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RAP1A (RAP11, member of RAS oncogene family)

Written2001-05Jean de Gunzburg
Laboratoire de Signalisation Intracellulaire et Oncogenöse INSERM U-528 Institut Curie Section de Recherche 26, rue d'Ulm, 75248 Paris Cedex 05, France

(Note : for Links provided by Atlas : click)

Identity

HGNC (Hugo) RAP1A
LocusID (NCBI) 5906
Atlas_Id 272
Location 1p13.2
Location_base_pair Starts at 112162405 and ends at 112259317 bp from pter ( according to hg19-Feb_2009)  [Mapping RAP1A.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)
MAGI3 (1p13.2) / RAP1A (1p13.2)PCDH7 (4p15.1) / RAP1A (1p13.2)RAP1A (1p13.2) / CD2 (1p13.1)
RAP1A (1p13.2) / EIF4A3 (17q25.3)RAP1A (1p13.2) / EIF4G1 (3q27.1)RAP1A (1p13.2) / RAP1A (1p13.2)
RAP1A (1p13.2) / SEL1L (14q31.1)TRAM1 (8q13.3) / RAP1A (1p13.2)

DNA/RNA

 
Description 6 coding exons covering 18095 bp on chromosome 1

Protein

Description Rap1 is a member of the Ras superfamily of monomeric GTPases, closely related to Ras. There are two isoforms, Rap1A and Rap1B that share 95% identity and are encoded by two different genes. Rap1 proteins share 50% identity with Ras proteins, including the regions involved in GDP/GTP binding (hence Rap1A has very similar biochemical properties to Ras), C-terminal CAAX domain leading to prenylation (geranylgeranylation in the case of Rap1A), and effector region identical to that of Ras proteins causing Ras and Rap1 to share some potential effectors
Expression ubiquitous ; higher in brain and hemopoïetic tissues
Localisation Rap1 is bound to membranes. In many cell types, it is found in a perinuclear compartment overlapping the Golgi. Rap1 proteins (A and B) are phosphorylated near the C-ter by cAMP-dependent protein kinase. This results in translocation of part of the Rap1 pool to the cytosol.
Function The function of Rap1 is still a matter of debate. Its overexpression is able to compete with the activation of Raf-1 by active Ras. Active Rap1B has been shown to activate the B-Raf kinase and the MEK-ERK cascade. In several cellular models, Rap1 has been shown to be involved in the regulation of integrin-mediated cell adhesion.
Homology 95% to Rap1B, 60% identical to Rap2, 50 % to Ras proteins

Mutations

Germinal unknown

Implicated in

Note
Entity no implication in pathologies characterized so far
  

Bibliography

Rap1 signalling: adhering to new models.
Bos JL, de Rooij J, Reedquist KA
Nature reviews. Molecular cell biology. 2001 ; 2 (5) : 369-377.
PMID 11331911
 

Citation

This paper should be referenced as such :
Gunzburg, J de
RAP1A (RAP1A, member of RAS oncogene family)
Atlas Genet Cytogenet Oncol Haematol. 2001;5(3):172-173.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/RAP1AID272.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(4;11)(q21;p15) NUP98/RAP1GDS1
t(4;11)(q23;p15) NUP98/RAP1GDS1

