENST00000379808.3_Splice_Site|NWD1_ENST00000524140.2_Splice_Site|NWD1_ENST00000549814.1_Splice_Site|NWD1_ENST00000523826.1_Splice_Site			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1								ATP binding (GO:0005524)	p.?(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TTGCCCACAGGTAGGTCCAGG	0.632																																																1	Unknown(1)	ovary(1)	19											17.0	15.0	16.0					19																	16870240		2168	4257	6425	16731240	SO:0001630	splice_region_variant	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1973+1G>A	19.37:g.16870240G>A		Somatic		Capture	SOLID	Phase_III	16731240	C9J021|Q68CT3	Splice_Site_SNP	SNP	ENST00000552788.1	37		SNP	44	Baylor	.	.	.	.	.	.	.	.	.	.	G	13.15	2.150887	0.37923	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5617	0.56286	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NWD1	16731240	1.000000	0.71417	0.986000	0.45419	0.235000	0.25334	7.485000	0.81204	2.044000	0.60594	0.542000	0.68232	.		0.632	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	Intron	Splice_Site_SNP
NCAN	1463	hgsc.bcm.edu	37	19	19334995	19334995	+	Missense_Mutation	SNP	G	G	A	rs112606625	byFrequency	TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr19:19334995G>A	ENST00000252575.6	+	4	740	c.641G>A	c.(640-642)cGc>cAc	p.R214H	NCAN_ENST00000538881.1_5'Flank	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	214	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.R214H(1)		breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	CTCTCTGACCGCACTGTTCGG	0.592																																																1	Substitution - Missense(1)	ovary(1)	19											68.0	58.0	61.0					19																	19334995		2203	4300	6503	19195995	SO:0001583	missense	1463			AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.641G>A	19.37:g.19334995G>A	ENSP00000252575:p.Arg214His	Somatic		Capture	SOLID	Phase_III	19195995	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556236	0.45487	.	.	ENSG00000130287	ENST00000539499;ENST00000252575	T	0.09445	2.98	4.75	2.62	0.31277	C-type lectin fold (1);Link (4);C-type lectin-like (1);	0.403904	0.18397	N	0.142478	T	0.05914	0.0154	N	0.17345	0.48	0.80722	D	1	B	0.27140	0.169	B	0.20384	0.029	T	0.32241	-0.9914	10	0.51188	T	0.08	-28.1963	5.7902	0.18357	0.3133:0.0:0.6867:0.0	.	214	O14594	NCAN_HUMAN	H	228;214	ENSP00000252575:R214H	ENSP00000252575:R214H	R	+	2	0	NCAN	19195995	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.136000	0.58004	0.997000	0.38969	0.561000	0.74099	CGC		0.592	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		Missense_Mutation
PKHD1	5314	hgsc.bcm.edu	37	6	51491869	51491869	+	Missense_Mutation	SNP	T	T	C			TCGA-25-1628-01	TCGA-25-1628-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr6:51491869T>C	ENST00000371117.3	-	66	11986	c.11711A>G	c.(11710-11712)aAt>aGt	p.N3904S		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3904					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.N3904S(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GATATGAATATTTTGATTATT	0.408																																																1	Substitution - Missense(1)	ovary(1)	6											261.0	261.0	261.0					6																	51491869		2203	4300	6503	51599828	SO:0001583	missense	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11711A>G	6.37:g.51491869T>C	ENSP00000360158:p.Asn3904Ser	Somatic		Capture	SOLID	Phase_III	51599828	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	SNP	52	Baylor	.	.	.	.	.	.	.	.	.	.	T	11.21	1.572620	0.28092	.	.	ENSG00000170927	ENST00000371117	D	0.85702	-2.02	5.19	1.34	0.21922	.	0.517350	0.17914	N	0.157738	T	0.49201	0.1543	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.10450	0.005	T	0.48864	-0.8997	10	0.66056	D	0.02	.	6.6735	0.23082	0.0:0.3181:0.0:0.6819	.	3904	P08F94	PKHD1_HUMAN	S	3904	ENSP00000360158:N3904S	ENSP00000360158:N3904S	N	-	2	0	PKHD1	51599828	0.269000	0.24143	0.006000	0.13384	0.008000	0.06430	0.343000	0.19944	0.140000	0.18849	0.533000	0.62120	AAT		0.408	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		Missense_Mutation
