#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	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_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
PTPRD	5789	broad.mit.edu	37	9	8454579	8454579	+	Intron	SNP	C	C	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr9:8454579C>A	ENST00000381196.4	-	31	4419				PTPRD_ENST00000486161.1_Splice_Site|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000540109.1_Intron|PTPRD_ENST00000356435.5_Intron|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Splice_Site|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000355233.5_Splice_Site|PTPRD_ENST00000360074.4_Intron|PTPRD_ENST00000358503.5_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CTATTCCTCACCTGTCGGGTT	0.408										TSP Lung(15;0.13)																												uc003zkp.3																			0				NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168						c.e18+1		Homo sapiens protein tyrosine phosphatase, receptor type, D (PTPRD), transcript variant 3, mRNA.							89.0	82.0	84.0					9																	8454579		1822	4081	5903	SO:0001627	intron_variant	5789				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr9:8454579C>A	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3876-4742G>T	9.37:g.8454579C>A		TSP Lung(15;0.13)	Somatic				PTPRD_uc003zkq.3_Splice_Site_p.R885_splice|PTPRD_uc003zkr.3_Intron|PTPRD_uc003zks.3_Intron|PTPRD_uc022bdj.1_Splice_Site_p.R882_splice|PTPRD_uc003zkk.3_Intron	p.R886_splice	NM_130392	NP_569076	WXS	Illumina GAIIx	Phase_I	P23468	PTPRD_HUMAN		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)	18	2760	-		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)	1292			Fibronectin type-III 6.		B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Splice_Site	SNP	ENST00000381196.4	37	c.2657_splice	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.514225	0.85389	.	.	ENSG00000153707	ENST00000355233;ENST00000397611;ENST00000486161	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0886	0.93217	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTPRD	8444579	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.435000	0.80391	2.517000	0.84864	0.591000	0.81541	.		0.408	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			5	18	0	0	0	1	0	5	18				
WT1-AS	51352	broad.mit.edu	37	11	32460511	32460511	+	RNA	SNP	T	T	C			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr11:32460511T>C	ENST00000395900.1	+	0	1389				WT1-AS_ENST00000426618.2_RNA|WT1-AS_ENST00000478367.1_RNA|WT1-AS_ENST00000525436.1_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000442957.1_RNA|WT1-AS_ENST00000459866.1_RNA	NR_023920.1		Q06250	WIT1_HUMAN	WT1 antisense RNA											endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6						CGAAGGTGCATAATTATTGCA	0.532																																						uc010rec.2																			0				endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6								Homo sapiens WT1 antisense RNA (non-protein coding) (WT1-AS), non-coding RNA.							55.0	55.0	55.0					11																	32460511		2202	4299	6501			51352							g.chr11:32460511T>C	BC002734		11p13	2012-10-19	2012-08-15	2012-01-25	ENSG00000183242	ENSG00000183242		"""Long non-coding RNAs"", ""-"""	18135	non-coding RNA	RNA, long non-coding	"""Wilms tumor associated protein"""	607899	"""Wilms tumor upstream neighbor 1"", ""WT1 antisense RNA (non-protein coding)"""	WIT1		2173145, 8406502, 17210670	Standard	NR_120546		Approved	WIT-1, WT1AS, WT1-AS1	uc010red.2	Q06250	OTTHUMG00000039557		11.37:g.32460511T>C			Somatic				WT1-AS_uc010red.2_Non-coding_Transcript|WT1-AS_uc021qfr.1_Non-coding_Transcript				WXS	Illumina GAIIx	Phase_I					1		+								Q4KMY0|Q96A27	RNA	SNP	ENST00000395900.1	37	c.1229T>C																																																																																					0.532	WT1-AS-001	KNOWN	basic	antisense	antisense	OTTHUMT00000095437.1	NR_023920		3	27	0	0	0	1	0	3	27				
CT45A5	441521	broad.mit.edu	37	X	134947924	134947924	+	Missense_Mutation	SNP	A	A	T			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chrX:134947924A>T	ENST00000463085.2	-	3	490	c.401T>A	c.(400-402)aTc>aAc	p.I134N	CT45A5_ENST00000370724.3_Missense_Mutation_p.I134N|CT45A4_ENST00000420087.2_Intron|CT45A5_ENST00000491480.1_Missense_Mutation_p.I134N			Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5	134										endometrium(1)|large_intestine(2)|lung(6)	9						AAGGCATCGGATTTCCTTCAC	0.378																																						uc004eze.3																			0		p.I134L(1)|p.E133*(1)		endometrium(1)|large_intestine(2)|lung(6)	9						c.(400-402)aTc>aAc		Homo sapiens cancer/testis antigen family 45, member A5 (CT45A5), transcript variant 1, mRNA.							204.0	170.0	182.0					X																	134947924		2187	4265	6452	SO:0001583	missense	441521							g.chrX:134947924A>T	AY743713	CCDS35406.1	Xq26.3	2009-03-12				ENSG00000269586			33270	protein-coding gene	gene with protein product	"""cancer/testis antigen CT45-5"""	300796				15905330	Standard	XM_006724759		Approved	CT45-5, CT45.5	uc022ces.1	Q6NSH3		ENST00000463085.2:c.401T>A	X.37:g.134947924A>T	ENSP00000424778:p.Ile134Asn		Somatic				CT45A5_uc022ces.1_Missense_Mutation_p.I134N|CT45A5_uc011mvu.2_Missense_Mutation_p.I134N	p.I134N	NM_001007551	NP_001165759	WXS	Illumina GAIIx	Phase_I	Q6NSH3	CT455_HUMAN			2	646	-			134					A8K842|B7ZMC5	Missense_Mutation	SNP	ENST00000463085.2	37	c.401T>A	CCDS35406.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.865520	0.32977	.	.	ENSG00000242284	ENST00000370724;ENST00000491480	T;T	0.54675	0.56;0.56	2.4	2.4	0.29515	.	0.235442	0.35555	U	0.003128	T	0.52386	0.1731	M	0.73962	2.25	0.09310	N	1	P	0.39022	0.655	B	0.42851	0.4	T	0.51505	-0.8697	10	0.87932	D	0	0.1753	6.0505	0.19783	1.0:0.0:0.0:0.0	.	134	Q6NSH3	CT455_HUMAN	N	134	ENSP00000359759:I134N;ENSP00000425997:I134N	ENSP00000359759:I134N	I	-	2	0	CT45A5	134775590	0.345000	0.24835	0.003000	0.11579	0.003000	0.03518	4.091000	0.57700	0.974000	0.38366	0.299000	0.19835	ATC		0.378	CT45A5-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472589.1	NM_001007551		35	55	0	0	0	1	0	35	55				