External links

Nomenclature
HGNC (Hugo)RAP1A   9855
Cards
AtlasRAP1AID272
Entrez_Gene (NCBI)RAP1A  5906  RAP1A, member of RAS oncogene family
AliasesC21KG; G-22K; KREV-1; KREV1; 
RAP1; SMGP21
GeneCards (Weizmann)RAP1A
Ensembl hg19 (Hinxton)ENSG00000116473 [Gene_View]  chr1:112162405-112259317 [Contig_View]  RAP1A [Vega]
Ensembl hg38 (Hinxton)ENSG00000116473 [Gene_View]  chr1:112162405-112259317 [Contig_View]  RAP1A [Vega]
ICGC DataPortalENSG00000116473
TCGA cBioPortalRAP1A
AceView (NCBI)RAP1A
Genatlas (Paris)RAP1A
WikiGenes5906
SOURCE (Princeton)RAP1A
Genomic and cartography
GoldenPath hg19 (UCSC)RAP1A  -     chr1:112162405-112259317 +  1p13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RAP1A  -     1p13.3   [Description]    (hg38-Dec_2013)
EnsemblRAP1A - 1p13.3 [CytoView hg19]  RAP1A - 1p13.3 [CytoView hg38]
Mapping of homologs : NCBIRAP1A [Mapview hg19]  RAP1A [Mapview hg38]
OMIM179520   
Gene and transcription
Genbank (Entrez)AB051846 AB451235 AB451360 AF493912 AK023457
RefSeq transcript (Entrez)NM_001010935 NM_001291896 NM_002884
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_032977 NW_004929290
Consensus coding sequences : CCDS (NCBI)RAP1A
Cluster EST : UnigeneHs.586618 [ NCBI ]
CGAP (NCI)Hs.586618
Alternative Splicing GalleryENSG00000116473
Gene ExpressionRAP1A [ NCBI-GEO ]   RAP1A [ EBI - ARRAY_EXPRESS ]   RAP1A [ SEEK ]   RAP1A [ MEM ]
Gene Expression Viewer (FireBrowse)RAP1A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5906
GTEX Portal (Tissue expression)RAP1A
Protein : pattern, domain, 3D structure
UniProt/SwissProtP62834 (Uniprot)
NextProtP62834  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP62834
Splice isoforms : SwissVarP62834 (Swissvar)
PhosPhoSitePlusP62834
Domaine pattern : Prosite (Expaxy)RAS (PS51421)   
Domains : Interpro (EBI)P-loop_NTPase    Small_GTP-bd_dom    Small_GTPase    Small_GTPase_Ras   
Domain families : Pfam (Sanger)Ras (PF00071)   
Domain families : Pfam (NCBI)pfam00071   
Domain families : Smart (EMBL)RAS (SM00173)  
DMDM Disease mutations5906
Blocks (Seattle)RAP1A
PDB (SRS)1C1Y    1GUA    3KUC    4KVG   
PDB (PDBSum)1C1Y    1GUA    3KUC    4KVG   
PDB (IMB)1C1Y    1GUA    3KUC    4KVG   
PDB (RSDB)1C1Y    1GUA    3KUC    4KVG   
Structural Biology KnowledgeBase1C1Y    1GUA    3KUC    4KVG   
SCOP (Structural Classification of Proteins)1C1Y    1GUA    3KUC    4KVG   
CATH (Classification of proteins structures)1C1Y    1GUA    3KUC    4KVG   
SuperfamilyP62834
Human Protein AtlasENSG00000116473
Peptide AtlasP62834
HPRD01545
IPIIPI00019345   IPI00877120   
Protein Interaction databases
DIP (DOE-UCLA)P62834
IntAct (EBI)P62834
FunCoupENSG00000116473
BioGRIDRAP1A
STRING (EMBL)RAP1A
ZODIACRAP1A
Ontologies - Pathways
QuickGOP62834
Ontology : AmiGOactivation of MAPKK activity  GTPase activity  protein binding  GTP binding  cytoplasm  early endosome  late endosome  cytosol  plasma membrane  intracellular protein transport  nucleocytoplasmic transport  signal transduction  metabolic process  protein transporter activity  positive regulation of neuron projection development  protein transport  Ras GTPase binding  Rap guanyl-nucleotide exchange factor activity  microvillus assembly  cell junction  guanyl-nucleotide exchange factor complex  protein complex binding  Rap protein signal transduction  negative regulation of collagen biosynthetic process  cellular response to drug  nerve growth factor signaling pathway  neuron projection  myelin sheath  positive regulation of GTPase activity  positive regulation of protein kinase activity  positive regulation of glucose import  perinuclear region of cytoplasm  positive regulation of phagocytosis  regulation of insulin secretion  establishment of endothelial barrier  extracellular exosome  positive regulation of ERK1 and ERK2 cascade  cellular response to cAMP  cellular response to glucose stimulus  response to antineoplastic agent  liver regeneration  regulation of cell junction assembly  cellular response to nerve growth factor stimulus  negative regulation of synaptic vesicle exocytosis  positive regulation of vasculogenesis  