RAB37	326624	hgsc.bcm.edu	37	17	72736931	72736931	+	Missense_Mutation	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr17:72736931G>A	ENST00000392613.5	+	2	174	c.118G>A	c.(118-120)Gtc>Atc	p.V40I	RAB37_ENST00000392615.5_Intron|RAB37_ENST00000392612.3_Intron|RAB37_ENST00000528438.1_Missense_Mutation_p.V13I|RAB37_ENST00000340415.3_Intron|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000392610.1_Missense_Mutation_p.V40I|RAB37_ENST00000392614.4_Missense_Mutation_p.V45I	NM_001006638.2	NP_001006639.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	40					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						AGACACAGGCGTCGGCAAAAC	0.567																																																0			17											153.0	154.0	153.0					17																	72736931		2203	4300	6503	70248526	SO:0001583	missense	326624			BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"""RAB, member RAS oncogene"""	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000392613.5:c.118G>A	17.37:g.72736931G>A	ENSP00000376389:p.Val40Ile	Somatic		Capture	SOLID	Phase_III	70248526	A8MXF5|A8MYT0|Q8IWA7	Missense_Mutation	SNP	ENST00000392613.5	37	CCDS32722.1	SNP	40	Baylor	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799506	0.70567	.	.	ENSG00000172794	ENST00000528438;ENST00000392614;ENST00000392613;ENST00000533530;ENST00000392610	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.27	5.27	0.74061	Small GTP-binding protein domain (1);	0.072360	0.53938	D	0.000052	D	0.91442	0.7299	M	0.93241	3.395	0.80722	D	1	P;P	0.50369	0.739;0.934	P;P	0.52627	0.503;0.704	D	0.93664	0.6984	10	0.87932	D	0	.	17.663	0.88197	0.0:0.0:1.0:0.0	.	45;40	A8MYT0;Q96AX2	.;RAB37_HUMAN	I	13;45;40;40;40	ENSP00000432086:V13I;ENSP00000376390:V45I;ENSP00000376389:V40I;ENSP00000376387:V40I	ENSP00000376387:V40I	V	+	1	0	RAB37	70248526	1.000000	0.71417	0.992000	0.48379	0.052000	0.14988	9.248000	0.95456	2.469000	0.83416	0.561000	0.74099	GTC		0.567	RAB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258872.2	NM_175738		Missense_Mutation
ROR1	4919	hgsc.bcm.edu	37	1	64608196	64608196	+	Missense_Mutation	SNP	C	C	G			TCGA-25-1628-01	TCGA-25-1628-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr1:64608196C>G	ENST00000371079.1	+	7	1412	c.1037C>G	c.(1036-1038)aCt>aGt	p.T346S	RP11-24J23.2_ENST00000424995.1_RNA|ROR1_ENST00000545203.1_5'UTR|ROR1_ENST00000371080.1_Missense_Mutation_p.T346S	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	346	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.T346S(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						CACACACACACTTTCACCGCC	0.552																																																1	Substitution - Missense(1)	ovary(1)	1											146.0	127.0	134.0					1																	64608196		2203	4300	6503	64380784	SO:0001583	missense	4919			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1037C>G	1.37:g.64608196C>G	ENSP00000360120:p.Thr346Ser	Somatic		Capture	SOLID	Phase_III	64380784	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	SNP	20	Baylor	.	.	.	.	.	.	.	.	.	.	C	4.645	0.119818	0.08881	.	.	ENSG00000185483	ENST00000371080;ENST00000371079;ENST00000544776	T;T	0.60424	0.33;0.19	6.08	5.15	0.70609	Kringle (4);Kringle-like fold (1);	0.153395	0.29830	N	0.011088	T	0.17916	0.0430	N	0.04297	-0.235	0.80722	D	1	B;B	0.12013	0.005;0.005	B;B	0.17979	0.006;0.02	T	0.14896	-1.0456	10	0.09338	T	0.73	.	17.0751	0.86584	0.0:0.8691:0.1309:0.0	.	346;346	Q01973;Q66K77	ROR1_HUMAN;.	S	346;346;349	ENSP00000360121:T346S;ENSP00000360120:T346S	ENSP00000360120:T346S	T	+	2	0	ROR1	64380784	0.987000	0.35691	1.000000	0.80357	0.233000	0.25261	1.423000	0.34837	1.545000	0.49373	0.655000	0.94253	ACT		0.552	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		Missense_Mutation