C19orf35	374872	broad.mit.edu	37	19	2278644	2278644	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr19:2278644T>C	ENST00000342063.3	-	3	644	c.551A>G	c.(550-552)gAc>gGc	p.D184G		NM_198532.2	NP_940934.1	Q6ZS72	CS035_HUMAN	chromosome 19 open reading frame 35	184										large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8				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)		ATACAGGGCGTCCCCGCTCTC	0.726																																						uc002lvn.2																			0				large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8						c.(550-552)gAc>gGc		Homo sapiens chromosome 19 open reading frame 35 (C19orf35), mRNA.							22.0	22.0	22.0					19																	2278644		2192	4289	6481	SO:0001583	missense	374872							g.chr19:2278644T>C	AK127680	CCDS12087.1	19p13.3	2012-10-26			ENSG00000188305	ENSG00000188305			24793	protein-coding gene	gene with protein product							Standard	NM_198532		Approved	FLJ45778	uc002lvn.2	Q6ZS72	OTTHUMG00000178460	ENST00000342063.3:c.551A>G	19.37:g.2278644T>C	ENSP00000345102:p.Asp184Gly		Somatic				SPPL2B_uc010dsw.1_Intron	p.D184G	NM_198532	NP_940934	WXS	Illumina GAIIx	Phase_I	Q6ZS72	CS035_HUMAN		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)	2	651	-			184						Missense_Mutation	SNP	ENST00000342063.3	37	c.551A>G	CCDS12087.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827991	0.32329	.	.	ENSG00000188305	ENST00000342063	T	0.29655	1.56	4.37	4.37	0.52481	.	.	.	.	.	T	0.46964	0.1420	M	0.72894	2.215	0.30669	N	0.753621	D	0.57257	0.979	P	0.55824	0.785	T	0.54159	-0.8335	9	0.72032	D	0.01	.	10.9441	0.47292	0.0:0.0:0.0:1.0	.	184	Q6ZS72	CS035_HUMAN	G	184	ENSP00000345102:D184G	ENSP00000345102:D184G	D	-	2	0	C19orf35	2229644	0.306000	0.24490	0.356000	0.25785	0.080000	0.17528	2.592000	0.46171	1.597000	0.50072	0.368000	0.22195	GAC		0.726	C19orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442080.1	NM_198532		6	9	0	0	0	1	0	6	9				
OR2T4	127074	broad.mit.edu	37	1	248525828	248525828	+	Missense_Mutation	SNP	G	G	T			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr1:248525828G>T	ENST00000366475.1	+	1	946	c.946G>T	c.(946-948)Gtg>Ttg	p.V316L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCTCACTCCAGTGGTGAACCC	0.463																																						uc001ieh.1																			0				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56						c.(946-948)Gtg>Ttg		Homo sapiens olfactory receptor, family 2, subfamily T, member 4 (OR2T4), mRNA.							149.0	146.0	147.0					1																	248525828		2203	4300	6503	SO:0001583	missense	127074				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248525828G>T	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.946G>T	1.37:g.248525828G>T	ENSP00000355431:p.Val316Leu		Somatic					p.V316L	NM_001004696	NP_001004696	WXS	Illumina GAIIx	Phase_I	Q8NH00	OR2T4_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		0	946	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		316					Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	c.946G>T	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	G	0.148	-1.094662	0.01858	.	.	ENSG00000196944	ENST00000366475	T	0.36699	1.24	3.0	2.04	0.26737	GPCR, rhodopsin-like superfamily (1);	0.173086	0.27442	N	0.019346	T	0.12178	0.0296	N	0.03324	-0.35	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.11941	-1.0567	10	0.23302	T	0.38	.	2.6383	0.04964	0.2801:0.0:0.4854:0.2345	.	316	Q8NH00	OR2T4_HUMAN	L	316	ENSP00000355431:V316L	ENSP00000355431:V316L	V	+	1	0	OR2T4	246592451	0.000000	0.05858	0.988000	0.46212	0.052000	0.14988	-1.318000	0.02705	1.498000	0.48600	0.585000	0.79938	GTG		0.463	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		73	100	0	0	0	1	0	73	100				
ZNF384	171017	broad.mit.edu	37	12	6781601	6781601	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr12:6781601G>A	ENST00000396801.3	-	8	1216	c.1009C>T	c.(1009-1011)Cgt>Tgt	p.R337C	ZNF384_ENST00000396795.1_Intron|ZNF384_ENST00000396799.2_Intron|ZNF384_ENST00000361959.3_Missense_Mutation_p.R337C|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000319770.3_Intron|ZNF384_ENST00000355772.4_Intron	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	337					nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						GAGTGGATACGGAGGTGCTGG	0.617			T	"""EWSR1, TAF15 """	ALL																																	uc010sfh.2				Dom	yes		12	12p13	171017	T	zinc finger protein 384 (CIZ/NMP4)			L	"""EWSR1, TAF15 """		ALL	EWSR1/ZNF384(4)	0				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						c.