CD58 Gene (Protein Coding)

CD58 Molecule

GC01M116514
GIFtS:
41
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] See more...

Aliases for CD58 Gene

Aliases for CD58 Gene

  • CD58 Molecule 2 3 5
  • CD58 Antigen, (Lymphocyte Function-Associated Antigen 3) 2 3
  • Lymphocyte Function-Associated Antigen 3 3 4
  • Surface Glycoprotein LFA-3 3 4
  • LFA3 3 4
  • Ag3 3 4
  • CD58 Antigen 4
  • LFA-3 3
  • CD58 5

External Ids for CD58 Gene

Previous HGNC Symbols for CD58 Gene

  • LFA3

Previous GeneCards Identifiers for CD58 Gene

  • GC01M117560
  • GC01M115939
  • GC01M116204
  • GC01M116403
  • GC01M116758
  • GC01M116858
  • GC01M117059
  • GC01M114916

Summaries for CD58 Gene

Entrez Gene Summary for CD58 Gene

  • 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]

GeneCards Summary for CD58 Gene

CD58 (CD58 Molecule) is a Protein Coding gene. Diseases associated with CD58 include Oral Lichen Planus and Paroxysmal Nocturnal Hemoglobinuria. Among its related pathways are Cell surface interactions at the vascular wall and Response to elevated platelet cytosolic Ca2+. Gene Ontology (GO) annotations related to this gene include signaling receptor binding.

UniProtKB/Swiss-Prot Summary for CD58 Gene

  • Ligand of the T-lymphocyte CD2 glycoprotein. This interaction is important in mediating thymocyte interactions with thymic epithelial cells, antigen-independent and -dependent interactions of T-lymphocytes with target cells and antigen-presenting cells and the T-lymphocyte rosetting with erythrocytes. In addition, the LFA-3/CD2 interaction may prime response by both the CD2+ and LFA-3+ cells.

Additional gene information for CD58 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CD58 Gene

Genomics for CD58 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CD58 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CD58 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CD58

Top Transcription factor binding sites by QIAGEN in the CD58 gene promoter:
  • CREB
  • deltaCREB
  • ER-alpha
  • Ik-2
  • IRF-2
  • Lmo2
  • LyF-1
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for CD58 Gene

Latest Assembly
chr1:116,500,390-116,571,039
(GRCh38/hg38)
Size:
70,650 bases
Orientation:
Minus strand

Previous Assembly
chr1:117,057,156-117,113,648
(GRCh37/hg19 by Entrez Gene)
Size:
56,493 bases
Orientation:
Minus strand

chr1:117,057,157-117,113,661
(GRCh37/hg19 by Ensembl)
Size:
56,505 bases
Orientation:
Minus strand

Genomic View for CD58 Gene

Genes around CD58 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD58 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD58 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CD58 Gene

Proteins for CD58 Gene

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  3. Assay products for research

  • Protein details for CD58 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P19256-LFA3_HUMAN
    Recommended name:
    Lymphocyte function-associated antigen 3
    Protein Accession:
    P19256
    Secondary Accessions:
    • A8K7G5
    • Q5U053
    • Q6IB65
    • Q96KI9

    Protein attributes for CD58 Gene

    Size:
    250 amino acids
    Molecular mass:
    28147 Da
    Quaternary structure:
    • Interacts with CD2 (PubMed:10380930, PubMed:3309127). Interacts with CMTM6 (PubMed:28813417).
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Three dimensional structures from OCA and Proteopedia for CD58 Gene

    Alternative splice isoforms for CD58 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CD58 Gene

Protein Expression for CD58 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CD58 Gene

  • Glycosylation at Asn40, Asn94, Asn109, Asn135, Asn169, and Asn195
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for CD58 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CD58 Gene

Domains & Families for CD58 Gene

Gene Families for CD58 Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Predicted membrane proteins

Protein Domains for CD58 Gene

InterPro:
Blocks:
  • Immunoglobulin subtype
ProtoNet:

Suggested Antigen Peptide Sequences for CD58 Gene

GenScript: Design optimal peptide antigens:
  • Surface glycoprotein LFA-3 (LFA3_HUMAN)
  • CD58 protein (Q9BRW0_HUMAN)
genes like me logo Genes that share domains with CD58: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CD58 Gene

Function for CD58 Gene

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  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for CD58 Gene

UniProtKB/Swiss-Prot Function:
Ligand of the T-lymphocyte CD2 glycoprotein. This interaction is important in mediating thymocyte interactions with thymic epithelial cells, antigen-independent and -dependent interactions of T-lymphocytes with target cells and antigen-presenting cells and the T-lymphocyte rosetting with erythrocytes. In addition, the LFA-3/CD2 interaction may prime response by both the CD2+ and LFA-3+ cells.
GENATLAS Biochemistry:
cell differentiation antigen CD58 (LFA-3),40-65kDa,identified by monoclonal antibodies G26,BRIC5,TS2/9,Ig superfamily,T cell restricted CD2 ligand

Phenotypes From GWAS Catalog for CD58 Gene

Gene Ontology (GO) - Molecular Function for CD58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IPI 17344209
GO:0005515 protein binding IPI 7544493
genes like me logo Genes that share ontologies with CD58: view
genes like me logo Genes that share phenotypes with CD58: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CD58

