Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

RNF139 (translocation in renal carcinoma, chromosome 8 gene)

Written2004-06Anita Bonné, Eric Schoenmakers, Ad Geurts van Kessel
Department of Human Genetics (417), P.O. Box 9101, 6500 HB Nijmegen, The Netherlands

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)TRC8
RCA1
HRCA1
Other aliasTRC8 (translocation in renal carcinoma, chromosome 8 gene)
MGC31961
8_125443572
HGNC (Hugo) RNF139
LocusID (NCBI) 11236
Atlas_Id 500
Location 8q24.13  [Link to chromosome band 8q24]
Location_base_pair Starts at 124474767 and ends at 124488618 bp from pter ( according to hg19-Feb_2009)  [Mapping RNF139.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
FHIT (3p14.2) / RNF139 (8q24.13)PTK2 (8q24.3) / RNF139 (8q24.13)RNF139 (8q24.13) / EIF2A (3q25.1)
RNF139 (8q24.13) / FHIT (3p14.2)

DNA/RNA

Description The TRC8 gene covers 13.96 kb. The gene contains 2 confirmed introns, 2 of which are alternative. The gene showed similarity to the hereditary basal cell carcinoma/segment polarity gene, 'patched' (PTCH) This similarity involved 2 regions of 'patched,' the putative sterol-sensing domain and the second extracellular loop that participates in the binding of sonic hedgehog (SHH). In the t(3;8) translocation, TRC8 was found to be fused to FHIT and disrupted within the sterol-sensing domain. In contrast, the FHIT coding region was maintained and expressed. In a series of sporadic renal carcinomas, an acquired TRC8 mutation was identified. By analogy to patched, TRC8 might function as a signaling receptor, and other pathway members, to be defined, are mutation candidates in malignant diseases involving the kidney and thyroid.

Protein

Description 664 amino acids
Localisation Plasma membrane
Function The protein encoded by this gene is a multi-membrane spanning protein containing a RING-H2 finger. This protein is located in the endoplasmic reticulum, and has been shown to possess ubiquitin ligase activity. This gene was found to be interrupted by a t(3:8) translocation in a family with hereditary renal and non-medulary thyroid cancer. Studies of the Drosophila counterpart suggested that this protein may interact with tumor suppressor protein VHL, as well as with COPS5/JAB1, a protein responsible for the degradation of tumor suppressor CDKN1B/P27KIP

Implicated in

Note
  
Entity t(3;8)(p14.2;q24.1) and hereditary renal cell cancer.
Disease familial renal cell cancer
Cytogenetics Disruption of the gene because of the t(3;8) translocation.
Hybrid/Mutated Gene FHIT/TRC8. Although studies demonstrated that the 3p14.2 breakpoint interrupted the fragile histidine triad gene (FHIT) in its 5-prime noncoding region, several reasons made it unlikely that FHIT is causally related to renal or other malignancies.
  

Bibliography

Sonic Hedgehog signalling in the developing and adult brain.
Charytoniuk D, Porcel B, Rodríguez Gomez J, Faure H, Ruat M, Traiffort E
Journal of physiology, Paris. 2002 ; 96 (1-2) : 9-16.
PMID 11755778
 
Hereditary renal-cell carcinoma associated with a chromosomal translocation.
Cohen AJ, Li FP, Berg S, Marchetto DJ, Tsai S, Jacobs SC, Brown RS
The New England journal of medicine. 1979 ; 301 (11) : 592-595.
PMID 470981
 
The hereditary renal cell carcinoma 3;8 translocation fuses FHIT to a patched-related gene, TRC8.
Gemmill RM, West JD, Boldog F, Tanaka N, Robinson LJ, Smith DI, Li F, Drabkin HA
Proceedings of the National Academy of Sciences of the United States of America. 1998 ; 95 (16) : 9572-9577.
PMID 9689122
 
RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination.
Lorick KL, Jensen JP, Fang S, Ong AM, Hatakeyama S, Weissman AM
Proceedings of the National Academy of Sciences of the United States of America. 1999 ; 96 (20) : 11364-11369.
PMID 10500182
 

