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Aliases for CD40 Gene

Aliases for CD40 Gene

  • CD40 Molecule 2 3 5
  • CD40 Molecule, TNF Receptor Superfamily Member 5 2 3
  • CD40L Receptor 3 4
  • TNFRSF5 3 4
  • CDW40 3 4
  • Bp50 3 4
  • Tumor Necrosis Factor Receptor Superfamily, Member 5 2
  • Tumor Necrosis Factor Receptor Superfamily Member 5 3
  • B Cell Surface Antigen CD40 3
  • B-Cell Surface Antigen CD40 4
  • B Cell-Associated Molecule 3
  • CD40 Antigen 4
  • P50 3

External Ids for CD40 Gene

Previous HGNC Symbols for CD40 Gene


Previous GeneCards Identifiers for CD40 Gene

  • GC20P044181
  • GC20P044746
  • GC20P041488

Summaries for CD40 Gene

Entrez Gene Summary for CD40 Gene

  • This gene is a member of the TNF-receptor superfamily. The encoded protein is a receptor on antigen-presenting cells of the immune system and is essential for mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. AT-hook transcription factor AKNA is reported to coordinately regulate the expression of this receptor and its ligand, which may be important for homotypic cell interactions. Adaptor protein TNFR2 interacts with this receptor and serves as a mediator of the signal transduction. The interaction of this receptor and its ligand is found to be necessary for amyloid-beta-induced microglial activation, and thus is thought to be an early event in Alzheimer disease pathogenesis. Mutations affecting this gene are the cause of autosomal recessive hyper-IgM immunodeficiency type 3 (HIGM3). Multiple alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Nov 2014]

GeneCards Summary for CD40 Gene

CD40 (CD40 Molecule) is a Protein Coding gene. Diseases associated with CD40 include Immunodeficiency With Hyper-Igm, Type 3 and Cd40 Ligand Deficiency. Among its related pathways are Regulation of activated PAK-2p34 by proteasome mediated degradation and HTLV-I infection. GO annotations related to this gene include enzyme binding and receptor activity. An important paralog of this gene is TNFRSF11A.

UniProtKB/Swiss-Prot for CD40 Gene

  • Receptor for TNFSF5/CD40LG. Transduces TRAF6- and MAP3K8-mediated signals that activate ERK in macrophages and B cells, leading to induction of immunoglobulin secretion.

Gene Wiki entry for CD40 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD40 Gene

Genomics for CD40 Gene

Regulatory Elements for CD40 Gene

Enhancers for CD40 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F046111 1.5 FANTOM5 Ensembl ENCODE 40.4 -6.8 -6750 1.0 HDGF PKNOX1 TBL1XR1 YBX1 BMI1 EGR1 ZNF366 SCRT2 ETV6 CREM CD40 NCOA5 PCIF1 SLC12A5 ENSG00000204044 ZNF663P SYS1 ZNF335 GC20P046113 RPL13P2
GH20F045967 1.2 ENCODE 45.5 -147.4 -147377 5.8 CREB3L1 ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 SP3 NFYC TBX21 NCOA5 CD40 ZNF335 TP53RK PCIF1 SLC2A10 ENSG00000271984 SYS1 FTLP1 RPL13P2
GH20F046107 1.6 FANTOM5 Ensembl ENCODE 34.1 -9.7 -9710 1.3 ATF1 CREB3L1 WRNIP1 ARID4B DMAP1 SLC30A9 ZNF143 ZMIZ1 SP3 NFYC CD40 SLC2A10 SPATA25 NEURL2 SLC12A5 ENSG00000204044 WFDC3 RPL13P2 SLC35C2 ZNF335
GH20F045334 1.8 FANTOM5 Ensembl ENCODE 25.4 -776.2 -776170 14.4 MLX ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC SSRP1 GLIS1 RCOR2 NCOA5 PCIF1 ZNF335 CD40 ZSWIM1 ENSG00000271984 ENSG00000233352 LOC105372630 ENSG00000237464 RPL5P2
GH20F045997 1.5 FANTOM5 Ensembl ENCODE 29.9 -118.9 -118850 4.8 PKNOX1 ZFP64 ZBTB11 ZEB2 ZNF623 ZNF781 ZNF518A NR2F2 ZNF264 SMARCA4 NCOA5 CD40 ZNF335 TP53RK SLC12A5 WFDC3 ENSG00000204044 PCIF1 DNTTIP1 ENSG00000271984
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CD40 on UCSC Golden Path with GeneCards custom track