(1009-1011)Cgt>Tgt		Homo sapiens zinc finger protein 384 (ZNF384), transcript variant 7, mRNA.							82.0	81.0	81.0					12																	6781601		1568	3582	5150	SO:0001583	missense	171017				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr12:6781601G>A	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"""Zinc fingers, C2H2-type"""	11955	protein-coding gene	gene with protein product		609951	"""trinucleotide repeat containing 1"""	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1009C>T	12.37:g.6781601G>A	ENSP00000380019:p.Arg337Cys		Somatic				ZNF384_uc001qqa.3_Intron|ZNF384_uc001qqd.3_Intron	p.R337C	NM_001135734	NP_001129206	WXS	Illumina GAIIx	Phase_I	Q8TF68	ZN384_HUMAN			7	1279	-			337					O15407|Q7Z722|Q8N938	Missense_Mutation	SNP	ENST00000396801.3	37	c.1009C>T	CCDS44817.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155156	0.78114	.	.	ENSG00000126746	ENST00000396801;ENST00000361959	T;T	0.02472	4.28;4.28	5.69	5.69	0.88448	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.20455	0.0492	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.69479	0.964	T	0.00619	-1.1641	10	0.87932	D	0	-8.9831	19.4149	0.94690	0.0:0.0:1.0:0.0	.	337	Q8TF68	ZN384_HUMAN	C	337	ENSP00000380019:R337C;ENSP00000354592:R337C	ENSP00000354592:R337C	R	-	1	0	ZNF384	6651862	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.773000	0.98989	2.676000	0.91093	0.655000	0.94253	CGT		0.617	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1			27	36	0	0	0	1	0	27	36				
XRN1	54464	broad.mit.edu	37	3	142031581	142031581	+	Silent	SNP	C	C	T	rs534878384		TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr3:142031581C>T	ENST00000264951.4	-	41	4794	c.4677G>A	c.(4675-4677)tcG>tcA	p.S1559S	XRN1_ENST00000392981.2_Silent_p.S1547S	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1559					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AGAGATGAGACGACGAAGGCA	0.443													C|||	1	0.000199681	0.0	0.0014	5008	,	,		15030	0.0		0.0	False		,,,				2504	0.0					uc003eus.3																			0		p.S1558L(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						c.(4675-4677)tcG>tcA		Homo sapiens 5'-3' exoribonuclease 1 (XRN1), transcript variant 1, mRNA.							118.0	122.0	121.0					3																	142031581		2203	4300	6503	SO:0001819	synonymous_variant	54464				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	Golgi apparatus|cytosol|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|RNA binding|protein binding	g.chr3:142031581C>T	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.4677G>A	3.37:g.142031581C>T			Somatic				XRN1_uc010huu.3_Silent_p.S1013S|XRN1_uc003eut.3_Silent_p.S1546S|XRN1_uc003euu.3_Silent_p.S1547S	p.S1559S	NM_019001	NP_061874	WXS	Illumina GAIIx	Phase_I	Q8IZH2	XRN1_HUMAN			40	4744	-			1559					Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	c.4677G>A	CCDS3123.1																																																																																				0.443	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		5	120	0	0	0	1	0	5	120				
PPP4R1	9989	broad.mit.edu	37	18	9588150	9588150	+	Silent	SNP	G	G	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr18:9588150G>A	ENST00000400556.3	-	6	595	c.522C>T	c.(520-522)tgC>tgT	p.C174C	PPP4R1_ENST00000580583.1_5'UTR|RP11-881L2.1_ENST00000584109.1_RNA|PPP4R1_ENST00000400555.3_Silent_p.C157C	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	174					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						TGAGGACAGGGCACACTTTGG	0.448																																					Melanoma(188;1232 2082 5061 11948 35994)	uc002koe.1																			0				large_intestine(1)|skin(2)	3						c.(520-522)tgC>tgT		Homo sapiens protein phosphatase 4, regulatory subunit 1 (PPP4R1), transcript variant 1, mRNA.							70.0	66.0	67.0					18																	9588150		1968	4170	6138	SO:0001819	synonymous_variant	9989				protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity	g.chr18:9588150G>A	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.522C>T	18.37:g.9588150G>A			Somatic				PPP4R1_uc010wzo.1_Silent_p.C131C|PPP4R1_uc002kod.1_Silent_p.C157C|PPP4R1_uc010wzp.1_Non-coding_Transcript	p.C174C	NM_001042388	NP_001035847	WXS	Illumina GAIIx	Phase_I	Q8TF05	PP4R1_HUMAN			5	640	-			174					Q99774|Q9UNQ7	Silent	SNP	ENST00000400556.3	37	c.522C>T	CCDS42412.1																																																																																				0.448	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		3	32	0	0	0	1	0	3	32				
OR4A5	81318	broad.mit.edu	37	11	51411842	51411842	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr11:51411842G>A	ENST00000319760.6	-	1	606	c.554C>T	c.(553-555)gCa>gTa	p.A185V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				GTCAGTGCATGCCAGTTCCAG	0.423																																						uc001nhi.2																			0		p.L184R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49						c.(553-555)gCa>gTa		Homo sapiens olfactory receptor, family 4, subfamily A, member 5 (OR4A5), mRNA.							64.0	56.0	59.0					11																	51411842		2201	4295	6496	SO:0001583	missense	81318				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:51411842G>A	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.554C>T	11.37:g.51411842G>A	ENSP00000367664:p.Ala185Val		Somatic					p.A185V	NM_001005272	NP_001005272	WXS	Illumina GAIIx	Phase_I	Q8NH83	OR4A5_HUMAN			0	607	-		all_lung(304;0.236)	185					Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	c.554C>T	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	1.278	-0.611133	0.03690	.	.	ENSG00000221840	ENST00000319760	T	0.00183	8.6	1.93	-0.111	0.13576	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000249	T	0.00210	0.0006	L	0.61036	1.89	0.09310	N	1	B	0.18013	0.025	B	0.30782	0.12	T	0.36237	-0.9756	10	0.40728	T	0.16	.	5.9532	0.19259	0.3154:0.0:0.6846:0.0	.	185	Q8NH83	OR4A5_HUMAN	V	185	ENSP00000367664:A185V	ENSP00000367664:A185V	A	-	2	0	OR4A5	51268418	0.003000	0.15002	0.325000	0.25375	0.035000	0.12851	1.327000	0.33746	-0.017000	0.14103	0.162000	0.16502	GCA		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		14	12	0	0	0	1	0	14	12				