Citation

This paper should be referenced as such :
Bonné, A ; Schoenmakers, EFPMG ; Geurts, van Kessel A
TRC8 (translocation in renal carcinoma, chromosome 8 gene)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(3):226-227.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TRC8ID500.html


Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Familial clear cell renal cancer


External links

Nomenclature
HGNC (Hugo)RNF139   17023
Cards
AtlasTRC8ID500
Entrez_Gene (NCBI)RNF139  11236  ring finger protein 139
AliasesHRCA1; RCA1; TRC8
GeneCards (Weizmann)RNF139
Ensembl hg19 (Hinxton)ENSG00000170881 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000170881 [Gene_View]  chr8:124474767-124488618 [Contig_View]  RNF139 [Vega]
ICGC DataPortalENSG00000170881
TCGA cBioPortalRNF139
AceView (NCBI)RNF139
Genatlas (Paris)RNF139
WikiGenes11236
SOURCE (Princeton)RNF139
Genetics Home Reference (NIH)RNF139
Genomic and cartography
GoldenPath hg38 (UCSC)RNF139  -     chr8:124474767-124488618 +  8q24.13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RNF139  -     8q24.13   [Description]    (hg19-Feb_2009)
EnsemblRNF139 - 8q24.13 [CytoView hg19]  RNF139 - 8q24.13 [CytoView hg38]
Mapping of homologs : NCBIRNF139 [Mapview hg19]  RNF139 [Mapview hg38]
OMIM144700   603046   
Gene and transcription
Genbank (Entrez)AA455970 AF064801 AK001602 AK025043 AK098519
RefSeq transcript (Entrez)NM_007218
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RNF139
Cluster EST : UnigeneHs.744151 [ NCBI ]
CGAP (NCI)Hs.744151
Alternative Splicing GalleryENSG00000170881
Gene ExpressionRNF139 [ NCBI-GEO ]   RNF139 [ EBI - ARRAY_EXPRESS ]   RNF139 [ SEEK ]   RNF139 [ MEM ]
Gene Expression Viewer (FireBrowse)RNF139 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)11236
GTEX Portal (Tissue expression)RNF139
Human Protein AtlasENSG00000170881-RNF139 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8WU17   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8WU17  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8WU17
Splice isoforms : SwissVarQ8WU17
Catalytic activity : Enzyme2.3.2.27 [ Enzyme-Expasy ]   2.3.2.272.3.2.27 [ IntEnz-EBI ]   2.3.2.27 [ BRENDA ]   2.3.2.27 [ KEGG ]   
PhosPhoSitePlusQ8WU17
Domaine pattern : Prosite (Expaxy)ZF_RING_2 (PS50089)   
Domains : Interpro (EBI)TRC8_N_dom    Znf_RING    Znf_RING-CH    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)TRC8_N (PF13705)    zf-RING_2 (PF13639)   
Domain families : Pfam (NCBI)pfam13705    pfam13639   
Domain families : Smart (EMBL)RING (SM00184)  RINGv (SM00744)  
Conserved Domain (NCBI)RNF139
DMDM Disease mutations11236
Blocks (Seattle)RNF139
SuperfamilyQ8WU17
Human Protein Atlas [tissue]ENSG00000170881-RNF139 [tissue]
Peptide AtlasQ8WU17
HPRD04333
IPIIPI00289584   IPI01010903   
Protein Interaction databases
DIP (DOE-UCLA)Q8WU17
IntAct (EBI)Q8WU17
FunCoupENSG00000170881
BioGRIDRNF139
STRING (EMBL)RNF139
ZODIACRNF139
Ontologies - Pathways
QuickGOQ8WU17
Ontology : AmiGOprotein polyubiquitination  protease binding  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  receptor activity  protein binding  endoplasmic reticulum  endoplasmic reticulum membrane  zinc ion binding  negative regulation of cell proliferation  integral component of membrane  protein ubiquitination  protein ubiquitination  ligase activity  negative regulation of translation  ubiquitin-like protein transferase activity  ubiquitin-dependent ERAD pathway  regulation of protein ubiquitination  protein destabilization  ERAD pathway  Derlin-1 retrotranslocation complex  proteasome-mediated ubiquitin-dependent protein catabolic process  endoplasmic reticulum quality control compartment  regulation of ER to Golgi vesicle-mediated transport  ubiquitin protein ligase activity  regulation of protein processing  ubiquitin protein ligase activity involved in ERAD pathway  endoplasmic reticulum mannose trimming  positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process  
