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ARHGEF12 (Rho guanine nucleotide exchange factor (GEF) 12)

Written2000-04Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesRho guanine nucleotide exchange factor (GEF) 12
Alias_symbol (synonym)KIAA0382
LARG
Other aliasLARG (Leukemia Associated Rho Guanine nucleotide exchange factor)
HGNC (Hugo) ARHGEF12
LocusID (NCBI) 23365
Atlas_Id 243
Location 11q23.3  [Link to chromosome band 11q23]
Location_base_pair Starts at 120207618 and ends at 120360645 bp from pter ( according to hg19-Feb_2009)  [Mapping ARHGEF12.png]
Local_order telomeric to MLL
Fusion genes
(updated 2016)
ARHGEF12 (11q23.3) / ANKRD29 (18q11.2)ARHGEF12 (11q23.3) / ARHGEF12 (11q23.3)ARHGEF12 (11q23.3) / CNTN5 (11q22.1)
ARHGEF12 (11q23.3) / HDAC9 (7p21.1)ARHGEF12 (11q23.3) / KMT2A (11q23.3)ARHGEF12 (11q23.3) / POU2F3 (11q23.3)
ARHGEF12 (11q23.3) / SIK3 (11q23.3)ARHGEF12 (11q23.3) / UQCC1 (20q11.22)ATP6AP2 (Xp11.4) / ARHGEF12 (11q23.3)
KCTD2 (17q25.1) / ARHGEF12 (11q23.3)KMT2A (11q23.3) / ARHGEF12 (11q23.3)SC5D (11q23.3) / ARHGEF12 (11q23.3)

DNA/RNA

Transcription 9501 bp mRNA; 4634 bp open reading frame

Protein

 
Description the gene encodes a guanine nucleotide exchange factor; 1544 amino acids; NH2- PDZ domain, Lsc homology (LH) domain, bipartite nuclear localization signal, Dbl homology (DH) domain, and a pleckstrin homology (PH) domain -COOH
Expression wide (leukocytes, spleen, prostate, testis, ovary, small intestine, colon, thymus)
Function PDZ domains are involved in protein-protein interactions in transmembrane signaling pathways; LH domains bind G proteins; nuclear localization signals are implicated in translocation of proteins from the cytoplasm to the nucleus; DH domains are responsible for the nucleotide exchange activity of guanine nucleotide exchange (GEF) toward Rho GTPases, PH domains function in membrane localization; Rho GEF are regulators of GTPases, and have oncogenic properties
Homology member of the family of Rho GEF factors, like dbl, vav, tiam, and BCR

Implicated in

Note
  
Entity acute non lymphocytic leukemia (AML) with apparently normal cromosomes 11 --> MLL- LARG
Note poorly defined: only 1 case to date, a 38 yr old male patient with occupational exposure; M4-AML; CR; death unrelated to the leukemia
Cytogenetics the case was 51,XY,+8,+19,+3mar; the interstitial deletion at 11q23 resulting in MLL-LARG fusion cannot be seen at the chromosome level
Hybrid/Mutated Gene 5' MLL fused at exon 6 with the 3' end of almost the entire LARG; LARG is oriented in a 5' to 3'direction, like MLL
Abnormal Protein excludes the NH2- PDZ domain of LARG, and includes most of LARG, from the Lsc homology (LH) domain to COOH
  

Bibliography

Identification of a gene at 11q23 encoding a guanine nucleotide exchange factor: evidence for its fusion with MLL in acute myeloid leukemia.
Kourlas PJ, Strout MP, Becknell B, Veronese ML, Croce CM, Theil KS, Krahe R, Ruutu T, Knuutila S, Bloomfield CD, Caligiuri MA
Proceedings of the National Academy of Sciences of the United States of America. 2000 ; 97 (5) : 2145-2150.
PMID 10681437
 

Citation

This paper should be referenced as such :
Huret, JL
ARHGEF12 (Rho guanine nucleotide exchange factor (GEF) 12)
Atlas Genet Cytogenet Oncol Haematol. 2000;4(2):58-59.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LARGID243.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  11q23 rearrangements (KMT2A) in leukaemia
del(11)(q23q23) KMT2A/ARHGEF12