Promoters for CD40 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for CD40 Gene

46,118,250 bp from pter
46,129,863 bp from pter
11,614 bases
Plus strand

Genomic View for CD40 Gene

Genes around CD40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD40 Gene

Proteins for CD40 Gene

  • Protein details for CD40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Tumor necrosis factor receptor superfamily member 5
    Protein Accession:
    Secondary Accessions:
    • E1P5S9
    • Q53GN5
    • Q5JY15
    • Q5U007
    • Q7M4Q8
    • Q86YK5
    • Q9BYU0

    Protein attributes for CD40 Gene

    277 amino acids
    Molecular mass:
    30619 Da
    Quaternary structure:
    • Monomer and homodimer. The variant form found in the bladder carcinoma cell line Hu549 does not form homodimers. Interacts with TRAF1, TRAF2, TRAF3, TRAF5 and TRAF6. Interacts with TRAF6 and MAP3K8; the interaction is required for ERK activation.

    Three dimensional structures from OCA and Proteopedia for CD40 Gene

    Alternative splice isoforms for CD40 Gene


neXtProt entry for CD40 Gene

Post-translational modifications for CD40 Gene

  • Glycosylation at Asn 153 and Asn 180
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for CD40

No data available for DME Specific Peptides for CD40 Gene

Domains & Families for CD40 Gene

Suggested Antigen Peptide Sequences for CD40 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 4 TNFR-Cys repeats.
  • Contains 4 TNFR-Cys repeats.
genes like me logo Genes that share domains with CD40: view

Function for CD40 Gene

Molecular function for CD40 Gene

UniProtKB/Swiss-Prot Function:
Receptor for TNFSF5/CD40LG. Transduces TRAF6- and MAP3K8-mediated signals that activate ERK in macrophages and B cells, leading to induction of immunoglobulin secretion.

Gene Ontology (GO) - Molecular Function for CD40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003823 antigen binding IEA --
GO:0004871 signal transducer activity TAS 9671306
GO:0004872 receptor activity IEA,TAS 10092834
GO:0005031 tumor necrosis factor-activated receptor activity IBA --
GO:0005515 protein binding IPI 7527023
genes like me logo Genes that share ontologies with CD40: view
genes like me logo Genes that share phenotypes with CD40: view

Human Phenotype Ontology for CD40 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CD40 Gene

MGI Knock Outs for CD40:

Animal Model Products

miRNA for CD40 Gene

miRTarBase miRNAs that target CD40

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CD40 Gene

Localization for CD40 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD40 Gene

Isoform I: Cell membrane; Single-pass type I membrane protein.
Isoform II: Secreted.

Subcellular locations from

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 CD40 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 3
nucleus 2
lysosome 2
endosome 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CD40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 10748139
genes like me logo Genes that share ontologies with CD40: view

Pathways & Interactions for CD40 Gene

genes like me logo Genes that share pathways with CD40: view

SIGNOR curated interactions for CD40 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CD40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001934 positive regulation of protein phosphorylation IMP 21410936
GO:0002376 immune system process IEA --
GO:0002768 immune response-regulating cell surface receptor signaling pathway IEA --
GO:0006461 protein complex assembly TAS 10748139
GO:0006874 cellular calcium ion homeostasis IMP 21410936
genes like me logo Genes that share ontologies with CD40: view

Drugs & Compounds for CD40 Gene

(79) Drugs for CD40 Gene - From: ClinicalTrials, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
rituximab Approved Pharma Therapeutic Antibodies 1654
Simvastatin Approved Pharma Competitive, Inhibitor HMG-CoA reductase inhibitor 510
CD40 ligand Pharma 0
Alkylating Agents Pharma 4694
Antibodies Pharma 6045

(50) Additional Compounds for CD40 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CD40: view

Transcripts for CD40 Gene

Unigene Clusters for CD40 Gene

CD40 molecule, TNF receptor superfamily member 5:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CD40 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8
SP1: - - -
SP2: - - - -
SP3: - - -
SP4: -

Relevant External Links for CD40 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CD40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CD40 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CD40 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.7), Breast (10.9), Platelet (10.2), and Gallbladder (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CD40 Gene

NURSA nuclear receptor signaling pathways regulating expression of CD40 Gene:


SOURCE GeneReport for Unigene cluster for CD40 Gene:


mRNA Expression by UniProt/SwissProt for CD40 Gene:

