Atlas of Genetics and Cytogenetics in Oncology and Haematology

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CD53 (CD53 molecule)

Written2007-12Pedro A Lazo
Instituto de Biologia Molecular y Celular del Cancer, CSIC-Universidad de Salamanca, campus Miguel de Unamuno, E-37007 Salamanca, Spain

(Note : for Links provided by Atlas : click)


Other namesTSPAN25
CD53 glycoprotein
CD53 tetraspan antigen
HGNC (Hugo) CD53
LocusID (NCBI) 963
Atlas_Id 983
Location 1p13.3  [Link to chromosome band 1p13]
Location_base_pair Starts at 111415722 and ends at 111442558 bp from pter ( according to hg19-Feb_2009)  [Mapping CD53.png]
Local_order Telomere-KCNA3--Q8NHC3---CD53---C1orf103---TMEM77---CEPT1---DENND2D-Centromere
  Map of chromosomal region 1p13.3
Fusion genes
(updated 2016)
HLCS (21q22.13) / CD53 (1p13.3)RBPMS (8p12) / CD53 (1p13.3)


  Exon-Intron structure of human CD53 gene.
Description Gene size: 26,77 Kbp; 8 exons.
Transcription Transcript length: 1,567 bps.


Note Size: 219 amino acids; 24341 Da; Four transmembrane domains.
Subcellular location: Plasma Membrane; endosomes.
  The CD53 protein has four transmembrane domains. Several residues are conserved and define the tetraspanin protein family. The protein is glycosylated (green) in its second extracellular loop. Internally the protein is palmitoylated (red lines). EC: extracellular.
Localisation Plasma membrane; endosomes; exoxomes.
Function Modifier of signal transduction.
Homology Member of the tetraspanin protein family.

Implicated in

Entity T-cell acute lymphoblastic leukemia
Cytogenetics t(1;22)(p13;q13)
Location of breakpoint in chromosome region 1p13.3 in a case of T-ALL with a t(1;22)(p13;q13). The CD53 gene is not structurally altered. It is not known if its level of expression is affected.
Abnormal Protein None


