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ACKR3 (atypical chemokine receptor 3)

Written2004-11Karin Broberg
Molecular biologist, Dep. of Occupational, Environmental Medicine, Lund University Hospital, SE-221 85 Lund, Sweden

(Note : for Links provided by Atlas : click)

Identity

Alias_namesCMKOR1
CXCR7
chemokine orphan receptor 1
chemokine (C-X-C motif) receptor 7
Alias_symbol (synonym)RDC1
GPR159
Other aliasCXCR7 (chemokine (C-X-C motif) receptor 7)
GPRN159
G protein-coupled receptor
G protein-coupled receptor RDC1 homolog
HGNC (Hugo) ACKR3
LocusID (NCBI) 57007
Atlas_Id 40108
Location 2q37.3  [Link to chromosome band 2q37]
Location_base_pair Starts at 236569737 and ends at 236582351 bp from pter ( according to hg19-Feb_2009)  [Mapping ACKR3.png]
Local_order Telomeric to IQCA
Centromeric to COPS8
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ACKR3 (2q37.3) / HMGA2 (12q14.3)CSGALNACT2 (10q11.21) / ACKR3 (2q37.3)HMGA2 (12q14.3) / ACKR3 (2q37.3)
ROBO1 (3p12.3) / ACKR3 (2q37.3)STAT4 (2q32.2) / ACKR3 (2q37.3)STAU2 (8q21.11) / ACKR3 (2q37.3)
Note RDC1 was originally thought to be the receptor for VIP.

DNA/RNA

Description The genomic size has been estimated to approximately 12.5-13.5 kb. RDC1 has previously been reported to contain only one exon of 1,09 kbp. However, the finding of a RDC1 transcript corresponding to four different regions with exon/intron boundaries in the BAC 514f21 suggests a more complex gene structure. The predicted amino acid sequence of exon 3 and 4 does not show any homology to the protein databases and, since they both contribute with stop codons, it could be questioned whether these sequences represent exons, or are part of an alternatively spliced 3' untranslated region of the gene.
Pseudogene None

Protein

Description 362 amino acids; 41522 Da
Expression RDC1 is expressed in embryological, juvenile as well as adult tissues. Expression has been reported in e.g. bladder, spleen, heart, skeletal muscle, peripheral nervous system and placenta.
Localisation Integral membrane protein
Function Orphan receptor, but its endogenous ligand has not yet been identified. The protein is also a coreceptor for human immunodeficiency viruses (HIV). RDC1 belongs to a family of G-protein coupled receptors, which includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide (G) binding proteins.
Homology RDC1 displays homology to other members of the large family of G-protein coupled receptors.

Mutations

Germinal Single nucleotide polymorphisms
Somatic Translocations involving RDC1 and HMGA2 has been reported in three lipomas (see below).

Implicated in

Note
  
Entity Lipoma,
Disease Benign adipocyte tumor
Prognosis Good
Cytogenetics Translocations involving 2q35-37 and 12q13-15 have been reported in six lipomas
Hybrid/Mutated Gene Fusion between RDC1 and HMGA2 has been reported in three lipomas with rearrangement involving 2q35-37 and 12q13-15. The breakpoint occurred after the third exon of HMGA2, the most common breakpoint of this gene, and in a previously unknown 3' part of the RDC1 gene. The RDC1 part of the fusion was over 300 bp.
Abnormal Protein The functional impact of this fusion is most likely a truncation of HMGA2, since the RDC1 part contributes with a stop codon one amino acid downstream of the breakpoint.
Oncogenesis Not yet established
  
  
Entity Tenosynovial giant cell tumours
Disease Benign tumor of synovium and tendon sheath
Prognosis Good
Cytogenetics Translocations involving 1p11-13 and 2q35-37 have been reported in eight cases of tenosynovial giant cell tumours.
Hybrid/Mutated Gene Four out of seven cases of tenosynovial giant cell tumours with aberrations of 2q35-37 had breakpoints in a BAC probe 260J21 (BACPAC, Oakland), which contains the RDC1 gene.
  

