CD58 CD58 molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD58provided by HGNC
Official Full Name: CD58 moleculeprovided by HGNC
Primary source: HGNC:HGNC:1688
See related: Ensembl:ENSG00000116815 MIM:153420; AllianceGenome:HGNC:1688
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: ag3; LFA3; LFA-3
Summary: This gene encodes a member of the immunoglobulin superfamily. The encoded protein is a ligand of the T lymphocyte CD2 protein, and functions in adhesion and activation of T lymphocytes. The protein is localized to the plasma membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]
Expression: Low expression observed in reference dataset See more
Orthologs: all
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Genomic context

Location:: 1p13.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (116514534..116571026, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (116524958..116581474, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (117057156..117113648, complement)

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?

From patient tissue correlates to molecular mechanisms of cancer immune evasion: the emerging role of CD58 and PD-L1 co-regulation via CMTM6.
Title: From patient tissue correlates to molecular mechanisms of cancer immune evasion: the emerging role of CD58 and PD-L1 co-regulation via CMTM6.
Association of CD58 rs12044852 and rs2300747 polymorphisms with the risk of multiple sclerosis: A systematic review and meta-analysis.
Title: Association of CD58 rs12044852 and rs2300747 polymorphisms with the risk of multiple sclerosis: A systematic review and meta-analysis.
rs10924104 in the expression enhancer motif of CD58 confers susceptibility to human autoimmune diseases.
Title: rs10924104 in the expression enhancer motif of CD58 confers susceptibility to human autoimmune diseases.
The CD2-CD58 axis: A novel marker predicting poor prognosis in patients with low-grade gliomas and potential therapeutic approaches.
Title: The CD2-CD58 axis: A novel marker predicting poor prognosis in patients with low-grade gliomas and potential therapeutic approaches.
CD58 acts as a tumor promotor in hepatocellular carcinoma via activating the AKT/GSK-3beta/beta-catenin pathway.
Title: CD58 acts as a tumor promotor in hepatocellular carcinoma via activating the AKT/GSK-3β/β-catenin pathway.
High Expression of CD58 and ALDH1A3 Predicts a Poor Prognosis in Basal-like Breast Cancer.
Title: High Expression of CD58 and ALDH1A3 Predicts a Poor Prognosis in Basal-like Breast Cancer.
Multidimensional single-cell analysis identifies a role for CD2-CD58 interactions in clinical antitumor T cell responses.
Title: Multidimensional single-cell analysis identifies a role for CD2-CD58 interactions in clinical antitumor T cell responses.
Higher Expression of WT1 With Lower CD58 Expression may be Biomarkers for Risk Stratification of Patients With Cytogenetically Normal Acute Myeloid Leukemia.
Title: Higher Expression of WT1 With Lower CD58 Expression may be Biomarkers for Risk Stratification of Patients With Cytogenetically Normal Acute Myeloid Leukemia.
CD58 Immunobiology at a Glance.
Title: CD58 Immunobiology at a Glance.
Rosetting T cells in Hodgkin lymphoma are activated by immunological synapse components HLA class II and CD58.
Title: Rosetting T cells in Hodgkin lymphoma are activated by immunological synapse components HLA class II and CD58.

Submit: New GeneRIF Correction See all GeneRIFs (54)

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
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data. 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
Envelope surface glycoprotein gp120	env	Molecular interactions of CD2 with LFA-3 and CD28 with B7-1 in conjunction with TCR occupancy prevent T cells from programmed apoptosis mediated by binding of CD4 to HIV-1 gp120, resulting in increased levels of IL-2 and IL-4 secretion from the T cells	PubMed
	env	Antibodies to LFA-3 block the early stages of HIV-1 infection by cell-free virus following HIV-1 gp120 binding to CD4	PubMed
Nef	nef	B lymphocytes exposed to supernatants from HIV-1 Nef-expressing macrophages have upregulated expression of receptors CD22, CD54, and CD58	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

AL033745 (e-PCR)
- UniSTS:93491

RH78061 (e-PCR)
- UniSTS:85069

D1S3454 (e-PCR)
- UniSTS:154706

D1S3262 (e-PCR)
- UniSTS:3453

PMC124986P3 (e-PCR)
- UniSTS:270479

SHGC-132861 (e-PCR)
- UniSTS:170929

AL010069 (e-PCR)
- UniSTS:24510

SHGC-53613 (e-PCR)
- UniSTS:50633

SHGC-106572 (e-PCR)
- UniSTS:169935

SHGC-75374 (e-PCR)
- UniSTS:54233

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell-cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in cellular response to tumor necrosis factor	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to type II interferon	IDA Inferred from Direct Assay more info	PubMed
involved_in heterotypic cell-cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interleukin-8 production	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in secretory granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: lymphocyte function-associated antigen 3

Names: CD58 antigen, (lymphocyte function-associated antigen 3); surface glycoprotein LFA-3

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_001144822.2 → NP_001138294.1 lymphocyte function-associated antigen 3 isoform 2

See identical proteins and their annotated locations for NP_001138294.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate segment in the 3' coding region compared to variant 1 that causes a frameshift. The resulting protein (isoform 2) has a distinct C-terminus, compared to isoform 1. This variant (2) also contains a unique 3' UTR compared to variant 1.

Source sequence(s)

AK291980

Consensus CDS

CCDS44199.1

UniProtKB/TrEMBL

B1AMW1

Related

ENSP00000409080.2, ENST00000457047.6

Conserved Domains (1) summary

cd05741
Location:39 → 120

Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
NM_001779.3 → NP_001770.1 lymphocyte function-associated antigen 3 isoform 1

See identical proteins and their annotated locations for NP_001770.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shortest transcript and encodes the longer isoform (1).

Source sequence(s)

AL355794, CA312671, Y00636

Consensus CDS

CCDS888.1

UniProtKB/Swiss-Prot

A8K7G5, P19256, Q5U053, Q6IB65, Q96KI9

UniProtKB/TrEMBL

B1AMW1

Related

ENSP00000358501.5, ENST00000369489.10

Conserved Domains (1) summary

cd05741
Location:39 → 120

Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins

RNA

NR_026665.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL355794, CD365881, X06296