CD53 CD53 molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD53provided by HGNC
Official Full Name: CD53 moleculeprovided by HGNC
Primary source: HGNC:HGNC:1686
See related: Ensembl:ENSG00000143119 MIM:151525; AllianceGenome:HGNC:1686
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MOX44; TSPAN25
Summary: The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. It contributes to the transduction of CD2-generated signals in T cells and natural killer cells and has been suggested to play a role in growth regulation. Familial deficiency of this gene has been linked to an immunodeficiency associated with recurrent infectious diseases caused by bacteria, fungi and viruses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Expression: Biased expression in lymph node (RPKM 181.8), appendix (RPKM 156.6) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (110871210..110899922)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (110885966..110914720)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (111413832..111442544)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Open conformation of tetraspanins shapes interaction partner networks on cell membranes.
Title: Open conformation of tetraspanins shapes interaction partner networks on cell membranes.
Tetraspanin CD53: an overlooked regulator of immune cell function.
Title: Tetraspanin CD53: an overlooked regulator of immune cell function.
Eight SNPs of CD53 were found to be associated with tuberculosis case.
Title: Association between CD53 genetic polymorphisms and tuberculosis cases.
In this study, significant and lineage-dependent association of CD53 locus with Tuberculosis (TB) onset was identified from the pathogen lineage-based genome-wide association study (GWAS).
Title: Pathogen lineage-based genome-wide association study identified CD53 as susceptible locus in tuberculosis.
CD53 is associated with population asthma risk via the functional promoter polymorphism -1560 C>T.
Title: CD53, a suppressor of inflammatory cytokine production, is associated with population asthma risk via the functional promoter polymorphism -1560 C>T.
SNP rs6679497 in gene CD53 showed significant association with TNFalpha levels (P=0.001); no association of this SNP was observed with osteoarthritis
Title: A genome-wide linkage scan reveals CD53 as an important regulator of innate TNF-alpha levels.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
Ligation of CD53 triggers a survival response and reduces the number of cells that enter apoptosis. The CD53 antigen interactions might contribute to cell survival in poorly vascularized regions of the tumor mass.
Title: Apoptosis protection and survival signal by the CD53 tetraspanin antigen.
Analysis of lymphocyte subsets showed that the total number of CD3+, CD4+, CD8+ and CD56+ lymphocytes increased after the intensive protocol before falling below pre-exercise values at 1 h post-exercise.
Title: The effects of intensive, moderate and downhill treadmill running on human blood lymphocytes expressing the adhesion/activation molecules CD54 (ICAM-1), CD18 (beta2 integrin) and CD53.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Human CD53 is relocalized from plasma membrane to a perinuclear area in the presence of HIV-1 Nef	PubMed
	nef	Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD53 (TSPAN25)	PubMed
Vpu	vpu	Human CD53 is relocalized from plasma membrane to a perinuclear area in the presence of HIV-1 Vpu	PubMed
	vpu	Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD53 (TSPAN25)	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S2090 (e-PCR)
- UniSTS:62744

RH69138 (e-PCR)
- UniSTS:10526

D1S2809 (e-PCR), detects polymorphism
- UniSTS:26167

D1S3453 (e-PCR)
- UniSTS:154705

RH102009 (e-PCR)
- UniSTS:96343

SHGC-12404 (e-PCR)
- UniSTS:8810

RH67893 (e-PCR)
- UniSTS:91242

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-membrane adaptor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of myoblast fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in receptor clustering	IDA Inferred from Direct Assay more info	PubMed
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cell-cell junction	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
located_in immunological synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in specific granule membrane	TAS Traceable Author Statement more info
located_in synapse	IEA Inferred from Electronic Annotation more info
located_in tertiary granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: leukocyte surface antigen CD53

Names: CD53 antigen; CD53 glycoprotein; CD53 tetraspan antigen; antigen MOX44 identified by monoclonal antibody MRC-OX44; cell surface antigen; cell surface glycoprotein CD53; tetraspanin-25; transmembrane glycoprotein; tspan-25

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_000560.4 → NP_000551.1 leukocyte surface antigen CD53 isoform 1

See identical proteins and their annotated locations for NP_000551.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

AL391064, BC040693, BG536920

Consensus CDS

CCDS829.1

UniProtKB/Swiss-Prot

B2R905, P19397, Q5U0D6

Related

ENSP00000271324.5, ENST00000271324.6

Conserved Domains (2) summary

cd03164
Location:104 → 186

CD53_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model ...

pfam00335
Location:9 → 206

Tetraspannin; Tetraspanin family
NM_001040033.2 → NP_001035122.1 leukocyte surface antigen CD53 isoform 1

See identical proteins and their annotated locations for NP_001035122.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AL391064, BC035456, CA453414

Consensus CDS

CCDS829.1

UniProtKB/Swiss-Prot

B2R905, P19397, Q5U0D6

Related

ENSP00000497382.1, ENST00000648608.1

Conserved Domains (2) summary

cd03164
Location:104 → 186

CD53_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model ...

pfam00335
Location:9 → 206

Tetraspannin; Tetraspanin family
NM_001320638.2 → NP_001307567.1 leukocyte surface antigen CD53 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AK298723, AL354713, AL391064

UniProtKB/TrEMBL

B4DQB5

Conserved Domains (2) summary

pfam00335
Location:9 → 110

Tetraspannin; Tetraspanin family

cl02781
Location:106 → 127

tetraspanin_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the ...