External links

Nomenclature
HGNC (Hugo)ARHGEF12   14193
Cards
AtlasLARGID243
Entrez_Gene (NCBI)ARHGEF12  23365  Rho guanine nucleotide exchange factor 12
AliasesLARG; PRO2792
GeneCards (Weizmann)ARHGEF12
Ensembl hg19 (Hinxton)ENSG00000196914 [Gene_View]  chr11:120207618-120360645 [Contig_View]  ARHGEF12 [Vega]
Ensembl hg38 (Hinxton)ENSG00000196914 [Gene_View]  chr11:120207618-120360645 [Contig_View]  ARHGEF12 [Vega]
ICGC DataPortalENSG00000196914
TCGA cBioPortalARHGEF12
AceView (NCBI)ARHGEF12
Genatlas (Paris)ARHGEF12
WikiGenes23365
SOURCE (Princeton)ARHGEF12
Genetics Home Reference (NIH)ARHGEF12
Genomic and cartography
GoldenPath hg19 (UCSC)ARHGEF12  -     chr11:120207618-120360645 +  11q23.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ARHGEF12  -     11q23.3   [Description]    (hg38-Dec_2013)
EnsemblARHGEF12 - 11q23.3 [CytoView hg19]  ARHGEF12 - 11q23.3 [CytoView hg38]
Mapping of homologs : NCBIARHGEF12 [Mapview hg19]  ARHGEF12 [Mapview hg38]
OMIM604763   
Gene and transcription
Genbank (Entrez)AB002380 AF119898 AF180681 AK294803 AK304316
RefSeq transcript (Entrez)NM_001198665 NM_001301084 NM_015313
RefSeq genomic (Entrez)NC_000011 NC_018922 NG_027960 NT_033899 NW_004929381
Consensus coding sequences : CCDS (NCBI)ARHGEF12
Cluster EST : UnigeneHs.24598 [ NCBI ]
CGAP (NCI)Hs.24598
Alternative Splicing GalleryENSG00000196914
Gene ExpressionARHGEF12 [ NCBI-GEO ]   ARHGEF12 [ EBI - ARRAY_EXPRESS ]   ARHGEF12 [ SEEK ]   ARHGEF12 [ MEM ]
Gene Expression Viewer (FireBrowse)ARHGEF12 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23365
GTEX Portal (Tissue expression)ARHGEF12
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NZN5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NZN5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NZN5
Splice isoforms : SwissVarQ9NZN5
PhosPhoSitePlusQ9NZN5
Domaine pattern : Prosite (Expaxy)DH_1 (PS00741)    DH_2 (PS50010)    PDZ (PS50106)    PH_DOMAIN (PS50003)   
Domains : Interpro (EBI)DH-domain    GDS_CDC24_CS    PDZ    PH_dom-like    PH_domain    RGS    RGS-like_dom   
Domain families : Pfam (Sanger)PDZ (PF00595)    PH_13 (PF16652)    RGS-like (PF09128)    RhoGEF (PF00621)   
Domain families : Pfam (NCBI)pfam00595    pfam16652    pfam09128    pfam00621   
Domain families : Smart (EMBL)PDZ (SM00228)  PH (SM00233)  RhoGEF (SM00325)  
Conserved Domain (NCBI)ARHGEF12
DMDM Disease mutations23365
Blocks (Seattle)ARHGEF12
PDB (SRS)1TXD    1X86    2OMJ    2OS6   
PDB (PDBSum)1TXD    1X86    2OMJ    2OS6   
PDB (IMB)1TXD    1X86    2OMJ    2OS6   
PDB (RSDB)1TXD    1X86    2OMJ    2OS6   
Structural Biology KnowledgeBase1TXD    1X86    2OMJ    2OS6   
SCOP (Structural Classification of Proteins)1TXD    1X86    2OMJ    2OS6   
CATH (Classification of proteins structures)1TXD    1X86    2OMJ    2OS6   
SuperfamilyQ9NZN5
Human Protein AtlasENSG00000196914
Peptide AtlasQ9NZN5
HPRD09207
IPIIPI00022164   IPI00339353   IPI00383302   
Protein Interaction databases
DIP (DOE-UCLA)Q9NZN5
IntAct (EBI)Q9NZN5
FunCoupENSG00000196914
BioGRIDARHGEF12
STRING (EMBL)ARHGEF12
ZODIACARHGEF12
Ontologies - Pathways
QuickGOQ9NZN5
Ontology : AmiGOG-protein coupled receptor binding  guanyl-nucleotide exchange factor activity  Rho guanyl-nucleotide exchange factor activity  GTPase activator activity  protein binding  cytoplasm  cytosol  G-protein coupled receptor signaling pathway  membrane  regulation of Rho protein signal transduction  intracellular signal transduction  positive regulation of apoptotic process  positive regulation of GTPase activity  positive regulation of GTPase activity  regulation of small GTPase mediated signal transduction  extracellular exosome  