Aberrant expression of tetraspanin molecules in B-cell chronic lymphoproliferative disorders and its correlation with normal B-cell maturation.
Barrena S, Almeida J, Yunta M, López A, Fern´ndez-Mosteirí N, Giralt M, Romero M, Perdiguer L, Delgado M, Orfao A, Lazo PA
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2005 ; 19 (8) : 1376-1383.
PMID 15931266
Increased expression of the tetraspanins CD53 and CD63 on apoptotic human neutrophils.
Beinert T, Münzing S, Possinger K, Krombach F
Journal of leukocyte biology. 2000 ; 67 (3) : 369-373.
PMID 10733097
Interleukin-2 receptor beta chain locus rearrangement in a T-cell acute lymphoblastic leukemia.
Berger R, Bernard OA
Pathologie-biologie. 2007 ; 55 (1) : 56-58.
PMID 16697123
HindIII RFLP in the human CD53 gene on 1p13.
Gallego MI, Varas F, Lazo PA
Human molecular genetics. 1994 ; 3 (9) : page 1711.
PMID 7833942
The human CD53 gene, coding for a four transmembrane domain protein, maps to chromosomal region 1p13.
Gonzalez ME, Pardo-Manuel de Villena F, Fernandez-Ruiz E, Rodriguez de Cordoba S, Lazo PA
Genomics. 1993 ; 18 (3) : 725-728.
PMID 8307585
Tetraspanin functions and associated microdomains.
Hemler ME
Nature reviews. Molecular cell biology. 2005 ; 6 (10) : 801-811.
PMID 16314869
Differential cooperation between regulatory sequences required for human CD53 gene expression.
Hern´ndez-Torres J, Yunta M, Lazo PA
The Journal of biological chemistry. 2001 ; 276 (38) : 35405-35413.
PMID 11443129
Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray.
Higgins JP, Shinghal R, Gill H, Reese JH, Terris M, Cohen RJ, Fero M, Pollack JR, van de Rijn M, Brooks JD
The American journal of pathology. 2003 ; 162 (3) : 925-932.
PMID 12598325
Genomic structure of the human CD53 gene.
Korí V, Horejsí V
Immunogenetics. 1993 ; 38 (4) : 272-279.
PMID 8319976
Functional implications of tetraspanin proteins in cancer biology.
Lazo PA
Cancer science. 2007 ; 98 (11) : 1666-1677.
PMID 17727684
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.
Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas MK, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA
Proceedings of the National Academy of Sciences of the United States of America. 2005 ; 102 (16) : 5814-5819.
PMID 15827123
The CD53 and CEACAM-1 genes are genetic targets for early B cell factor.
Månsson R, Lagergren A, Hansson F, Smith E, Sigvardsson M
European journal of immunology. 2007 ; 37 (5) : 1365-1376.
PMID 17429843
Transmembrane-4 superfamily proteins CD81 (TAPA-1), CD82, CD63, and CD53 specifically associated with integrin alpha 4 beta 1 (CD49d/CD29).
Mannion BA, Berditchevski F, Kraeft SK, Chen LB, Hemler ME
Journal of immunology (Baltimore, Md. : 1950). 1996 ; 157 (5) : 2039-2047.
PMID 8757325
Recurrent infectious diseases in human CD53 deficiency.
Mollinedo F, Font´n G, Barasoain I, Lazo PA
Clinical and diagnostic laboratory immunology. 1997 ; 4 (2) : 229-231.
PMID 9067662
Gamma-glutamyl transpeptidase, an ecto-enzyme regulator of intracellular redox potential, is a component of TM4 signal transduction complexes.
Nichols TC, Guthridge JM, Karp DR, Molina H, Fletcher DR, Holers VM
European journal of immunology. 1998 ; 28 (12) : 4123-4129.
PMID 9862348
CD53, a protein with four membrane-spanning domains, mediates signal transduction in human monocytes and B cells.
Olweus J, Lund-Johansen F, Horejsi V
Journal of immunology (Baltimore, Md. : 1950). 1993 ; 151 (2) : 707-716.
PMID 8335905
Cross-linking of CD53 promotes activation of resting human B lymphocytes.
Rasmussen AM, Blomhoff HK, Stokke T, Horejsi V, Smeland EB
Journal of immunology (Baltimore, Md. : 1950). 1994 ; 153 (11) : 4997-5007.
PMID 7963560
Supramolecular complexes of MHC class I, MHC class II, CD20, and tetraspan molecules (CD53, CD81, and CD82) at the surface of a B cell line JY.
Szölló J, Horejsí V, Bene L, Angelisov´ P, Damjanovich S
Journal of immunology (Baltimore, Md. : 1950). 1996 ; 157 (7) : 2939-2946.
PMID 8816400
Chromosomal localization of the Ox-44 (CD53) leukocyte antigen gene in man and rodents.
Taguchi T, Bellacosa A, Zhou JY, Gilbert DJ, Lazo PA, Copeland NG, Jenkins NA, Tsichlis PN, Testa JR
Cytogenetics and cell genetics. 1993 ; 64 (3-4) : 217-221.
PMID 8404042
Determination of stromal signatures in breast carcinoma.
West RB, Nuyten DS, Subramanian S, Nielsen TO, Corless CL, Rubin BP, Montgomery K, Zhu S, Patel R, Hernandez-Boussard T, Goldblum JR, Brown PO, van de Vijver M, van de Rijn M
PLoS biology. 2005 ; 3 (6) : page e187.
PMID 15869330
Apoptosis protection and survival signal by the CD53 tetraspanin antigen.
Yunta M, Lazo PA
Oncogene. 2003 ; 22 (8) : 1219-1224.
PMID 12606948


This paper should be referenced as such :
Lazo, PA
CD53 (CD53 molecule)
Atlas Genet Cytogenet Oncol Haematol. 2008;12(4):303-305.
Free journal version : [ pdf ]   [ DOI ]
On line version :