SPOCK3	50859	hgsc.bcm.edu	37	4	167656170	167656170	+	Nonsense_Mutation	SNP	C	C	A			TCGA-25-1628-01	TCGA-25-1628-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr4:167656170C>A	ENST00000357154.3	-	12	1350	c.1213G>T	c.(1213-1215)Gaa>Taa	p.E405*	SPOCK3_ENST00000421836.2_Nonsense_Mutation_p.E354*|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Nonsense_Mutation_p.E402*|SPOCK3_ENST00000502330.1_Nonsense_Mutation_p.E405*|SPOCK3_ENST00000541637.1_Nonsense_Mutation_p.E307*|SPOCK3_ENST00000534949.1_Nonsense_Mutation_p.E309*|SPOCK3_ENST00000541354.1_Nonsense_Mutation_p.E285*|SPOCK3_ENST00000506886.1_Nonsense_Mutation_p.E405*|SPOCK3_ENST00000535728.1_Nonsense_Mutation_p.E273*|SPOCK3_ENST00000511269.1_Nonsense_Mutation_p.E402*|SPOCK3_ENST00000511531.1_Nonsense_Mutation_p.E405*|SPOCK3_ENST00000512681.1_Nonsense_Mutation_p.E307*|SPOCK3_ENST00000510741.1_Nonsense_Mutation_p.E362*|SPOCK3_ENST00000504953.1_Nonsense_Mutation_p.E402*	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	405	Asp-rich.			E -> G (in Ref. 4; BAG58265). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)	p.E402*(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		atatcgtcttcatcatcctca	0.353																																																1	Substitution - Nonsense(1)	ovary(1)	4											192.0	178.0	183.0					4																	167656170		2203	4299	6502	167892745	SO:0001587	stop_gained	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1213G>T	4.37:g.167656170C>A	ENSP00000349677:p.Glu405*	Somatic		Capture	SOLID	Phase_III	167892745	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Nonsense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	SNP	29	Baylor	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416478	0.42918	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949	.	.	.	5.14	5.14	0.70334	.	0.549955	0.18619	N	0.135918	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-29.1078	17.55	0.87873	0.0:1.0:0.0:0.0	.	.	.	.	X	405;402;402;405;405;405;362;285;307;402;273;354;307;309	.	ENSP00000349677:E405X	E	-	1	0	SPOCK3	167892745	0.996000	0.38824	0.367000	0.25926	0.006000	0.05464	3.653000	0.54446	2.561000	0.86390	0.637000	0.83480	GAA		0.353	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			Nonsense_Mutation
SYDE1	85360	hgsc.bcm.edu	37	19	15222225	15222225	+	Silent	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr19:15222225G>A	ENST00000342784.2	+	5	1423	c.1392G>A	c.(1390-1392)ctG>ctA	p.L464L	SYDE1_ENST00000600440.1_Silent_p.L397L|SYDE1_ENST00000600252.1_Silent_p.L121L	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	464	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)	p.L464L(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						CTGAGGACCTGTACCCCGATA	0.582																																																1	Substitution - coding silent(1)	ovary(1)	19											168.0	136.0	147.0					19																	15222225		2203	4300	6503	15083225	SO:0001819	synonymous_variant	85360			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.1392G>A	19.37:g.15222225G>A		Somatic		Capture	SOLID	Phase_III	15083225	Q7L2I8|Q8N6J2|Q9H8K4	Silent	SNP	ENST00000342784.2	37	CCDS12324.1	SNP	48	Baylor																																																																																				0.582	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		Silent
TP53	7157	hgsc.bcm.edu	37	17	7579536	7579536	+	Nonsense_Mutation	SNP	C	C	A			TCGA-25-1628-01	TCGA-25-1628-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr17:7579536C>A	ENST00000269305.4	-	4	340	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	TP53_ENST00000359597.4_Nonsense_Mutation_p.E51*|TP53_ENST00000445888.2_Nonsense_Mutation_p.E51*|TP53_ENST00000455263.2_Nonsense_Mutation_p.E51*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Nonsense_Mutation_p.E51*|TP53_ENST00000413465.2_Nonsense_Mutation_p.E51*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	51	Interaction with HRMT1L2.				apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.E51*(6)|p.E51fs*6(3)|p.E51fs*59(1)|p.I50fs*4(1)|p.D48fs*55(1)|p.E51fs*72(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AACCATTGTTCAATATCGTCC	0.592		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	23	Whole gene deletion(8)|Substitution - Nonsense(6)|Deletion - Frameshift(6)|Insertion - Frameshift(3)	ovary(5)|bone(4)|skin(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|kidney(1)|breast(1)|prostate(1)|pancreas(1)	17											169.0	168.0	168.0					17																	7579536		2203	4300	6503	7520261	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.151G>T	17.37:g.7579536C>A	ENSP00000269305:p.Glu51*	Somatic		Capture	SOLID	Phase_III	7520261	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	SNP	29	Baylor	.	