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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 4-1BB Pathway and Allograft rejection. 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

Additional gene information for CD40 Gene

No data available for CIViC summary , 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
GH20H046111 1.8 FANTOM5 Ensembl ENCODE dbSUPER 50.1 -6.9 -6874 0.8 HDGF PKNOX1 TBL1XR1 BMI1 YBX1 ZNF366 ZNF207 ATF7 ETV6 RUNX3 CD40 NCOA5 PCIF1 SLC12A5 SLC12A5-AS1 ZNF663P SYS1 NEURL2 ZNF335 GC20P046113
GH20H045967 1.5 ENCODE dbSUPER 39 -147.4 -147377 5.8 ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 SP3 NFYC ZFP41 MEF2D NCOA5 ZNF335 PCIF1 SLC35C2 TP53RK ZNF663P CD40 ZNF334 ENSG00000271984 PIGT
GH20H046107 1.4 FANTOM5 ENCODE dbSUPER 25.3 -9.7 -9728 1.3 CTCF EBF1 BATF RAD21 RELA POLR2A EED SMC3 ZNF143 ATF7 CD40 SPATA25 SLC12A5 SLC12A5-AS1 WFDC3 RPL13P2 SLC35C2 ZNF335 GC20P046113
GH20H045334 2 FANTOM5 Ensembl ENCODE dbSUPER 14.7 -776.2 -776170 14.4 MLX ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A SSRP1 GLIS1 NCOA5 PCIF1 ZNF335 ZSWIM1 SPATA25 SNX21 CD40 ENSG00000233352 LOC105372630 RPL5P2
GH20H046002 1.4 FANTOM5 Ensembl ENCODE 20.6 -113.7 -113650 3.6 BCOR ZMYM3 MAX POLR2A EED ETV6 RUNX3 IKZF2 CHD2 CBFB CD40 ZNF335 NCOA5 SLC12A5 PCIF1 PLTP MMP9 FTLP1
- 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
ENSR00000137758 250 1401 RB1 SIN3A BATF ZNF143 ATF7 ETV6 RUNX3 IKZF2 SMARCA5 SMAD5

Genomic Locations for CD40 Gene

Genomic Locations for CD40 Gene
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 Asn153 and Asn180
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for CD40 (CD40)
  • Abcam antibodies for CD40

No data available for DME Specific Peptides for CD40 Gene

Domains & Families for CD40 Gene

Gene Families for CD40 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • CD markers
  • Disease related genes
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for CD40 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for CD40 Gene

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.

Phenotypes From GWAS Catalog for CD40 Gene

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

Clone Products

  • Addgene plasmids for CD40

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

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,ISS --
GO:0005887 integral component of plasma membrane TAS 10748139
genes like me logo Genes that share ontologies with CD40: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CD40 Gene

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

(82) 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 1771
Simvastatin Approved Pharma Competitive, Inhibitor 528
nivolumab Approved Pharma Therapeutic Antibodies, Immunotherapies 499
Dacetuzumab Investigational Pharma antibody 0
CD40 ligand Pharma 0

(49) 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:

Clone Products

  • Addgene plasmids for CD40

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 CGAP 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.

Evidence on tissue expression from TISSUES for CD40 Gene

  • Blood(4.8)
  • Kidney(4.4)
  • Lymph node(4)
  • Spleen(4)
  • Bone marrow(2.8)
  • Skin(2.7)
  • Lung(2.6)
  • Intestine(2.5)
  • Heart(2.4)
  • Liver(2.2)
  • Nervous system(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CD40 Gene

Germ Layers:
  • mesoderm
  • immune
  • lymphatic
  • blood
  • bone marrow
  • lymph node
  • white blood cell
genes like me logo Genes that share expression patterns with CD40: view

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 33
  • 99.4 (n)
(Canis familiaris)
Mammalia CD40 33 34
  • 79.34 (n)
(Bos Taurus)
Mammalia CD40 33 34
  • 76.65 (n)
(Mus musculus)
Mammalia Cd40 33 16 34
  • 71.29 (n)
(Rattus norvegicus)
Mammalia Cd40 33
  • 70.56 (n)
(Monodelphis domestica)
Mammalia CD40 34
  • 55 (a)
(Gallus gallus)
Aves CD40 33 34
  • 52.58 (n)
(Anolis carolinensis)
Reptilia CD40 34
  • 37 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd40 33
  • 47.77 (n)
(Danio rerio)
Actinopterygii cd40 34
  • 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 Pathogenic, Immunodeficiency with hyper-IgM 3 (HIGM3) [MIM:606843] 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
VAR_077569 Immunodeficiency with hyper-IgM 3 (HIGM3) [MIM:606843]

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

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

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: HGMD, 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
  • higmx-1
acute myocarditis
immunodeficiency, x-linked, with hyper-igm
  • immunodeficiency with hyper igm type 1
  • myocardial inflammation
- 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, ECO:0000269 PubMed:26545377}. 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 ML (Genes and immunity 2009) 3 22 45 60
  2. [Association between inflammatory cytokine CD40 gene polymorphism and risk of acute coronary syndrome]. (PMID: 19099972) Tian CX … Huang CX (Zhonghua xin xue guan bing za zhi 2008) 3 22 45 60
  3. Association analysis of CD40 polymorphisms with asthma and the level of serum total IgE. (PMID: 17255560) Park JH … Shin HD (American journal of respiratory and critical care medicine 2007) 3 22 45 60
  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 SS … Kehry MR (Biochemistry 1998) 3 4 22 60
  5. A genome-wide association study identifies three new risk loci for Kawasaki disease. (PMID: 22446962) Onouchi Y … US Kawasaki Disease Genetics Consortium (Nature genetics 2012) 3 45 60

Products for CD40 Gene

  • Addgene plasmids for CD40

Sources for CD40 Gene

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