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ARHGAP20 (Rho GTPase activating protein 20)

Written2006-08Claudia Kalla
DKFZ, Div. Molecular Genetics (B060), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany

(Note : for Links provided by Atlas : click)

Identity

Other namesKIAA1391
RARHOGAP
HGNC (Hugo) ARHGAP20
LocusID (NCBI) 57569
Atlas_Id 42979
Location 11q23.1  [Link to chromosome band 11q23]
Location_base_pair Starts at 110447759 and ends at 110582773 bp from pter ( according to hg19-Feb_2009)  [Mapping ARHGAP20.png]
Local_order telomeric to ATM
Fusion genes
(updated 2016)
ARHGAP20 (11q23.1) / BRWD3 (Xq21.1)BRWD3 (Xq21.1) / ARHGAP20 (11q23.1)

DNA/RNA

 
  Genomic organization (A) and transcript variants (B) of ARHGAP20.
(A) Gene structure (drawn to scale): black boxes represent exons.
(B) Transcripts (drawn to scale): boxes, exons; UTR, untranslated region; light shaded box, coding region; shaded and dark shaded boxes, nucleotide sequences coding for protein domains (PH: pleckstrin homology domain, RA: ras association domain; RhoGAP: RhoGAP domain).
Description 19 exons spanning 136.1 kb genomic DNA.
Transcription 5.9-6.2 kb mRNA, coding sequence: 3.5-3.6 kb
Alternative splicing of the first 5 exons results in the expression of 5 transcript variants (ARHGAP20-1e, ARHGAP20-1d, ARHGAP20-1ad, ARHGAP20-1be, ARHGAP20-1c).
Pseudogene None.

Protein

 
  Schematic representation of ARHGAP20 protein variants as deduced from the transcripts. Hatched box, amino-terminal extension of unknown function; PH: pleckstrin homology domain, RA: ras association domain; RhoGAP: RhoGAP domain.
Description The amino-terminal region shows significant homology to a pleckstrin homology (PH) domain commonly found in eukaryotic signaling proteins. Adjacent to the PH domain a Ras association (RA) domain is postulated, which is found in proteins involved in GTPase-mediated signaling processes. The central section of the protein contains a RhoGAP domain, which is crucial for the regulation of Rho-like GTPases by Rho GTPase-activating proteins in the course of transmitting diverse intracellular signals.
Expression Predominantly expressed in brain, but transcripts were also detected in peripheral blood lymphocytes.
Localisation Cytoplasm
Function The presence of a RhoGAP domain in combination with PH and RA modules indicates that ARHGAP20 is involved in the regulation of Rho-family GTPases. ARHGAP20 was shown to be activated by Rap1 and to induce inactivation of Rho, resulting in the neurite outgrowth.
Homology Mouse: RarhoGAP (RhoGAP having the RA domain), Arhgap20.
Rat: RahoGAP (RhoGAP having the RA domain), Arhgap20.

Mutations

Note Single nucleotide polymorphism 1785T/C (transcript variant ARHGAP20-1ad, AY496263).
Germinal None detected.
Somatic In the tumour cells of one case of B-cell chronic lymphocytic leukemia, the missense mutation 2995T>G (S999A; transcript variant ARHGAP20-1ad, AY496263) was found.

Implicated in

Note
Entity B-cell chronic lymphocytic leukemia (B-CLL).
Note In the tumour cells of two B-CLL cases, ARHGAP20 was found affected by translocations that rearranged the gene with BRWD3 (Xq21) and a novel gene on 13q14 (unpublished data), respectively. No fusion transcripts were generated. ARHGAP20 transcript expression is significantly upregulated in B-CLL lymphocytes vs. CD19+ control B cells.
  
Entity t(X;11)(q21;q23)
Disease B-cell chronic lymphocytic leukemia (B-CLL).
Cytogenetics t(X;11)(q21;q23)
Hybrid/Mutated Gene ARHGAP20 - BRWD3
Abnormal Protein None detected.
  
Entity t(11;13)(q23;q14)
Disease B-cell chronic lymphocytic leukemia (B-CLL).
Cytogenetics t(11;13)(q23;14)
Hybrid/Mutated Gene ARHGAP20 - novel gene on 13q14 (unpublished data)
Abnormal Protein None detected.
  