.	.	.	.	.	.	.	.	.	C	15.05	2.718125	0.48622	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	3.77	0.663	0.17885	.	1.997220	0.02241	N	0.065738	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	0.6634	5.7343	0.18057	0.0:0.6465:0.0:0.3535	.	.	.	.	X	51	.	ENSP00000269305:E51X	E	-	1	0	TP53	7520261	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.943000	0.03917	0.194000	0.20326	0.561000	0.74099	GAA		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		Nonsense_Mutation
TUBA4A	7277	hgsc.bcm.edu	37	2	220115939	220115939	+	Missense_Mutation	SNP	T	T	C			TCGA-25-1628-01	TCGA-25-1628-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr2:220115939T>C	ENST00000248437.4	-	4	655	c.482A>G	c.(481-483)tAt>tGt	p.Y161C	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000392088.2_Missense_Mutation_p.Y146C|TUBA4A_ENST00000498660.1_5'UTR	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	161					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.Y146C(1)|p.Y161C(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	TTTCTTGCCATAGTCAACAGA	0.577																																																2	Substitution - Missense(2)	ovary(2)	2											55.0	62.0	60.0					2																	220115939		2203	4300	6503	219824183	SO:0001583	missense	7277			AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"""Tubulins"""	12407	protein-coding gene	gene with protein product		191110	"""tubulin, alpha 1 (testis specific)"", ""tubulin, alpha 1"""	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.482A>G	2.37:g.220115939T>C	ENSP00000248437:p.Tyr161Cys	Somatic		Capture	SOLID	Phase_III	219824183	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	37	CCDS2438.1	SNP	49	Baylor	.	.	.	.	.	.	.	.	.	.	T	12.45	1.941602	0.34283	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000398989;ENST00000427737;ENST00000456818;ENST00000447205	T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.28	5.28	0.74379	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000001	D	0.92606	0.7651	H	0.99090	4.425	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94449	0.7665	10	0.87932	D	0	.	11.1756	0.48596	0.1375:0.0:0.0:0.8625	.	161	P68366	TBA4A_HUMAN	C	161;146;8;146;184;146	ENSP00000248437:Y161C;ENSP00000375938:Y146C;ENSP00000396212:Y8C;ENSP00000408194:Y146C;ENSP00000416992:Y184C;ENSP00000396061:Y146C	ENSP00000248437:Y161C	Y	-	2	0	TUBA4A	219824183	0.995000	0.38212	1.000000	0.80357	0.996000	0.88848	2.468000	0.45102	2.224000	0.72417	0.533000	0.62120	TAT		0.577	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		Missense_Mutation
WDR7	23335	hgsc.bcm.edu	37	18	54603085	54603085	+	Silent	SNP	G	G	A			TCGA-25-1628-01	TCGA-25-1628-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1628-01	TCGA-25-1628-10	g.chr18:54603085G>A	ENST00000254442.3	+	23	3991	c.3780G>A	c.(3778-3780)tcG>tcA	p.S1260S	WDR7_ENST00000357574.3_Silent_p.S1227S|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1260					hematopoietic progenitor cell differentiation (GO:0002244)			p.S1260S(2)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		ATGCCCTCTCGCTCATTGCCA	0.527																																																2	Substitution - coding silent(2)	ovary(1)|breast(1)	18											84.0	85.0	85.0					18																	54603085		2203	4300	6503	52754083	SO:0001819	synonymous_variant	23335			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.3780G>A	18.37:g.54603085G>A		Somatic		Capture	SOLID	Phase_III	52754083	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Silent	SNP	ENST00000254442.3	37	CCDS11962.1	SNP	38	Baylor																																																																																				0.527	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			Silent