Bibliography

Fusion of RDC1 with HMGA2 in lipomas as the result of chromosome aberrations involving 2q35-37 and 12q13-15.
Broberg K, Zhang M, Strömbeck B, Isaksson M, Nilsson M, Mertens F, Mandahl N, Panagopoulos I
International journal of oncology. 2002 ; 21 (2) : 321-326.
PMID 12118328
 
Vascular gene expression in nonneoplastic and malignant brain.
Madden SL, Cook BP, Nacht M, Weber WD, Callahan MR, Jiang Y, Dufault MR, Zhang X, Zhang W, Walter-Yohrling J, Rouleau C, Akmaev VR, Wang CJ, Cao X, St Martin TB, Roberts BL, Teicher BA, Klinger KW, Stan RV, Lucey B, Carson-Walter EB, Laterra J, Walter KA
The American journal of pathology. 2004 ; 165 (2) : 601-608.
PMID 15277233
 
RDC1 may not be VIP receptor.
Nagata S, Ishihara T, Robberecht P, Libert F, Parmentier M, Christophe J, Vassart G
Trends in pharmacological sciences. 1992 ; 13 (3) : 102-103.
PMID 1315461
 
Molecular cytogenetic mapping of recurrent chromosomal breakpoints in tenosynovial giant cell tumors.
Nilsson M, Höglund M, Panagopoulos I, Sciot R, Dal Cin P, Debiec-Rychter M, Mertens F, Mandahl N
Virchows Archiv : an international journal of pathology. 2002 ; 441 (5) : 475-480.
PMID 12447678
 
A putative G protein-coupled receptor, RDC1, is a novel coreceptor for human and simian immunodeficiency viruses.
Shimizu N, Soda Y, Kanbe K, Liu HY, Mukai R, Kitamura T, Hoshino H
Journal of virology. 2000 ; 74 (2) : 619-626.
PMID 10623723
 
Cloning and expression of the human vasoactive intestinal peptide receptor.
Sreedharan SP, Robichon A, Peterson KE, Goetzl EJ
Proceedings of the National Academy of Sciences of the United States of America. 1991 ; 88 (11) : 4986-4990.
PMID 1675791
 

Citation

This paper should be referenced as such :
Broberg, K
CMKOR1 (chemokine orphan receptor 1)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(1):1-2.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CMKOR1ID40108ch2q37.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  Soft Tissues: Lipoma / benign lipomatous tumors
Soft Tissues: Ordinary lipoma with t(1;12)(p32;q14) HMGA2/PPAP2B
Soft tissue tumors: an overview