External links

HGNC (Hugo)CD53   1686
Entrez_Gene (NCBI)CD53  963  CD53 molecule
AliasesMOX44; TSPAN25
GeneCards (Weizmann)CD53
Ensembl hg19 (Hinxton)ENSG00000143119 [Gene_View]  chr1:111415722-111442558 [Contig_View]  CD53 [Vega]
Ensembl hg38 (Hinxton)ENSG00000143119 [Gene_View]  chr1:111415722-111442558 [Contig_View]  CD53 [Vega]
ICGC DataPortalENSG00000143119
TCGA cBioPortalCD53
AceView (NCBI)CD53
Genatlas (Paris)CD53
SOURCE (Princeton)CD53
Genetics Home Reference (NIH)CD53
Genomic and cartography
GoldenPath hg19 (UCSC)CD53  -     chr1:111415722-111442558 +  1p13   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CD53  -     1p13   [Description]    (hg38-Dec_2013)
EnsemblCD53 - 1p13 [CytoView hg19]  CD53 - 1p13 [CytoView hg38]
Mapping of homologs : NCBICD53 [Mapview hg19]  CD53 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK298723 AK313582 BC035456 BC040693 BG536920
RefSeq transcript (Entrez)NM_000560 NM_001040033 NM_001320638
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_032977 NW_004929290
Consensus coding sequences : CCDS (NCBI)CD53
Cluster EST : UnigeneHs.443057 [ NCBI ]
CGAP (NCI)Hs.443057
Alternative Splicing GalleryENSG00000143119
Gene ExpressionCD53 [ NCBI-GEO ]   CD53 [ EBI - ARRAY_EXPRESS ]   CD53 [ SEEK ]   CD53 [ MEM ]
Gene Expression Viewer (FireBrowse)CD53 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)963
GTEX Portal (Tissue expression)CD53
Protein : pattern, domain, 3D structure
UniProt/SwissProtP19397 (Uniprot)
NextProtP19397  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP19397
Splice isoforms : SwissVarP19397 (Swissvar)
Domaine pattern : Prosite (Expaxy)TM4_1 (PS00421)   
Domains : Interpro (EBI)Tetraspanin    Tetraspanin/Peripherin    Tetraspanin_CS    Tetraspanin_EC2   
Domain families : Pfam (Sanger)Tetraspannin (PF00335)   
Domain families : Pfam (NCBI)pfam00335   
DMDM Disease mutations963
Blocks (Seattle)CD53
Human Protein AtlasENSG00000143119
Peptide AtlasP19397
IPIIPI00018307   IPI00909520   
Protein Interaction databases
IntAct (EBI)P19397
Ontologies - Pathways
Ontology : AmiGOimmunological synapse  protein binding  plasma membrane  integral component of plasma membrane  cell-cell junction  signal transduction  cell surface receptor signaling pathway  cell surface  extracellular exosome  positive regulation of myoblast fusion  
Ontology : EGO-EBIimmunological synapse  protein binding  plasma membrane  integral component of plasma membrane  cell-cell junction  signal transduction  cell surface receptor signaling pathway  cell surface  extracellular exosome  positive regulation of myoblast fusion  
NDEx NetworkCD53
Atlas of Cancer Signalling NetworkCD53
Wikipedia pathwaysCD53
Orthology - Evolution
GeneTree (enSembl)ENSG00000143119
Phylogenetic Trees/Animal Genes : TreeFamCD53
Homologs : HomoloGeneCD53
Homology/Alignments : Family Browser (UCSC)CD53
Gene fusions - Rearrangements
Fusion : MitelmanHLCS/CD53 [21q22.13/1p13.3]  [t(1;21)(p13;q22)]  
Fusion: TCGAHLCS 21q22.13 CD53 1p13.3 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCD53 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CD53
Exome Variant ServerCD53
ExAC (Exome Aggregation Consortium)CD53 (select the gene name)
Genetic variants : HAPMAP963
Genomic Variants (DGV)CD53 [DGVbeta]
DECIPHER (Syndromes)1:111415722-111442558  ENSG00000143119
CONAN: Copy Number AnalysisCD53 
ICGC Data PortalCD53 
TCGA Data PortalCD53 
Broad Tumor PortalCD53
OASIS PortalCD53 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCD53 
Mutations and Diseases : HGMDCD53
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 CD53
DgiDB (Drug Gene Interaction Database)CD53
DoCM (Curated mutations)CD53 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CD53 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry CD53
NextProtP19397 [Medical]
Huge Navigator CD53 [HugePedia]
snp3D : Map Gene to Disease963
BioCentury BCIQCD53
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD963
Chemical/Pharm GKB GenePA26225
Clinical trialCD53
canSAR (ICR)CD53 (select the gene name)
PubMed42 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 10 11:35:09 CEST 2016

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