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RNF213 (lymphoma oligomerization partner on chromosome 17)

Written2003-08Jean-Loup Huret, Sylvie Senon
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Other namesALO17 (ALK lymphoma oligomerization partner on chromosome 17)
HGNC (Hugo) RNF213
LocusID (NCBI) 57674
Atlas_Id 480
Location 17q25.3  [Link to chromosome band 17q25]
Location_base_pair Starts at 78234660 and ends at 78372581 bp from pter ( according to hg19-Feb_2009)  [Mapping RNF213.png]
Fusion genes
(updated 2016)
ARHGDIA (17q25.3) / RNF213 (17q25.3)FRA10AC1 (10q23.33) / RNF213 (17q25.3)RNF213 (17q25.3) / ALK (2p23.2)
RNF213 (17q25.3) / BAIAP2 (17q25.3)RNF213 (17q25.3) / CA11 (19q13.33)RNF213 (17q25.3) / ETV5 (3q27.2)
RNF213 (17q25.3) / IL22RA1 (1p36.11)RNF213 (17q25.3) / MYC (8q24.21)RNF213 (17q25.3) / PPM1L (3q25.33)
RNF213 (17q25.3) / PRPF38B (1p13.3)RNF213 (17q25.3) / PSAP (10q22.1)RNF213 (17q25.3) / RNF213 (17q25.3)
RNF213 (17q25.3) / SIT1 (9p13.3)RNF213 (17q25.3) / SLC26A11 (17q25.3)RNF213 (17q25.3) / SLC37A1 (21q22.3)
RNF213 (17q25.3) / TPP1 (11p15.4)RPL10 (Xq28) / RNF213 (17q25.3)RPS6KB1 (17q23.1) / RNF213 (17q25.3)
RPTOR (17q25.3) / RNF213 (17q25.3)SLC16A3 (17q25.3) / RNF213 (17q25.3)TBC1D16 (17q25.3) / RNF213 (17q25.3)
UBE2O (17q25.1) / RNF213 (17q25.3)cytochrome_b () / RNF213 (17q25.3)

DNA/RNA

Transcription alternate spicing; 5185 and 5332 bp cDNA

Protein

Description 1550 and 1599 amino acids if the sequence is complete; putative zinc finger in the N term, and AraC motif in the C term

Implicated in

Note
Entity Anaplasic large cell lymphoma (ALCL) with t(2;17)(p23;q25) --> ALK- ALO17
Disease ALCL are high grade non Hodgkin lymphomas; ALK+ ALCL are ALCL where ALK is involved in a fusion gene; ALK+ ALCL represent 50 to 60 % of ALCL cases (they are CD30+, ALK+;); belong to the "cytoplasmic ALK+" subset.
Prognosis Althouth presenting as a high grade tumour, a 80% five yr survival is associated with this anomaly
Hybrid/Mutated Gene 5' ALO17 - 3' ALK
Abnormal Protein NH2 ALO17 - COOH ALK
  

Bibliography

Identification of novel fusion partners of ALK, the anaplastic lymphoma kinase, in anaplastic large-cell lymphoma and inflammatory myofibroblastic tumor.
Cools J, Wlodarska I, Somers R, Mentens N, Pedeutour F, Maes B, De Wolf-Peeters C, Pauwels P, Hagemeijer A, Marynen P
Genes, chromosomes & cancer. 2002 ; 34 (4) : 354-362.
PMID 12112524
 

Citation

This paper should be referenced as such :
Huret, JL ; Senon, S
ALO17 (ALK lymphoma oligomerization partner on chromosome 17)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(4):220-220.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ALO17ID480.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  Anaplastic large cell lymphoma (ALCL)
t(2;17)(p23;q25) RNF213/ALK