External links

Nomenclature
HGNC (Hugo)ACKR3   23692
Cards
AtlasCMKOR1ID40108ch2q37
Entrez_Gene (NCBI)ACKR3  57007  atypical chemokine receptor 3
AliasesCMKOR1; CXC-R7; CXCR-7; CXCR7; 
GPR159; RDC-1; RDC1
GeneCards (Weizmann)ACKR3
Ensembl hg19 (Hinxton)ENSG00000144476 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000144476 [Gene_View]  chr2:236569737-236582351 [Contig_View]  ACKR3 [Vega]
ICGC DataPortalENSG00000144476
TCGA cBioPortalACKR3
AceView (NCBI)ACKR3
Genatlas (Paris)ACKR3
WikiGenes57007
SOURCE (Princeton)ACKR3
Genetics Home Reference (NIH)ACKR3
Genomic and cartography
GoldenPath hg38 (UCSC)ACKR3  -     chr2:236569737-236582351 +  2q37.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)ACKR3  -     2q37.3   [Description]    (hg19-Feb_2009)
EnsemblACKR3 - 2q37.3 [CytoView hg19]  ACKR3 - 2q37.3 [CytoView hg38]
Mapping of homologs : NCBIACKR3 [Mapview hg19]  ACKR3 [Mapview hg38]
OMIM610376   
Gene and transcription
Genbank (Entrez)AF030297 AK291659 BC008459 BC036661 BM925428
RefSeq transcript (Entrez)NM_001047841 NM_020311
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)ACKR3
Cluster EST : UnigeneHs.471751 [ NCBI ]
CGAP (NCI)Hs.471751
Alternative Splicing GalleryENSG00000144476
Gene ExpressionACKR3 [ NCBI-GEO ]   ACKR3 [ EBI - ARRAY_EXPRESS ]   ACKR3 [ SEEK ]   ACKR3 [ MEM ]
Gene Expression Viewer (FireBrowse)ACKR3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)57007
GTEX Portal (Tissue expression)ACKR3
Human Protein AtlasENSG00000144476-ACKR3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP25106   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP25106  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP25106
Splice isoforms : SwissVarP25106
PhosPhoSitePlusP25106
Domaine pattern : Prosite (Expaxy)G_PROTEIN_RECEP_F1_1 (PS00237)    G_PROTEIN_RECEP_F1_2 (PS50262)   
Domains : Interpro (EBI)ACKR3    GPCR_Rhodpsn    GPCR_Rhodpsn_7TM   
Domain families : Pfam (Sanger)7tm_1 (PF00001)   
Domain families : Pfam (NCBI)pfam00001   
Conserved Domain (NCBI)ACKR3
DMDM Disease mutations57007
Blocks (Seattle)ACKR3
SuperfamilyP25106
Human Protein Atlas [tissue]ENSG00000144476-ACKR3 [tissue]
Peptide AtlasP25106
HPRD09882
IPIIPI00012733   IPI00917980   
Protein Interaction databases
DIP (DOE-UCLA)P25106
IntAct (EBI)P25106
FunCoupENSG00000144476
BioGRIDACKR3
STRING (EMBL)ACKR3
ZODIACACKR3
Ontologies - Pathways
QuickGOP25106
Ontology : AmiGOangiogenesis  vasculogenesis  scavenger receptor activity  protein binding  nucleus  endosome  early endosome  plasma membrane  plasma membrane  clathrin-coated pit  chemotaxis  cell adhesion  G-protein coupled receptor signaling pathway  cell surface  coreceptor activity  integral component of membrane  viral process  C-X-C chemokine receptor activity  C-X-C chemokine binding  receptor internalization  intracellular membrane-bounded organelle  perinuclear region of cytoplasm  recycling endosome  chemokine-mediated signaling pathway  positive regulation of ERK1 and ERK2 cascade  negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage  positive regulation of mesenchymal stem cell migration  
Ontology : EGO-EBIangiogenesis  vasculogenesis  scavenger receptor activity  protein binding  nucleus  endosome  early endosome  plasma membrane  plasma membrane  clathrin-coated pit  chemotaxis  cell adhesion  G-protein coupled receptor signaling pathway  cell surface  coreceptor activity  integral component of membrane  viral process  C-X-C chemokine receptor activity  C-X-C chemokine binding  receptor internalization  intracellular membrane-bounded organelle  perinuclear region of cytoplasm  recycling endosome  chemokine-mediated signaling pathway  positive regulation of ERK1 and ERK2 cascade  negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage  positive regulation of mesenchymal stem cell migration  
Pathways : KEGGCytokine-cytokine receptor interaction   
REACTOMEP25106 [protein]
REACTOME PathwaysR-HSA-418594 [pathway]   
NDEx NetworkACKR3
Atlas of Cancer Signalling NetworkACKR3
Wikipedia pathwaysACKR3
Orthology - Evolution
OrthoDB57007
GeneTree (enSembl)ENSG00000144476
Phylogenetic Trees/Animal Genes : TreeFamACKR3
HOVERGENP25106
HOGENOMP25106
Homologs : HomoloGeneACKR3
Homology/Alignments : Family Browser (UCSC)ACKR3
Gene fusions - Rearrangements
Fusion : MitelmanHMGA2/ACKR3 [12q14.3/2q37.3]  [t(2;12)(q37;q14)]  [t(3;12)(q28;q14)]  
Fusion : MitelmanSTAT4/ACKR3 [2q32.2/2q37.3]  [t(2;2)(q32;q37)]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerACKR3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ACKR3
dbVarACKR3
ClinVarACKR3
1000_GenomesACKR3 
Exome Variant ServerACKR3
ExAC (Exome Aggregation Consortium)ENSG00000144476
GNOMAD BrowserENSG00000144476
Genetic variants : HAPMAP57007
Genomic Variants (DGV)ACKR3 [DGVbeta]
DECIPHERACKR3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisACKR3 
Mutations
ICGC Data PortalACKR3 
TCGA Data PortalACKR3 
Broad Tumor PortalACKR3
OASIS PortalACKR3 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDACKR3
BioMutasearch ACKR3
DgiDB (Drug Gene Interaction Database)ACKR3
DoCM (Curated mutations)ACKR3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ACKR3 (select a term)
intoGenACKR3
NCG5 (London)ACKR3
Cancer3DACKR3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610376   
Orphanet
MedgenACKR3
Genetic Testing Registry ACKR3
NextProtP25106 [Medical]
TSGene57007
GENETestsACKR3
Target ValidationACKR3
Huge Navigator ACKR3 [HugePedia]
snp3D : Map Gene to Disease57007
BioCentury BCIQACKR3
ClinGenACKR3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD57007
Chemical/Pharm GKB GenePA162383053
Clinical trialACKR3
Miscellaneous
canSAR (ICR)ACKR3 (select the gene name)
Probes
Litterature
PubMed167 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineACKR3
EVEXACKR3
GoPubMedACKR3
iHOPACKR3
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 : Thu Oct 12 16:19:16 CEST 2017

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