Tissue specificity: B-cells and in primary carcinomas.
genes like me logo Genes that share expression patterns with CD40: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CD40 Gene

Orthologs for CD40 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD40 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CD40 34
  • 99.4 (n)
(Canis familiaris)
Mammalia CD40 34 35
  • 79.34 (n)
(Bos Taurus)
Mammalia CD40 34 35
  • 76.65 (n)
(Mus musculus)
Mammalia Cd40 34 16 35
  • 71.29 (n)
(Rattus norvegicus)
Mammalia Cd40 34
  • 70.56 (n)
(Monodelphis domestica)
Mammalia CD40 35
  • 55 (a)
(Gallus gallus)
Aves CD40 34 35
  • 52.58 (n)
(Anolis carolinensis)
Reptilia CD40 35
  • 37 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd40 34
  • 47.77 (n)
(Danio rerio)
Actinopterygii cd40 35
  • 25 (a)
Species where no ortholog for CD40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CD40 Gene

Gene Tree for CD40 (if available)
Gene Tree for CD40 (if available)

Paralogs for CD40 Gene

(3) SIMAP similar genes for CD40 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CD40: view

Variants for CD40 Gene

Sequence variations from dbSNP and Humsavar for CD40 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs28931586 Immunodeficiency with hyper-IgM 3 (HIGM3) [MIM:606843], Pathogenic 46,122,349(+) AATAC(C/T)GCGAC nc-transcript-variant, reference, missense
rs750234130 Bladder carcinoma cell line Hu549 46,121,871(+) TAAAC(A/G)GTCAG nc-transcript-variant, reference, missense
VAR_039301 Bladder carcinoma cell line Hu549
VAR_039303 Bladder carcinoma cell line Hu549
rs11086998 -- 46,128,885(+) AGGCC(C/G)CCCAC nc-transcript-variant, reference, synonymous-codon, missense, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for CD40 Gene

Variant ID Type Subtype PubMed ID
nsv833993 CNV gain 17160897
nsv586135 CNV loss 21841781
nsv1138961 CNV deletion 24896259
nsv1057686 CNV loss 25217958
esv2758796 CNV loss 17122850

Variation tolerance for CD40 Gene

Residual Variation Intolerance Score: 58.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.02; 20.88% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CD40 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD40 Gene

Disorders for CD40 Gene

MalaCards: The human disease database

(40) MalaCards diseases for CD40 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency with hyper-igm, type 3
  • cd40 deficiency
cd40 ligand deficiency
  • immunodeficiency with hyper-igm, type 1
acute myocarditis
hyperimmunoglobulin syndrome
immunodeficiency, x-linked, with hyper-igm
  • immunodeficiency with hyper-igm, type 1
- elite association - COSMIC cancer census association via MalaCards
Search CD40 in MalaCards View complete list of genes associated with diseases


  • Immunodeficiency with hyper-IgM 3 (HIGM3) [MIM:606843]: A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections. {ECO:0000269 PubMed:11675497}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CD40

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CD40: view

No data available for Genatlas for CD40 Gene

Publications for CD40 Gene

  1. Individual and epistatic effects of genetic polymorphisms of B-cell co-stimulatory molecules on susceptibility to pemphigus foliaceus. (PMID: 19421221) Malheiros D. … Petzl-Erler M.L. (Genes Immun. 2009) 3 22 46 64
  2. [Association between inflammatory cytokine CD40 gene polymorphism and risk of acute coronary syndrome]. (PMID: 19099972) Tian C.X. … Huang C.X. (Zhonghua Xin Xue Guan Bing Za Zhi 2008) 3 22 46 64
  3. Association analysis of CD40 polymorphisms with asthma and the level of serum total IgE. (PMID: 17255560) Park J.H. … Shin H.D. (Am. J. Respir. Crit. Care Med. 2007) 3 22 46 64
  4. CD40-tumor necrosis factor receptor-associated factor (TRAF) interactions: regulation of CD40 signaling through multiple TRAF binding sites and TRAF hetero-oligomerization. (PMID: 9718306) Pullen S.S. … Kehry M.R. (Biochemistry 1998) 3 4 22 64
  5. A genome-wide association study identifies three new risk loci for Kawasaki disease. (PMID: 22446962) Onouchi Y. … . (Nat. Genet. 2012) 3 46 64

Products for CD40 Gene

Sources for CD40 Gene

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