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RAP1GDS1 (RAP1, GTP-GDP dissociation stimulator 1)

Written2003-10Franck Viguié
Laboratoire de Cytogenetique - Service d'Hematologie Biologique, Hopital Hotel-Dieu - 75181 Paris Cedex 04, France

(Note : for Links provided by Atlas : click)

Identity

Other namesRAP1
GTP-GDP dissociation stimulator 1
HGNC (Hugo) RAP1GDS1
LocusID (NCBI) 5910
Atlas_Id 400
Location 4q23  [Link to chromosome band 4q23]
Location_base_pair Starts at 99182527 and ends at 99365012 bp from pter ( according to hg19-Feb_2009)  [Mapping RAP1GDS1.png]
Fusion genes
(updated 2016)
NUP98 (11p15.4) / RAP1GDS1 (4q23)RAP1GDS1 (4q23) / GSTCD (4q24)RAP1GDS1 (4q23) / KLF5 (13q22.1)
RAP1GDS1 (4q23) / NUP98 (11p15.4)RAP1GDS1 (4q23) / RAP1GDS1 (4q23)UNC5C (4q22.3) / RAP1GDS1 (4q23)

DNA/RNA

Description 181.2 kb - 15 exons
Transcription mRNA 2487 bases

Protein

Description rap1gds, also refered as smgGDS - 61.1 kDa, 558 aa. Contains in major part an armadillo motif, which is composed of tandemly repeated sequences of 43 amino acid residues.
Expression Ubiquitary, high level of expression in central nervous system.
Function Acts as guanine nucleotide exchange factor (GEF). Activates GDP/GTP exchange reaction on numerous small proteins with GTPase activity (G proteins) containing a C-terminal polybasic region (PBR), including Ras and Rho family GTPases such as rap1a, rap1b, K-ras, rac1, rac2, rhoA, ralB. These proteins play a pivotal role in cell proliferation, differentiation and oncogenic transformation.
Homology With other mammalian rap1gds1 proteins.

Implicated in

Note
Entity t(4;11)(q21;p15).
Disease T cell acute lymphocytic leukemia.
Cytogenetics Additional anomalies in 2/3 cases.
Hybrid/Mutated Gene Quasi totality of RAP1GDS1 fused with 5' part of NUP98.
Abnormal Protein Chimeric protein 5' -NUP98 - RAP1GDS1 - 3'.
  

Bibliography

The (4;11)(q21;p15) translocation fuses the NUP98 and RAP1GDS1 genes and is recurrent in T-cell acute lymphocytic leukemia.
Hussey DJ, Nicola M, Moore S, Peters GB, Dobrovic A
Blood. 1999 ; 94 (6) : 2072-2079.
PMID 10477737
 
t(4;11)(q21;p15) translocation involving NUP98 and RAP1GDS1 genes: characterization of a new subset of T acute lymphoblastic leukaemia.
Mecucci C, La Starza R, Negrini M, Sabbioni S, Crescenzi B, Leoni P, Di Raimondo F, Krampera M, Cimino G, Tafuri A, Cuneo A, Vitale A, Foá R
British journal of haematology. 2000 ; 109 (4) : 788-793.
PMID 10929031
 
SmgGDS displays differential binding and exchange activity towards different Ras isoforms.
Vikis HG, Stewart S, Guan KL
Oncogene. 2002 ; 21 (15) : 2425-2432.
PMID 11948427
 
Inhibition of adenylate cyclase activity by galanin in rat insulinoma cells is mediated by the G-protein Gi3.
de Mazancourt P, Goldsmith PK, Weinstein LS
The Biochemical journal. 1994 ; 303 ( Pt 2) : 369-375.
PMID 7526840
 

Citation

This paper should be referenced as such :
Viguié, F
RAP1GDS1 (RAP1, GTP-GDP dissociation stimulator 1)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(1):6-6.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/RAP1GDS1ID400.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(4;11)(q21;p15) NUP98/RAP1GDS1
t(4;11)(q23;p15) NUP98/RAP1GDS1
T-lineage acute lymphoblastic leukemia (T-ALL)