RSRC2	65117	broad.mit.edu	37	12	123001975	123001975	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr12:123001975C>T	ENST00000331738.7	-	5	546	c.401G>A	c.(400-402)cGc>cAc	p.R134H	RSRC2_ENST00000354654.2_Missense_Mutation_p.R86H	NM_023012.5	NP_075388.2	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2	134	Ser-rich.						poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|urinary_tract(2)	24	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		ACTACGATGGCGTCTGAAATT	0.398																																						uc001ucr.3																			0				breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|urinary_tract(2)	24						c.(400-402)cGc>cAc		Homo sapiens arginine/serine-rich coiled-coil 2 (RSRC2), transcript variant 1, mRNA.							74.0	69.0	71.0					12																	123001975		2203	4300	6503	SO:0001583	missense	65117							g.chr12:123001975C>T	AF161432	CCDS31920.1	12q24.31	2007-02-13			ENSG00000111011	ENSG00000111011			30559	protein-coding gene	gene with protein product						17203224	Standard	NM_023012		Approved	FLJ11021	uc001ucr.3	Q7L4I2	OTTHUMG00000167572	ENST00000331738.7:c.401G>A	12.37:g.123001975C>T	ENSP00000330188:p.Arg134His		Somatic				RSRC2_uc001uco.3_5'UTR|RSRC2_uc001ucp.3_Missense_Mutation_p.R75H|RSRC2_uc001ucs.3_5'UTR|RSRC2_uc001uct.3_Missense_Mutation_p.R86H|RSRC2_uc021rfm.1_Missense_Mutation_p.R134H	p.R134H	NM_023012	NP_075388	WXS	Illumina GAIIx	Phase_I	Q7L4I2	RSRC2_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)	4	561	-	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		134			Ser-rich.		Q6N040|Q6NW16|Q9H864	Missense_Mutation	SNP	ENST00000331738.7	37	c.401G>A	CCDS31920.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.961886|3.961886	0.74016|0.74016	.|.	.|.	ENSG00000111011|ENSG00000111011	ENST00000526560|ENST00000331738;ENST00000354654;ENST00000418773;ENST00000344591	T|T;T;T	0.55588|0.27256	0.51|1.68;1.68;1.68	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|0.366154	.|0.31989	.|N	.|0.006759	T|T	0.36138|0.36138	0.0956|0.0956	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D	.|0.69078	.|0.997;0.997;0.997;0.997	.|D;D;D;D	.|0.74674	.|0.984;0.923;0.984;0.923	T|T	0.41502|0.41502	-0.9505|-0.9505	7|10	0.87932|0.72032	D|D	0|0.01	.|.	18.8274|18.8274	0.92124|0.92124	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|134;86;134;75	.|F5GXM2;Q7L4I2-2;Q7L4I2;E1B6W4	.|.;.;RSRC2_HUMAN;.	T|H	28|134;86;134;75	ENSP00000446470:A28T|ENSP00000330188:R134H;ENSP00000346678:R86H;ENSP00000343315:R75H	ENSP00000446470:A28T|ENSP00000330188:R134H	A|R	-|-	1|2	0|0	RSRC2|RSRC2	121567928|121567928	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.927000|0.927000	0.56198|0.56198	6.411000|6.411000	0.73298|0.73298	2.528000|2.528000	0.85240|0.85240	0.558000|0.558000	0.71614|0.71614	GCC|CGC		0.398	RSRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395096.3	NM_023012		3	28	0	0	0	1	0	3	28				
TTK	7272	broad.mit.edu	37	6	80715612	80715612	+	Missense_Mutation	SNP	A	A	G			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr6:80715612A>G	ENST00000369798.2	+	2	163	c.52A>G	c.(52-54)Aac>Gac	p.N18D	TTK_ENST00000230510.3_Missense_Mutation_p.N18D|TTK_ENST00000509894.1_Missense_Mutation_p.N18D	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	18					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		TTCCATAATGAACAAAGTGAG	0.313																																						uc003pjc.3																			0				endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53						c.(52-54)Aac>Gac		Homo sapiens TTK protein kinase (TTK), transcript variant 1, mRNA.							81.0	86.0	85.0					6																	80715612		2203	4300	6503	SO:0001583	missense	7272				mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr6:80715612A>G		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.52A>G	6.37:g.80715612A>G	ENSP00000358813:p.Asn18Asp		Somatic				TTK_uc003pjb.4_Missense_Mutation_p.N18D	p.N18D	NM_003318	NP_003309	WXS	Illumina GAIIx	Phase_I	P33981	TTK_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0321)	1	163	+		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)	18					A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	c.52A>G	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.801807	0.31869	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798;ENST00000502580;ENST00000511260;ENST00000504040	D;D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	4.84	4.84	0.62591	.	0.272821	0.42053	D	0.000780	T	0.68577	0.3016	L	0.34521	1.04	0.23325	N	0.997908	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.55617	-0.8113	10	0.24483	T	0.36	.	8.357	0.32335	0.9121:0.0:0.0879:0.0	.	18;18	P33981;A8K8U5	TTK_HUMAN;.	D	18	ENSP00000422936:N18D;ENSP00000230510:N18D;ENSP00000358813:N18D;ENSP00000424851:N18D;ENSP00000421636:N18D;ENSP00000427483:N18D	ENSP00000230510:N18D	N	+	1	0	TTK	80772331	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.701000	0.54793	1.817000	0.53016	0.379000	0.24179	AAC		0.313	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			7	56	0	0	0	1	0	7	56				