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CD58 Gene

Localization for CD58 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD58 Gene

[Isoform 1]: Cell membrane. Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CD58 gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 2
nucleus 2
cytosol 2
lysosome 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CD58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane NAS 7544493
GO:0009986 cell surface IBA,IDA 15345303
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CD58: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CD58 Gene

Pathways & Interactions for CD58 Gene

genes like me logo Genes that share pathways with CD58: view

Gene Ontology (GO) - Biological Process for CD58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032757 positive regulation of interleukin-8 production IMP 19109405
GO:0034113 heterotypic cell-cell adhesion IDA 15345303
GO:0043312 neutrophil degranulation TAS --
GO:0050900 leukocyte migration TAS --
GO:0071346 cellular response to interferon-gamma IDA 19109405
genes like me logo Genes that share ontologies with CD58: view

No data available for SIGNOR curated interactions for CD58 Gene

Drugs & Compounds for CD58 Gene

Products:

  1. Drug products for research

(11) Drugs for CD58 Gene - From: PharmGKB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Interferon beta-1a Approved, Investigational Pharma 229
Interferon beta-1b Approved Pharma 100

(7) Additional Compounds for CD58 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CD58: view

Transcripts for CD58 Gene

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mRNA/cDNA for CD58 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CD58

Alternative Splicing Database (ASD) splice patterns (SP) for CD58 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6
SP1: -
SP2: - -
SP3:
SP4: - - -

Relevant External Links for CD58 Gene

GeneLoc Exon Structure for
CD58

Expression for CD58 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CD58 Gene

mRNA expression in normal human tissues for CD58 Gene
mRNA expression by BioGPS for CD58 GenemRNA expression by GTEx for CD58 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD58 Gene

This gene is overexpressed in Whole Blood (x4.9).

Protein differential expression in normal tissues from HIPED for CD58 Gene

This gene is overexpressed in Bone marrow stromal cell (32.1) and Serum (12.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CD58 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CD58

SOURCE GeneReport for Unigene cluster for CD58 Gene:

Hs.34341

Evidence on tissue expression from TISSUES for CD58 Gene

  • Blood(4.6)
  • Intestine(4.5)
  • Bone marrow(2.8)
  • Lymph node(2.8)
  • Spleen(2.8)
  • Heart(2.5)
  • Skin(2.4)
  • Kidney(2.2)
  • Lung(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with CD58: view

Primer products for research

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CD58 Gene

Orthologs for CD58 Gene

This gene was present in the common ancestor of mammals.

Orthologs for CD58 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CD58 30 31
  • 98.4 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CD58 30 31
  • 66.19 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CD58 31
  • 49 (a)
 OneToOne
Species where no ortholog for CD58 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for CD58 Gene

ENSEMBL:
Gene Tree for CD58 (if available)
TreeFam:
Gene Tree for CD58 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CD58: view image

Paralogs for CD58 Gene

No data available for Paralogs for CD58 Gene

Variants for CD58 Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CD58 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs17426456 - p.Ser15Gly

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CD58 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CD58 Gene

Variant ID Type Subtype PubMed ID
esv1003883 CNV deletion 20482838
esv2209199 CNV deletion 18987734
esv2512482 CNV deletion 19546169
esv2663968 CNV deletion 23128226
esv2716607 CNV deletion 23290073
esv3303707 CNV mobile element insertion 20981092
esv3433 CNV loss 18987735
esv3434570 CNV insertion 20981092
esv3539978 CNV deletion 23714750
esv7455 CNV loss 19470904

Variation tolerance for CD58 Gene

Residual Variation Intolerance Score: 72.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.93; 35.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CD58 Gene

Human Gene Mutation Database (HGMD)
CD58
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD58

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD58 Gene

Disorders for CD58 Gene

MalaCards: The human disease database

(11) MalaCards diseases for CD58 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
oral lichen planus
  • oral lichenoid lesions
paroxysmal nocturnal hemoglobinuria
  • marchiafava-micheli disease
psoriatic arthritis
  • psoriatic arthritis, susceptibility to
actinic prurigo
  • polymorphic light eruption, hereditary; hple
hemoglobinuria
- elite association - COSMIC cancer census association via MalaCards
Search CD58 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CD58

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CD58: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CD58 Gene

Publications for CD58 Gene

  1. Gene structure, promoter characterization, and basis for alternative mRNA splicing of the human CD58 gene. (PMID: 9510189) Wallich R … Meuer S (Journal of immunology (Baltimore, Md. : 1950) 1998) 2 3 4 23
  2. The role of the CD58 locus in multiple sclerosis. (PMID: 19237575) De Jager PL … Hafler DA (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 23 41
  3. Crystal structure of the CD2-binding domain of CD58 (lymphocyte function-associated antigen 3) at 1.8-A resolution. (PMID: 10200255) Ikemizu S … Davis SJ (Proceedings of the National Academy of Sciences of the United States of America 1999) 3 4 23
  4. CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity. (PMID: 28813417) Burr ML … Dawson MA (Nature 2017) 3 4
  5. Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. (PMID: 22190364) Patsopoulos NA … de Bakker PI (Annals of neurology 2011) 3 41

ExternalLinks

View latest publications for CD58 gene in Mastermind

Products for CD58 Gene

  • Addgene plasmids for CD58

Sources for CD58 Gene