External links

Nomenclature
HGNC (Hugo)RAP1GDS1   9859
Cards
AtlasRAP1GDS1ID400
Entrez_Gene (NCBI)RAP1GDS1  5910  Rap1 GTPase-GDP dissociation stimulator 1
AliasesGDS1; SmgGDS
GeneCards (Weizmann)RAP1GDS1
Ensembl hg19 (Hinxton)ENSG00000138698 [Gene_View]  chr4:99182527-99365012 [Contig_View]  RAP1GDS1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000138698 [Gene_View]  chr4:99182527-99365012 [Contig_View]  RAP1GDS1 [Vega]
ICGC DataPortalENSG00000138698
TCGA cBioPortalRAP1GDS1
AceView (NCBI)RAP1GDS1
Genatlas (Paris)RAP1GDS1
WikiGenes5910
SOURCE (Princeton)RAP1GDS1
Genomic and cartography
GoldenPath hg19 (UCSC)RAP1GDS1  -     chr4:99182527-99365012 +  4q23   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RAP1GDS1  -     4q23   [Description]    (hg38-Dec_2013)
EnsemblRAP1GDS1 - 4q23 [CytoView hg19]  RAP1GDS1 - 4q23 [CytoView hg38]
Mapping of homologs : NCBIRAP1GDS1 [Mapview hg19]  RAP1GDS1 [Mapview hg38]
OMIM179502   
Gene and transcription
Genbank (Entrez)AF215923 AF237413 AI800264 AK055032 AK295156
RefSeq transcript (Entrez)NM_001100426 NM_001100427 NM_001100428 NM_001100429 NM_001100430 NM_021159
RefSeq genomic (Entrez)NC_000004 NC_018915 NT_016354 NW_004929320
Consensus coding sequences : CCDS (NCBI)RAP1GDS1
Cluster EST : UnigeneHs.132858 [ NCBI ]
CGAP (NCI)Hs.132858
Alternative Splicing GalleryENSG00000138698
Gene ExpressionRAP1GDS1 [ NCBI-GEO ]   RAP1GDS1 [ EBI - ARRAY_EXPRESS ]   RAP1GDS1 [ SEEK ]   RAP1GDS1 [ MEM ]
Gene Expression Viewer (FireBrowse)RAP1GDS1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5910
GTEX Portal (Tissue expression)RAP1GDS1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP52306 (Uniprot)
NextProtP52306  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP52306
Splice isoforms : SwissVarP52306 (Swissvar)
PhosPhoSitePlusP52306
Domaine pattern : Prosite (Expaxy)ARM_REPEAT (PS50176)   
Domains : Interpro (EBI)ARM-like    ARM-type_fold    Armadillo   
Domain families : Pfam (Sanger)Arm (PF00514)   
Domain families : Pfam (NCBI)pfam00514   
Domain families : Smart (EMBL)ARM (SM00185)  
DMDM Disease mutations5910
Blocks (Seattle)RAP1GDS1
SuperfamilyP52306
Human Protein AtlasENSG00000138698
Peptide AtlasP52306
HPRD11763
IPIIPI00607591   IPI00856100   IPI00619924   IPI00424869   IPI00855767   IPI00855727   IPI00968047   IPI00967638   IPI00964475   IPI00967154   IPI00966126   IPI00965229   IPI00967796   IPI00966423   IPI00967339   IPI00964784   IPI00965386   
Protein Interaction databases
DIP (DOE-UCLA)P52306
IntAct (EBI)P52306
FunCoupENSG00000138698
BioGRIDRAP1GDS1
STRING (EMBL)RAP1GDS1
ZODIACRAP1GDS1
Ontologies - Pathways
QuickGOP52306
Ontology : AmiGOGTPase activator activity  protein binding  mitochondrion  endoplasmic reticulum  cytosol  small GTPase mediated signal transduction  negative regulation of endoplasmic reticulum calcium ion concentration  positive regulation of GTPase activity  positive regulation of mitochondrial calcium ion concentration  extracellular exosome  
Ontology : EGO-EBIGTPase activator activity  protein binding  mitochondrion  endoplasmic reticulum  cytosol  small GTPase mediated signal transduction  negative regulation of endoplasmic reticulum calcium ion concentration  positive regulation of GTPase activity  positive regulation of mitochondrial calcium ion concentration  extracellular exosome  
NDEx Network
Atlas of Cancer Signalling NetworkRAP1GDS1
Wikipedia pathwaysRAP1GDS1
Orthology - Evolution
OrthoDB5910
GeneTree (enSembl)ENSG00000138698
Phylogenetic Trees/Animal Genes : TreeFamRAP1GDS1
Homologs : HomoloGeneRAP1GDS1
Homology/Alignments : Family Browser (UCSC)RAP1GDS1
Gene fusions - Rearrangements
Fusion : MitelmanNUP98/RAP1GDS1 [11p15.4/4q23]  [t(4;11)(q23;p15)]  
Fusion: TCGARAP1GDS1 4q23 GSTCD 4q24 HNSC
Fusion : TICdbNUP98 [11p15.4]  -  RAP1GDS1 [4q23]
Polymorphisms : SNP, variants
NCBI Variation ViewerRAP1GDS1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RAP1GDS1
dbVarRAP1GDS1
ClinVarRAP1GDS1
1000_GenomesRAP1GDS1 
Exome Variant ServerRAP1GDS1
ExAC (Exome Aggregation Consortium)RAP1GDS1 (select the gene name)
Genetic variants : HAPMAP5910
Genomic Variants (DGV)RAP1GDS1 [DGVbeta]
Mutations
ICGC Data PortalRAP1GDS1 
TCGA Data PortalRAP1GDS1 
Broad Tumor PortalRAP1GDS1
OASIS PortalRAP1GDS1 [ Somatic mutations - Copy number]
Cancer Gene: CensusRAP1GDS1 
Somatic Mutations in Cancer : COSMICRAP1GDS1 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch RAP1GDS1
DgiDB (Drug Gene Interaction Database)RAP1GDS1
DoCM (Curated mutations)RAP1GDS1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RAP1GDS1 (select a term)
intoGenRAP1GDS1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)4:99182527-99365012  ENSG00000138698
CONAN: Copy Number AnalysisRAP1GDS1 
Mutations and Diseases : HGMDRAP1GDS1
OMIM179502   
MedgenRAP1GDS1
Genetic Testing Registry RAP1GDS1
NextProtP52306 [Medical]
TSGene5910
GENETestsRAP1GDS1
Huge Navigator RAP1GDS1 [HugePedia]
snp3D : Map Gene to Disease5910
BioCentury BCIQRAP1GDS1
ClinGenRAP1GDS1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5910
Chemical/Pharm GKB GenePA34221
Clinical trialRAP1GDS1
Miscellaneous
canSAR (ICR)RAP1GDS1 (select the gene name)
Probes
Litterature
PubMed35 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRAP1GDS1
EVEXRAP1GDS1
GoPubMedRAP1GDS1
iHOPRAP1GDS1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Aug 10 18:58:44 CEST 2016

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