SMG6	23293	broad.mit.edu	37	17	2203563	2203563	+	Silent	SNP	G	G	T	rs200691961		TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr17:2203563G>T	ENST00000263073.6	-	2	534	c.484C>A	c.(484-486)Cgg>Agg	p.R162R	SMG6_ENST00000544865.1_Silent_p.R131R	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	162	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCCTCCACCCGACTGGCGGAT	0.468																																					Melanoma(59;28 1088 11621 25887 46638 50814)	uc002fub.1																			0		p.R162L(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						c.(484-486)Cgg>Agg		Homo sapiens smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans) (SMG6), transcript variant 1, mRNA.							156.0	170.0	165.0					17																	2203563		2203	4300	6503	SO:0001819	synonymous_variant	23293				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding	g.chr17:2203563G>T	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.484C>A	17.37:g.2203563G>T			Somatic				SMG6_uc002fud.2_Silent_p.R131R	p.R162R	NM_017575	NP_060045	WXS	Illumina GAIIx	Phase_I	Q86US8	EST1A_HUMAN			1	539	-			162			Interaction with telomeric DNA.		B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	c.484C>A	CCDS11016.1																																																																																				0.468	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			9	211	0	0	0	1	0	9	211				
RNF7	9616	broad.mit.edu	37	3	141462360	141462360	+	Missense_Mutation	SNP	T	T	G			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr3:141462360T>G	ENST00000273480.3	+	2	323	c.185T>G	c.(184-186)cTt>cGt	p.L62R	RNF7_ENST00000480908.1_Intron|RNF7_ENST00000393000.3_Missense_Mutation_p.L60V	NM_014245.4|NM_183237.2	NP_055060.1|NP_899060.1	Q9UBF6	RBX2_HUMAN	ring finger protein 7	62					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of apoptotic process (GO:0043066)|protein neddylation (GO:0045116)|protein ubiquitination (GO:0016567)|response to redox state (GO:0051775)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|NEDD8 ligase activity (GO:0019788)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|upper_aerodigestive_tract(1)	5						GATGCCTGTCTTAGATGTCAA	0.358																																						uc003eud.3																			0		p.L62V(1)		kidney(1)|lung(3)|upper_aerodigestive_tract(1)	5						c.(184-186)cTt>cGt		Homo sapiens ring finger protein 7 (RNF7), transcript variant 1, mRNA.							254.0	243.0	247.0					3																	141462360		2203	4300	6503	SO:0001583	missense	9616				anti-apoptosis|induction of apoptosis by oxidative stress|protein neddylation|response to redox state	cytoplasm|nucleus	NEDD8 ligase activity|copper ion binding|protein binding|zinc ion binding	g.chr3:141462360T>G	AF092878	CCDS3118.1, CCDS43158.1, CCDS56283.1	3q22-q24	2008-07-18			ENSG00000114125	ENSG00000114125		"""RING-type (C3HC4) zinc fingers"""	10070	protein-coding gene	gene with protein product	"""sensitive to apoptosis, zinc RING finger protein SAG, regulator of cullins 2"""	603863				10082581, 10230407	Standard	NM_014245		Approved	SAG, ROC2, CKBBP1	uc003eud.3	Q9UBF6	OTTHUMG00000141305	ENST00000273480.3:c.185T>G	3.37:g.141462360T>G	ENSP00000273480:p.Leu62Arg		Somatic				RNF7_uc021xet.1_Non-coding_Transcript|RNF7_uc003eue.3_Non-coding_Transcript|RNF7_uc003euc.3_Missense_Mutation_p.L60V|RNF7_uc021xeu.1_Intron	p.L62R	NM_014245	NP_055060	WXS	Illumina GAIIx	Phase_I	Q9UBF6	RBX2_HUMAN			1	318	+			62					A8K1H9|A8MTB5|C9JYL3|D3DNF7|D3DNF8|Q9BXN8|Q9Y5M7	Missense_Mutation	SNP	ENST00000273480.3	37	c.185T>G	CCDS3118.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.09|17.09	3.299787|3.299787	0.60195|0.60195	.|.	.|.	ENSG00000114125|ENSG00000114125	ENST00000273480|ENST00000393000	T|.	0.46063|.	0.88|.	5.92|5.92	5.92|5.92	0.95590|0.95590	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.42200|0.42200	0.1192|0.1192	.|.	.|.	.|.	0.22947|0.22947	N|N	0.998528|0.998528	D|B	0.89917|0.22683	1.0|0.073	D|B	0.78314|0.24394	0.991|0.053	T|T	0.35847|0.35847	-0.9772|-0.9772	9|8	0.87932|0.45353	D|T	0|0.12	.|.	16.3782|16.3782	0.83418|0.83418	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	62|60	Q9UBF6|Q9UBF6-3	RBX2_HUMAN|.	R|V	62|60	ENSP00000273480:L62R|.	ENSP00000273480:L62R|ENSP00000376725:L60V	L|L	+|+	2|1	0|2	RNF7|RNF7	142945050|142945050	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.804000|6.804000	0.75186|0.75186	2.277000|2.277000	0.76020|0.76020	0.528000|0.528000	0.53228|0.53228	CTT|TTA		0.358	RNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280602.1	NM_014245		23	54	0	0	0	1	0	23	54				
CCNT1	904	broad.mit.edu	37	12	49087741	49087741	+	Missense_Mutation	SNP	G	G	T			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr12:49087741G>T	ENST00000261900.3	-	9	1478	c.1256C>A	c.(1255-1257)gCa>gAa	p.A419E		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	419					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						GGCAGCATATGCATATTGTGA	0.463																																						uc001rsd.4																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						c.(1255-1257)gCa>gAa		Homo sapiens cyclin T1 (CCNT1), mRNA.							150.0	156.0	154.0					12																	49087741		2203	4300	6503	SO:0001583	missense	904				cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding	g.chr12:49087741G>T	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1256C>A	12.37:g.49087741G>T	ENSP00000261900:p.Ala419Glu		Somatic				CCNT1_uc009zkz.2_Missense_Mutation_p.A134E|CCNT1_uc021qxk.1_5'Flank	p.A419E	NM_001240	NP_001231	WXS	Illumina GAIIx	Phase_I	O60563	CCNT1_HUMAN			8	1579	-			419					A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	37	c.1256C>A	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.105726	0.77096	.	