External links

Nomenclature
HGNC (Hugo)RNF213   14539
Cards
AtlasALO17ID480
Entrez_Gene (NCBI)RNF213  57674  ring finger protein 213
AliasesALO17; C17orf27; KIAA1618; MYMY2; 
MYSTR; NET57
GeneCards (Weizmann)RNF213
Ensembl hg19 (Hinxton)ENSG00000173821 [Gene_View]  chr17:78234660-78372581 [Contig_View]  RNF213 [Vega]
Ensembl hg38 (Hinxton)ENSG00000173821 [Gene_View]  chr17:78234660-78372581 [Contig_View]  RNF213 [Vega]
ICGC DataPortalENSG00000173821
TCGA cBioPortalRNF213
AceView (NCBI)RNF213
Genatlas (Paris)RNF213
WikiGenes57674
SOURCE (Princeton)RNF213
Genomic and cartography
GoldenPath hg19 (UCSC)RNF213  -     chr17:78234660-78372581 +  17q25.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RNF213  -     17q25.3   [Description]    (hg38-Dec_2013)
EnsemblRNF213 - 17q25.3 [CytoView hg19]  RNF213 - 17q25.3 [CytoView hg38]
Mapping of homologs : NCBIRNF213 [Mapview hg19]  RNF213 [Mapview hg38]
OMIM607151   613768   
Gene and transcription
Genbank (Entrez)AB046774 AB046838 AB537889 AF397204 AF397205
RefSeq transcript (Entrez)NM_001256071 NM_020914 NM_020954
RefSeq genomic (Entrez)NC_000017 NC_018928 NG_031980 NT_010783 NW_004929407
Consensus coding sequences : CCDS (NCBI)RNF213
Cluster EST : UnigeneHs.745415 [ NCBI ]
CGAP (NCI)Hs.745415
Alternative Splicing GalleryENSG00000173821
Gene ExpressionRNF213 [ NCBI-GEO ]   RNF213 [ EBI - ARRAY_EXPRESS ]   RNF213 [ SEEK ]   RNF213 [ MEM ]
Gene Expression Viewer (FireBrowse)RNF213 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)57674
GTEX Portal (Tissue expression)RNF213
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ63HN8 (Uniprot)
NextProtQ63HN8  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ63HN8
Splice isoforms : SwissVarQ63HN8 (Swissvar)
PhosPhoSitePlusQ63HN8
Domaine pattern : Prosite (Expaxy)ZF_RING_2 (PS50089)   
Domains : Interpro (EBI)AAA+_ATPase    P-loop_NTPase    RNF213    Znf_C3HC4_RING-type    Znf_RING    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)zf-C3HC4 (PF00097)   
Domain families : Pfam (NCBI)pfam00097   
Domain families : Smart (EMBL)AAA (SM00382)  RING (SM00184)  
DMDM Disease mutations57674
Blocks (Seattle)RNF213
SuperfamilyQ63HN8
Human Protein AtlasENSG00000173821
Peptide AtlasQ63HN8
HPRD10716
IPIIPI00965321   IPI00470478   IPI00642126   IPI00217287   IPI00782972   IPI00103821   IPI00828098   
Protein Interaction databases
DIP (DOE-UCLA)Q63HN8
IntAct (EBI)Q63HN8
FunCoupENSG00000173821
BioGRIDRNF213
STRING (EMBL)RNF213
ZODIACRNF213
Ontologies - Pathways
QuickGOQ63HN8
Ontology : AmiGOprotein polyubiquitination  angiogenesis  sprouting angiogenesis  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  protein binding  nucleolus  cytoplasm  cytosol  ubiquitin-dependent protein catabolic process  zinc ion binding  membrane  protein ubiquitination  ligase activity  ATPase activity  protein homooligomerization  protein autoubiquitination  negative regulation of non-canonical Wnt signaling pathway  
Ontology : EGO-EBIprotein polyubiquitination  angiogenesis  sprouting angiogenesis  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  protein binding  nucleolus  cytoplasm  cytosol  ubiquitin-dependent protein catabolic process  zinc ion binding  membrane  protein ubiquitination  ligase activity  ATPase activity  protein homooligomerization  protein autoubiquitination  negative regulation of non-canonical Wnt signaling pathway  