Ontology : EGO-EBIprotein polyubiquitination  protease binding  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  receptor activity  protein binding  endoplasmic reticulum  endoplasmic reticulum membrane  zinc ion binding  negative regulation of cell proliferation  integral component of membrane  protein ubiquitination  protein ubiquitination  ligase activity  negative regulation of translation  ubiquitin-like protein transferase activity  ubiquitin-dependent ERAD pathway  regulation of protein ubiquitination  protein destabilization  ERAD pathway  Derlin-1 retrotranslocation complex  proteasome-mediated ubiquitin-dependent protein catabolic process  endoplasmic reticulum quality control compartment  regulation of ER to Golgi vesicle-mediated transport  ubiquitin protein ligase activity  regulation of protein processing  ubiquitin protein ligase activity involved in ERAD pathway  endoplasmic reticulum mannose trimming  positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process  
NDEx NetworkRNF139
Atlas of Cancer Signalling NetworkRNF139
Wikipedia pathwaysRNF139
Orthology - Evolution
OrthoDB11236
GeneTree (enSembl)ENSG00000170881
Phylogenetic Trees/Animal Genes : TreeFamRNF139
HOVERGENQ8WU17
HOGENOMQ8WU17
Homologs : HomoloGeneRNF139
Homology/Alignments : Family Browser (UCSC)RNF139
Gene fusions - Rearrangements
Fusion : MitelmanPTK2/RNF139 [8q24.3/8q24.13]  [t(8;8)(q24;q24)]  
Fusion : MitelmanRNF139/EIF2A [8q24.13/3q25.1]  [t(3;8)(q25;q24)]  
Fusion: TCGA_MDACCPTK2 8q24.3 RNF139 8q24.13 LUAD
Fusion: TCGA_MDACCRNF139 8q24.13 EIF2A 3q25.1 LUAD
Tumor Fusion PortalRNF139
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRNF139 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RNF139
dbVarRNF139
ClinVarRNF139
1000_GenomesRNF139 
Exome Variant ServerRNF139
ExAC (Exome Aggregation Consortium)ENSG00000170881
GNOMAD BrowserENSG00000170881
Genetic variants : HAPMAP11236
Genomic Variants (DGV)RNF139 [DGVbeta]
DECIPHERRNF139 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRNF139 
Mutations
ICGC Data PortalRNF139 
TCGA Data PortalRNF139 
Broad Tumor PortalRNF139
OASIS PortalRNF139 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRNF139  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRNF139
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch RNF139
DgiDB (Drug Gene Interaction Database)RNF139
DoCM (Curated mutations)RNF139 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RNF139 (select a term)
intoGenRNF139
NCG5 (London)RNF139
Cancer3DRNF139(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM144700    603046   
Orphanet23138   
DisGeNETRNF139
MedgenRNF139
Genetic Testing Registry RNF139
NextProtQ8WU17 [Medical]
TSGene11236
GENETestsRNF139
Target ValidationRNF139
Huge Navigator RNF139 [HugePedia]
snp3D : Map Gene to Disease11236
BioCentury BCIQRNF139
ClinGenRNF139
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD11236
Chemical/Pharm GKB GenePA134945850
Clinical trialRNF139
Miscellaneous
canSAR (ICR)RNF139 (select the gene name)
Probes
Litterature
PubMed21 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRNF139
EVEXRNF139
GoPubMedRNF139
iHOPRNF139
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 21 15:05:20 CET 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.