.	ENSG00000129315	ENST00000261900	T	0.19669	2.13	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.38506	0.1043	L	0.46157	1.445	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	T	0.01894	-1.1252	10	0.22706	T	0.39	-10.7242	18.0305	0.89282	0.0:0.0:1.0:0.0	.	419	O60563	CCNT1_HUMAN	E	419	ENSP00000261900:A419E	ENSP00000261900:A419E	A	-	2	0	CCNT1	47374008	1.000000	0.71417	0.995000	0.50966	0.961000	0.63080	9.594000	0.98254	2.634000	0.89283	0.561000	0.74099	GCA		0.463	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		81	102	0	0	0	1	0	81	102				
KRT35	3886	broad.mit.edu	37	17	39635994	39635994	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr17:39635994C>T	ENST00000393989.1	-	2	553	c.511G>A	c.(511-513)Gag>Aag	p.E171K	KRT35_ENST00000246639.2_Missense_Mutation_p.E141K	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	171	Coil 1B.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				TTGTCAATCTCCACCACCAGC	0.488																																						uc002hws.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						c.(511-513)Gag>Aag		Homo sapiens keratin 35 (KRT35), mRNA.							186.0	187.0	187.0					17																	39635994		2203	4300	6503	SO:0001583	missense	3886				anatomical structure morphogenesis	intermediate filament	protein binding|structural molecule activity	g.chr17:39635994C>T	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6453	protein-coding gene	gene with protein product	"""hard keratin type I 5"""	602764	"""keratin, hair, acidic, 5"""	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.511G>A	17.37:g.39635994C>T	ENSP00000377558:p.Glu171Lys		Somatic					p.E171K	NM_002280	NP_002271	WXS	Illumina GAIIx	Phase_I	Q92764	KRT35_HUMAN			1	554	-		Breast(137;0.000286)	171			Coil 1B.|Rod.		O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	c.511G>A	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836446	0.50951	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.90324	-2.65;-2.65	5.1	4.13	0.48395	Filament (1);	0.124173	0.36893	N	0.002359	D	0.88097	0.6345	M	0.64170	1.965	0.24401	N	0.994703	B	0.11235	0.004	B	0.12837	0.008	T	0.81765	-0.0783	10	0.87932	D	0	.	10.2721	0.43489	0.0:0.2832:0.5815:0.1353	.	171	Q92764	KRT35_HUMAN	K	141;171	ENSP00000246639:E141K;ENSP00000377558:E171K	ENSP00000246639:E141K	E	-	1	0	KRT35	36889520	0.005000	0.15991	1.000000	0.80357	0.982000	0.71751	-0.024000	0.12435	1.366000	0.46076	-0.165000	0.13383	GAG		0.488	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		20	146	0	0	0	1	0	20	146				
DSC3	1825	broad.mit.edu	37	18	28602425	28602425	+	Silent	SNP	C	C	T	rs374250811		TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr18:28602425C>T	ENST00000360428.4	-	7	899	c.819G>A	c.(817-819)ccG>ccA	p.P273P	DSC3_ENST00000434452.1_Silent_p.P273P	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	273	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GCATTGTGTCCGGTTCATCTC	0.438																																						uc002kwj.4																			0				endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						c.(817-819)ccG>ccA		Homo sapiens desmocollin 3 (DSC3), transcript variant Dsc3a, mRNA.		C	,	1,4405	2.1+/-5.4	0,1,2202	149.0	128.0	135.0		819,819	-9.8	0.0	18		135	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DSC3	NM_001941.3,NM_024423.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	273/897,273/840	28602425	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1825				homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding	g.chr18:28602425C>T	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.819G>A	18.37:g.28602425C>T			Somatic				DSC3_uc002kwi.4_Silent_p.P273P	p.P273P	NM_001941	NP_001932	WXS	Illumina GAIIx	Phase_I	Q14574	DSC3_HUMAN	OV - Ovarian serous cystadenocarcinoma(10;0.125)		6	974	-			273			Cadherin 2.		A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	37	c.819G>A	CCDS32810.1																																																																																				0.438	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		22	34	0	0	0	1	0	22	34				
TMEM53	79639	broad.mit.edu	37	1	45120353	45120353	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr1:45120353G>A	ENST00000372237.3	-	3	875	c.712C>T	c.(712-714)Cgc>Tgc	p.R238C	TMEM53_ENST00000372242.3_Intron|TMEM53_ENST00000372243.3_Intron|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372235.3_Missense_Mutation_p.R208C|TMEM53_ENST00000476724.1_5'UTR	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	238						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					AGGACCCGGCGTGCCAGGCGT	0.602																																						uc001cmc.3																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10						c.(712-714)Cgc>Tgc		Homo sapiens transmembrane protein 53 (TMEM53), mRNA.							95.0	106.0	102.0					1																	45120353		2203	4300	6503	SO:0001583	missense	79639					integral to membrane		g.chr1:45120353G>A		CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.712C>T	1.37:g.45120353G>A	ENSP00000361311:p.Arg238Cys		Somatic				TMEM53_uc001cmd.3_Missense_Mutation_p.R165C|TMEM53_uc009vxh.1_Missense_Mutation_p.R121C|TMEM53_uc010ola.1_Missense_Mutation_p.R121C	p.R238C	NM_024587	NP_078863	WXS	Illumina GAIIx	Phase_I	Q6P2H8	TMM53_HUMAN			2	748	-	Acute lymphoblastic leukemia(166;0.155)		238					B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Missense_Mutation	SNP	ENST00000372237.3	37	c.712C>T	CCDS511.