NDEx NetworkRNF213
Atlas of Cancer Signalling NetworkRNF213
Wikipedia pathwaysRNF213
Orthology - Evolution
OrthoDB57674
GeneTree (enSembl)ENSG00000173821
Phylogenetic Trees/Animal Genes : TreeFamRNF213
Homologs : HomoloGeneRNF213
Homology/Alignments : Family Browser (UCSC)RNF213
Gene fusions - Rearrangements
Fusion : MitelmanARHGDIA/RNF213 [17q25.3/17q25.3]  [t(17;17)(q25;q25)]  
Fusion : MitelmanRNF213/ALK [17q25.3/2p23.2]  [t(2;17)(p23;q25)]  
Fusion : MitelmanRNF213/ETV5 [17q25.3/3q27.2]  [t(3;17)(q27;q25)]  
Fusion : MitelmanRNF213/IL22RA1 [17q25.3/1p36.11]  [t(1;17)(p36;q25)]  
Fusion : MitelmanRNF213/MYC [17q25.3/8q24.21]  [t(8;17)(q24;q25)]  
Fusion : MitelmanRNF213/SLC26A11 [17q25.3/17q25.3]  [t(17;17)(q25;q25)]  
Fusion : MitelmanRPS6KB1/RNF213 [17q23.1/17q25.3]  [t(17;17)(q23;q25)]  
Fusion : MitelmanRPTOR/RNF213 [17q25.3/17q25.3]  [t(17;17)(q25;q25)]  
Fusion : MitelmanTBC1D16/RNF213 [17q25.3/17q25.3]  [t(17;17)(q25;q25)]  
Fusion : MitelmanUBE2O/RNF213 [17q25.1/17q25.3]  [t(17;17)(q25;q25)]  
Fusion: TCGAARHGDIA 17q25.3 RNF213 17q25.3 LUAD
Fusion: TCGARNF213 17q25.3 ETV5 3q27.2 BRCA
Fusion: TCGARNF213 17q25.3 IL22RA1 1p36.11 BLCA
Fusion: TCGARNF213 17q25.3 SLC26A11 17q25.3 BRCA
Fusion: TCGARPS6KB1 17q23.1 RNF213 17q25.3 BRCA
Fusion: TCGARPTOR 17q25.3 RNF213 17q25.3 BRCA
Fusion: TCGAUBE2O 17q25.1 RNF213 17q25.3 BRCA
Fusion : TICdbRNF213 [17q25.3]  -  ALK [2p23.2]
Fusion Cancer (Beijing)RNF213 [17q25.3]  -  SLC26A11 [17q25.3]  [FUSC001666]
Fusion Cancer (Beijing)cytochrome_b [RNF213]  -  17q25.3 [FUSC004466]
Polymorphisms : SNP, variants
NCBI Variation ViewerRNF213 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RNF213
dbVarRNF213
ClinVarRNF213
1000_GenomesRNF213 
Exome Variant ServerRNF213
ExAC (Exome Aggregation Consortium)RNF213 (select the gene name)
Genetic variants : HAPMAP57674
Genomic Variants (DGV)RNF213 [DGVbeta]
Mutations
ICGC Data PortalRNF213 
TCGA Data PortalRNF213 
Broad Tumor PortalRNF213
OASIS PortalRNF213 [ Somatic mutations - Copy number]
Cancer Gene: CensusRNF213 
Somatic Mutations in Cancer : COSMICRNF213 
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 RNF213
DgiDB (Drug Gene Interaction Database)RNF213
DoCM (Curated mutations)RNF213 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RNF213 (select a term)
intoGenRNF213
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:78234660-78372581  ENSG00000173821
CONAN: Copy Number AnalysisRNF213 
Mutations and Diseases : HGMDRNF213
OMIM607151    613768   
MedgenRNF213
Genetic Testing Registry RNF213
NextProtQ63HN8 [Medical]
TSGene57674
GENETestsRNF213
Huge Navigator RNF213 [HugePedia]
snp3D : Map Gene to Disease57674
BioCentury BCIQRNF213
ClinGenRNF213
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD57674
Chemical/Pharm GKB GenePA162401681
Clinical trialRNF213
Miscellaneous
canSAR (ICR)RNF213 (select the gene name)
Probes
Litterature
PubMed57 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRNF213
EVEXRNF213
GoPubMedRNF213
iHOPRNF213
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Sep 28 15:57:46 CEST 2016

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