Bibliography

Identification of RARhoGAP, a novel putative RhoGAP gene expressed in male germ cells.
Curry BJ, Su H, Law EG, McLaughlin EA, Nixon B, Aitken RJ
Genomics. 2004 ; 84 (2) : 406-418.
PMID 15234003
 
Translocation t(X;11)(q13;q23) in B-cell chronic lymphocytic leukemia disrupts two novel genes.
Kalla C, Nentwich H, Schlotter M, Mertens D, Wildenberger K, Döhner H, Stilgenbauer S, Lichter P
Genes, chromosomes & cancer. 2005 ; 42 (2) : 128-143.
PMID 15543602
 
Identification and characterization of human KIAA1391 and mouse Kiaa1391 genes encoding novel RhoGAP family proteins with RA domain and ANXL repeats.
Katoh M, Katoh M
International journal of oncology. 2003 ; 23 (5) : 1471-1476.
PMID 14532992
 
Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro.
Nagase T, Kikuno R, Ishikawa KI, Hirosawa M, Ohara O
DNA research : an international journal for rapid publication of reports on genes and genomes. 2000 ; 7 (1) : 65-73.
PMID 10718198
 
RA-RhoGAP, Rap-activated Rho GTPase-activating protein implicated in neurite outgrowth through Rho.
Yamada T, Sakisaka T, Hisata S, Baba T, Takai Y
The Journal of biological chemistry. 2005 ; 280 (38) : 33026-33034.
PMID 16014623
 

Citation

This paper should be referenced as such :
Kalla, C
ARHGAP20 (Rho GTPase activating protein 20)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(1):1-3.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ARHGAP20ID42979ch11q23.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(X;11)(q21;q23) BRWD3/ARHGAP20