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171698	0.38315	.	.	ENSG00000126106	ENST00000372237;ENST00000372235	.	.	.	5.54	5.54	0.83059	.	0.486297	0.24793	N	0.035551	T	0.56920	0.2018	L	0.38838	1.175	0.50632	D	0.999881	B	0.17852	0.024	B	0.12156	0.007	T	0.52305	-0.8593	9	0.52906	T	0.07	.	19.4772	0.94994	0.0:0.0:1.0:0.0	.	238	Q6P2H8	TMM53_HUMAN	C	238;208	.	ENSP00000361309:R208C	R	-	1	0	TMEM53	44892940	1.000000	0.71417	0.870000	0.34147	0.473000	0.32948	6.039000	0.70972	2.602000	0.87976	0.563000	0.77884	CGC		0.602	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587		31	48	0	0	0	1	0	31	48				
FAM187B	148109	broad.mit.edu	37	19	35719205	35719205	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr19:35719205G>A	ENST00000324675.3	-	1	427	c.379C>T	c.(379-381)Ccc>Tcc	p.P127S		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	127						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TTCTGCAGGGGCCTCTGACCC	0.562																																						uc002nyk.1																			0				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						c.(379-381)Ccc>Tcc		Homo sapiens family with sequence similarity 187, member B (FAM187B), mRNA.							113.0	107.0	109.0					19																	35719205		2203	4300	6503	SO:0001583	missense	148109					integral to membrane		g.chr19:35719205G>A	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.379C>T	19.37:g.35719205G>A	ENSP00000323355:p.Pro127Ser		Somatic					p.P127S	NM_152481	NP_689694	WXS	Illumina GAIIx	Phase_I	Q17R55	F187B_HUMAN			0	424	-			127					Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	37	c.379C>T	CCDS12448.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.528018	0.64860	.	.	ENSG00000177558	ENST00000324675	T	0.28666	1.6	5.26	2.91	0.33838	.	0.000000	0.49916	D	0.000121	T	0.49150	0.1540	M	0.66939	2.045	0.36347	D	0.859828	D	0.76494	0.999	D	0.68765	0.96	T	0.60870	-0.7177	10	0.59425	D	0.04	-42.912	11.4746	0.50291	0.0:0.3513:0.6487:0.0	.	127	Q17R55	F187B_HUMAN	S	127	ENSP00000323355:P127S	ENSP00000323355:P127S	P	-	1	0	FAM187B	40411045	0.979000	0.34478	0.863000	0.33907	0.021000	0.10359	1.948000	0.40303	1.308000	0.44962	0.655000	0.94253	CCC		0.562	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481		48	72	0	0	0	1	0	48	72				
OR4C3	256144	broad.mit.edu	37	11	48347139	48347139	+	Missense_Mutation	SNP	A	A	G	rs386753296		TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr11:48347139A>G	ENST00000319856.4	+	1	668	c.647A>G	c.(646-648)aAt>aGt	p.N216S		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						GCCTGCACCAATACGTATGTC	0.507																																						uc010rhv.2																			0				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						c.(646-648)aAt>aGt		Homo sapiens olfactory receptor, family 4, subfamily C, member 3 (OR4C3), mRNA.							224.0	164.0	184.0					11																	48347139		2201	4298	6499	SO:0001583	missense	256144				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:48347139A>G	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"""GPCR / Class A : Olfactory receptors"""	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.647A>G	11.37:g.48347139A>G	ENSP00000321419:p.Asn216Ser		Somatic					p.N216S	NM_001004702	NP_001004702	WXS	Illumina GAIIx	Phase_I	Q8NH37	OR4C3_HUMAN			0	647	+			189					B2RNF2|Q6IFB3	Missense_Mutation	SNP	ENST00000319856.4	37	c.647A>G	CCDS31489.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.560907	0.27827	.	.	ENSG00000176547	ENST00000319856;ENST00000395239	T	0.00091	8.74	5.78	5.78	0.91487	GPCR, rhodopsin-like superfamily (1);	0.901795	0.09503	N	0.793384	T	0.00178	0.0005	L	0.28192	0.835	0.26075	N	0.981161	B	0.23058	0.079	B	0.32928	0.155	T	0.57112	-0.7867	10	0.87932	D	0	.	14.2031	0.65716	1.0:0.0:0.0:0.0	.	189	Q8NH37	OR4C3_HUMAN	S	216;79	ENSP00000321419:N216S	ENSP00000321419:N216S	N	+	2	0	OR4C3	48303715	0.405000	0.25336	0.742000	0.31022	0.051000	0.14879	5.005000	0.63972	2.245000	0.73994	0.391000	0.25812	AAT		0.507	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		10	37	0	0	0	1	0	10	37				
IGKV1OR22-5	28850	broad.mit.edu	37	22	17385392	17385392	+	IGR	SNP	T	T	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr22:17385392T>A								AC007064.24 (33376 upstream) : GAB4 (57433 downstream)																							GTCATCTGGATGTCACATCTG	0.453																																						uc011agg.1																			0													Homo sapiens isolate N1858K immunoglobulin kappa light chain variable region (IGKV1-12) mRNA, partial cds.							127.0	125.0	125.0					22																	17385392		1189	2528	3717	SO:0001628	intergenic_variant	28940							g.chr22:17385392T>A																													22.37:g.17385392T>A			Somatic								WXS	Illumina GAIIx	Phase_I					0		-									RNA	SNP		37	c.4A>T																																																																																				0	0.453									8	124	0	0	0	1	0	8	124				