Ontology : EGO-EBIG-protein coupled receptor binding  guanyl-nucleotide exchange factor activity  Rho guanyl-nucleotide exchange factor activity  GTPase activator activity  protein binding  cytoplasm  cytosol  G-protein coupled receptor signaling pathway  membrane  regulation of Rho protein signal transduction  intracellular signal transduction  positive regulation of apoptotic process  positive regulation of GTPase activity  positive regulation of GTPase activity  regulation of small GTPase mediated signal transduction  extracellular exosome  
Pathways : KEGGVascular smooth muscle contraction    Axon guidance    Regulation of actin cytoskeleton    Tuberculosis    Proteoglycans in cancer   
REACTOMEQ9NZN5 [protein]
REACTOME Pathways193648 [pathway]   194840 [pathway]   416482 [pathway]   416572 [pathway]   
NDEx NetworkARHGEF12
Atlas of Cancer Signalling NetworkARHGEF12
Wikipedia pathwaysARHGEF12
Orthology - Evolution
OrthoDB23365
GeneTree (enSembl)ENSG00000196914
Phylogenetic Trees/Animal Genes : TreeFamARHGEF12
HOVERGENQ9NZN5
HOGENOMQ9NZN5
Homologs : HomoloGeneARHGEF12
Homology/Alignments : Family Browser (UCSC)ARHGEF12
Gene fusions - Rearrangements
Fusion : MitelmanARHGEF12/CNTN5 [11q23.3/11q22.1]  
Fusion : MitelmanARHGEF12/SIK3 [11q23.3/11q23.3]  [t(11;11)(q23;q23)]  
Fusion : MitelmanKCTD2/ARHGEF12 [17q25.1/11q23.3]  [t(11;17)(q23;q25)]  
Fusion : MitelmanSC5D/ARHGEF12 [11q23.3/11q23.3]  [t(11;11)(q23;q23)]  
Fusion : COSMICKMT2A [11q23.3]  -  ARHGEF12 [11q23.3]  [fusion_1846]  [fusion_1847]  
Fusion: TCGAARHGEF12 11q23.3 CNTN5 11q22.1 LUAD
Fusion: TCGAARHGEF12 11q23.3 SIK3 11q23.3 BRCA
Fusion: TCGASC5DL ARHGEF12 11q23.3 LUAD
Fusion : TICdbKMT2A [11q23.3]  -  ARHGEF12 [11q23.3]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerARHGEF12 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ARHGEF12
dbVarARHGEF12
ClinVarARHGEF12
1000_GenomesARHGEF12 
Exome Variant ServerARHGEF12
ExAC (Exome Aggregation Consortium)ARHGEF12 (select the gene name)
Genetic variants : HAPMAP23365
Genomic Variants (DGV)ARHGEF12 [DGVbeta]
DECIPHER (Syndromes)11:120207618-120360645  ENSG00000196914
CONAN: Copy Number AnalysisARHGEF12 
Mutations
ICGC Data PortalARHGEF12 
TCGA Data PortalARHGEF12 
Broad Tumor PortalARHGEF12
OASIS PortalARHGEF12 [ Somatic mutations - Copy number]
Cancer Gene: CensusARHGEF12 
Somatic Mutations in Cancer : COSMICARHGEF12  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDARHGEF12
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 ARHGEF12
DgiDB (Drug Gene Interaction Database)ARHGEF12
DoCM (Curated mutations)ARHGEF12 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ARHGEF12 (select a term)
intoGenARHGEF12
NCG5 (London)ARHGEF12
Cancer3DARHGEF12(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604763   
Orphanet
MedgenARHGEF12
Genetic Testing Registry ARHGEF12
NextProtQ9NZN5 [Medical]
TSGene23365
GENETestsARHGEF12
Huge Navigator ARHGEF12 [HugePedia]
snp3D : Map Gene to Disease23365
BioCentury BCIQARHGEF12
ClinGenARHGEF12
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23365
Chemical/Pharm GKB GenePA24969
Clinical trialARHGEF12
Miscellaneous
canSAR (ICR)ARHGEF12 (select the gene name)
Other databaseHUGE: A Database of Human Unidentified Gene-Encoded Large Proteins
Probes
Litterature
PubMed62 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineARHGEF12
EVEXARHGEF12
GoPubMedARHGEF12
iHOPARHGEF12
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:43:27 CET 2017

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jlhuret@AtlasGeneticsOncology.org.