External links

Nomenclature
HGNC (Hugo)ARHGAP20   18357
Cards
AtlasARHGAP20ID42979ch11q23
Entrez_Gene (NCBI)ARHGAP20  57569  Rho GTPase activating protein 20
AliasesRARHOGAP
GeneCards (Weizmann)ARHGAP20
Ensembl hg19 (Hinxton)ENSG00000137727 [Gene_View]  chr11:110447759-110582773 [Contig_View]  ARHGAP20 [Vega]
Ensembl hg38 (Hinxton)ENSG00000137727 [Gene_View]  chr11:110447759-110582773 [Contig_View]  ARHGAP20 [Vega]
ICGC DataPortalENSG00000137727
TCGA cBioPortalARHGAP20
AceView (NCBI)ARHGAP20
Genatlas (Paris)ARHGAP20
WikiGenes57569
SOURCE (Princeton)ARHGAP20
Genomic and cartography
GoldenPath hg19 (UCSC)ARHGAP20  -     chr11:110447759-110582773 -  11q23.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ARHGAP20  -     11q23.2   [Description]    (hg38-Dec_2013)
EnsemblARHGAP20 - 11q23.2 [CytoView hg19]  ARHGAP20 - 11q23.2 [CytoView hg38]
Mapping of homologs : NCBIARHGAP20 [Mapview hg19]  ARHGAP20 [Mapview hg38]
OMIM609568   
Gene and transcription
Genbank (Entrez)AB037812 AI936560 AK292290 AK307602 AY496263
RefSeq transcript (Entrez)NM_001258415 NM_001258416 NM_001258417 NM_001258418 NM_020809
RefSeq genomic (Entrez)NC_000011 NC_018922 NT_033899 NW_004929381
Consensus coding sequences : CCDS (NCBI)ARHGAP20
Cluster EST : UnigeneHs.6136 [ NCBI ]
CGAP (NCI)Hs.6136
Alternative Splicing GalleryENSG00000137727
Gene ExpressionARHGAP20 [ NCBI-GEO ]   ARHGAP20 [ EBI - ARRAY_EXPRESS ]   ARHGAP20 [ SEEK ]   ARHGAP20 [ MEM ]
Gene Expression Viewer (FireBrowse)ARHGAP20 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)57569
GTEX Portal (Tissue expression)ARHGAP20
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9P2F6 (Uniprot)
NextProtQ9P2F6  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9P2F6
Splice isoforms : SwissVarQ9P2F6 (Swissvar)
PhosPhoSitePlusQ9P2F6
Domaine pattern : Prosite (Expaxy)RA (PS50200)    RHOGAP (PS50238)   
Domains : Interpro (EBI)PH_dom-like    PH_domain    RA_dom    Rho_GTPase_activation_prot    RhoGAP_dom    Ubiquitin-rel_dom   
Domain families : Pfam (Sanger)RA (PF00788)    RhoGAP (PF00620)   
Domain families : Pfam (NCBI)pfam00788    pfam00620   
Domain families : Smart (EMBL)PH (SM00233)  RhoGAP (SM00324)  
DMDM Disease mutations57569
Blocks (Seattle)ARHGAP20
PDB (SRS)3MSX   
PDB (PDBSum)3MSX   
PDB (IMB)3MSX   
PDB (RSDB)3MSX   
Structural Biology KnowledgeBase3MSX   
SCOP (Structural Classification of Proteins)3MSX   
CATH (Classification of proteins structures)3MSX   
SuperfamilyQ9P2F6
Human Protein AtlasENSG00000137727
Peptide AtlasQ9P2F6
HPRD10657
IPIIPI00012622   IPI00478558   IPI00844419   IPI00844483   IPI00844252   
Protein Interaction databases
DIP (DOE-UCLA)Q9P2F6
IntAct (EBI)Q9P2F6
FunCoupENSG00000137727
BioGRIDARHGAP20
STRING (EMBL)ARHGAP20
ZODIACARHGAP20
Ontologies - Pathways
QuickGOQ9P2F6
Ontology : AmiGOGTPase activator activity  cytosol  signal transduction  positive regulation of GTPase activity  positive regulation of GTPase activity  regulation of small GTPase mediated signal transduction  
Ontology : EGO-EBIGTPase activator activity  cytosol  signal transduction  positive regulation of GTPase activity  positive regulation of GTPase activity  regulation of small GTPase mediated signal transduction  
REACTOMEQ9P2F6 [protein]
REACTOME PathwaysR-HSA-194840 Rho GTPase cycle [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkARHGAP20
Wikipedia pathwaysARHGAP20
Orthology - Evolution
OrthoDB57569
GeneTree (enSembl)ENSG00000137727
Phylogenetic Trees/Animal Genes : TreeFamARHGAP20
Homologs : HomoloGeneARHGAP20
Homology/Alignments : Family Browser (UCSC)ARHGAP20
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerARHGAP20 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ARHGAP20
dbVarARHGAP20
ClinVarARHGAP20
1000_GenomesARHGAP20 
Exome Variant ServerARHGAP20
ExAC (Exome Aggregation Consortium)ARHGAP20 (select the gene name)
Genetic variants : HAPMAP57569
Genomic Variants (DGV)ARHGAP20 [DGVbeta]
Mutations
ICGC Data PortalARHGAP20 
TCGA Data PortalARHGAP20 
Broad Tumor PortalARHGAP20
OASIS PortalARHGAP20 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICARHGAP20 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch ARHGAP20
DgiDB (Drug Gene Interaction Database)ARHGAP20
DoCM (Curated mutations)ARHGAP20 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ARHGAP20 (select a term)
intoGenARHGAP20
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)11:110447759-110582773  ENSG00000137727
CONAN: Copy Number AnalysisARHGAP20 
Mutations and Diseases : HGMDARHGAP20
OMIM609568   
MedgenARHGAP20
Genetic Testing Registry ARHGAP20
NextProtQ9P2F6 [Medical]
TSGene57569
GENETestsARHGAP20
Huge Navigator ARHGAP20 [HugePedia]
snp3D : Map Gene to Disease57569
BioCentury BCIQARHGAP20
ClinGenARHGAP20
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD57569
Chemical/Pharm GKB GenePA134963885
Clinical trialARHGAP20
Miscellaneous
canSAR (ICR)ARHGAP20 (select the gene name)
Probes
Litterature
PubMed13 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineARHGAP20
EVEXARHGAP20
GoPubMedARHGAP20
iHOPARHGAP20
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Aug 10 18:47:08 CEST 2016

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