CT45A5	441521	broad.mit.edu	37	X	134947928	134947928	+	Missense_Mutation	SNP	C	C	G			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chrX:134947928C>G	ENST00000463085.2	-	3	486	c.397G>C	c.(397-399)Gaa>Caa	p.E133Q	CT45A5_ENST00000370724.3_Missense_Mutation_p.E133Q|CT45A4_ENST00000420087.2_Intron|CT45A5_ENST00000491480.1_Missense_Mutation_p.E133Q			Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5	133								p.E133*(1)		endometrium(1)|large_intestine(2)|lung(6)	9						CATCGGATTTCCTTCACTACT	0.388																																						uc004eze.3																			1	Substitution - Nonsense(1)	p.E133*(2)	lung(1)	endometrium(1)|large_intestine(2)|lung(6)	9						c.(397-399)Gaa>Caa		Homo sapiens cancer/testis antigen family 45, member A5 (CT45A5), transcript variant 1, mRNA.							209.0	174.0	186.0					X																	134947928		2188	4266	6454	SO:0001583	missense	441521							g.chrX:134947928C>G	AY743713	CCDS35406.1	Xq26.3	2009-03-12				ENSG00000269586			33270	protein-coding gene	gene with protein product	"""cancer/testis antigen CT45-5"""	300796				15905330	Standard	XM_006724759		Approved	CT45-5, CT45.5	uc022ces.1	Q6NSH3		ENST00000463085.2:c.397G>C	X.37:g.134947928C>G	ENSP00000424778:p.Glu133Gln		Somatic				CT45A5_uc022ces.1_Missense_Mutation_p.E133Q|CT45A5_uc011mvu.2_Missense_Mutation_p.E133Q	p.E133Q	NM_001007551	NP_001165759	WXS	Illumina GAIIx	Phase_I	Q6NSH3	CT455_HUMAN			2	642	-			133					A8K842|B7ZMC5	Missense_Mutation	SNP	ENST00000463085.2	37	c.397G>C	CCDS35406.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.788780	0.31685	.	.	ENSG00000242284	ENST00000370724;ENST00000491480	T;T	0.62105	0.05;0.05	2.4	1.46	0.22682	.	0.000000	0.85682	U	0.000000	T	0.74152	0.3679	M	0.80332	2.49	0.09310	N	1	D	0.67145	0.996	D	0.75484	0.986	T	0.63042	-0.6725	10	0.87932	D	0	-3.4548	5.7026	0.17891	0.3195:0.6805:0.0:0.0	.	133	Q6NSH3	CT455_HUMAN	Q	133	ENSP00000359759:E133Q;ENSP00000425997:E133Q	ENSP00000359759:E133Q	E	-	1	0	CT45A5	134775594	0.998000	0.40836	0.013000	0.15412	0.005000	0.04900	2.054000	0.41335	0.206000	0.20587	0.365000	0.22127	GAA		0.388	CT45A5-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472589.1	NM_001007551		35	57	0	0	0	1	0	35	57				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		24	27	0	0	0	1	0	24	27				
TTC39C	125488	broad.mit.edu	37	18	21660663	21660663	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chr18:21660663T>A	ENST00000317571.3	+	5	811	c.575T>A	c.(574-576)tTg>tAg	p.L192*	TTC39C_ENST00000578150.1_3'UTR|TTC39C_ENST00000304621.6_Nonsense_Mutation_p.L131*|RP11-403A21.3_ENST00000578443.1_RNA	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	192										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						GAAGAGTCCTTGACTTCTGAT	0.448																																						uc002kuw.3																			0				breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						c.(574-576)tTg>tAg		Homo sapiens tetratricopeptide repeat domain 39C (TTC39C), transcript variant 1, mRNA.							136.0	130.0	132.0					18																	21660663		2203	4300	6503	SO:0001587	stop_gained	125488						binding	g.chr18:21660663T>A	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.575T>A	18.37:g.21660663T>A	ENSP00000323645:p.Leu192*		Somatic				TTC39C_uc002kuu.3_Nonsense_Mutation_p.L131*	p.L192*	NM_001135993	NP_694943	WXS	Illumina GAIIx	Phase_I	Q8N584	TT39C_HUMAN			4	1027	+			192					B7WP63|J3QRR1|Q0VAJ2|Q8N284	Nonsense_Mutation	SNP	ENST00000317571.3	37	c.575T>A	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	t	34	5.359971	0.95877	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	.	.	.	5.2	4.03	0.46877	.	0.595344	0.16935	N	0.193507	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9486	10.1785	0.42952	0.0:0.0772:0.0:0.9228	.	.	.	.	X	131;192	.	ENSP00000306598:L131X	L	+	2	0	TTC39C	19914661	1.000000	0.71417	0.977000	0.42913	0.924000	0.55760	3.312000	0.51927	1.069000	0.40788	0.451000	0.29950	TTG		0.448	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		24	44	0	0	0	1	0	24	44				
RNF128	79589	broad.mit.edu	37	X	106016280	106016281	+	Frame_Shift_Ins	INS	-	-	T			TCGA-ET-A3BT-01A-11D-A19J-08	TCGA-ET-A3BT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fd99f617-2855-4379-ab0f-87b67b471767	0f39fc31-07ab-4d8d-9bd2-510277dd467a	g.chrX:106016280_106016281insT	ENST00000255499.2	+	2	872_873	c.622_623insT	c.(622-624)attfs	p.I208fs	RNF128_ENST00000324342.3_Frame_Shift_Ins_p.I182fs	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	208					negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						TCACTATTCAATTTTTTTCGTT	0.391																																						uc004eml.3																			0				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						c.(622-624)attfs		Homo sapiens ring finger protein 128 (RNF128), transcript variant 1, mRNA.																																				SO:0001589	frameshift_variant	79589					endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding	g.chrX:106016280_106016281insT	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"""RING-type (C3HC4) zinc fingers"""	21153	protein-coding gene	gene with protein product		300439	"""ring finger protein 128"""				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.629dupT	X.37:g.106016287_106016287dupT	ENSP00000255499:p.Ile208fs		Somatic				RNF128_uc004emk.3_Frame_Shift_Ins_p.I182fs	p.I208fs	NM_194463	NP_919445	WXS	Illumina GAIIx	Phase_I	Q8TEB7	RN128_HUMAN			1	872_873	+			208					A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Frame_Shift_Ins	INS	ENST00000255499.2	37	c.622_623insT	CCDS14521.1																																																																																				0.391	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		49	90						49	90	---	---	---	---