Ontology : EGO-EBIactivation of MAPKK activity  GTPase activity  protein binding  GTP binding  cytoplasm  early endosome  late endosome  cytosol  plasma membrane  intracellular protein transport  nucleocytoplasmic transport  signal transduction  metabolic process  protein transporter activity  positive regulation of neuron projection development  protein transport  Ras GTPase binding  Rap guanyl-nucleotide exchange factor activity  microvillus assembly  cell junction  guanyl-nucleotide exchange factor complex  protein complex binding  Rap protein signal transduction  negative regulation of collagen biosynthetic process  cellular response to drug  nerve growth factor signaling pathway  neuron projection  myelin sheath  positive regulation of GTPase activity  positive regulation of protein kinase activity  positive regulation of glucose import  perinuclear region of cytoplasm  positive regulation of phagocytosis  regulation of insulin secretion  establishment of endothelial barrier  extracellular exosome  positive regulation of ERK1 and ERK2 cascade  cellular response to cAMP  cellular response to glucose stimulus  response to antineoplastic agent  liver regeneration  regulation of cell junction assembly  cellular response to nerve growth factor stimulus  negative regulation of synaptic vesicle exocytosis  positive regulation of vasculogenesis  
Pathways : BIOCARTAIntegrin Signaling Pathway [Genes]    Signaling of Hepatocyte Growth Factor Receptor [Genes]   
Pathways : KEGGMAPK signaling pathway    Ras signaling pathway    Rap1 signaling pathway    Chemokine signaling pathway    Focal adhesion    Leukocyte transendothelial migration    Long-term potentiation    Neurotrophin signaling pathway    Pancreatic secretion    Renal cell carcinoma   
REACTOMEP62834 [protein]
REACTOME PathwaysR-HSA-170984 ARMS-mediated activation [pathway]
REACTOME PathwaysR-HSA-381676 Glucagon-like Peptide-1 (GLP1) regulates insulin secretion [pathway]
REACTOME PathwaysR-HSA-392517 Rap1 signalling [pathway]
REACTOME PathwaysR-HSA-5674135 MAP2K and MAPK activation [pathway]
REACTOME PathwaysR-HSA-372708 p130Cas linkage to MAPK signaling for integrins [pathway]
REACTOME PathwaysR-HSA-354192 Integrin alphaIIb beta3 signaling [pathway]
REACTOME PathwaysR-HSA-354194 GRB2:SOS provides linkage to MAPK signaling for Integrins [pathway]
REACTOME PathwaysR-HSA-170968 Frs2-mediated activation [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkRAP1A
Wikipedia pathwaysRAP1A
Orthology - Evolution
OrthoDB5906
GeneTree (enSembl)ENSG00000116473
Phylogenetic Trees/Animal Genes : TreeFamRAP1A
Homologs : HomoloGeneRAP1A
Homology/Alignments : Family Browser (UCSC)RAP1A
Gene fusions - Rearrangements
Fusion : MitelmanMAGI3/RAP1A [1p13.2/1p13.2]  [t(1;1)(p13;p13)]  
Fusion : MitelmanRAP1A/CD2 [1p13.2/1p13.1]  [t(1;1)(p13;p13)]  
Fusion: TCGAMAGI3 1p13.2 RAP1A 1p13.2 BRCA
Fusion: TCGARAP1A 1p13.2 CD2 1p13.1 HNSC
Polymorphisms : SNP, variants
NCBI Variation ViewerRAP1A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RAP1A
dbVarRAP1A
ClinVarRAP1A
1000_GenomesRAP1A 
Exome Variant ServerRAP1A
ExAC (Exome Aggregation Consortium)RAP1A (select the gene name)
Genetic variants : HAPMAP5906
Genomic Variants (DGV)RAP1A [DGVbeta]
Mutations
ICGC Data PortalRAP1A 
TCGA Data PortalRAP1A 
Broad Tumor PortalRAP1A
OASIS PortalRAP1A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRAP1A 
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 RAP1A
DgiDB (Drug Gene Interaction Database)RAP1A
DoCM (Curated mutations)RAP1A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RAP1A (select a term)
intoGenRAP1A
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)1:112162405-112259317  ENSG00000116473
CONAN: Copy Number AnalysisRAP1A 
Mutations and Diseases : HGMDRAP1A
OMIM179520   
MedgenRAP1A
Genetic Testing Registry RAP1A
NextProtP62834 [Medical]
TSGene5906
GENETestsRAP1A
Huge Navigator RAP1A [HugePedia]
snp3D : Map Gene to Disease5906
BioCentury BCIQRAP1A
ClinGenRAP1A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5906
Chemical/Pharm GKB GenePA34217
Clinical trialRAP1A
Miscellaneous
canSAR (ICR)RAP1A (select the gene name)
Probes
Litterature
PubMed186 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRAP1A
EVEXRAP1A
GoPubMedRAP1A
iHOPRAP1A
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat May 28 11:28:58 CEST 2016

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