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CD40 Gene(Protein Coding)

CD40 Molecule

GCID:
GC20P046118
GIFtS:
55
Genes Participants
UDN Logo

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
  • 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
  • CDW40 3
  • CDw40 4
  • P50 3

External Ids for CD40 Gene

Previous HGNC Symbols for CD40 Gene

  • TNFRSF5

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 Akt Signaling and NF-kappa B signaling pathway. Gene Ontology (GO) annotations related to this gene include enzyme binding. 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

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for CD40 Gene

Promoters and enhancers for CD40 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH20J046117 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 673.5 +0.9 873 3.3 HDGF SMAD1 RB1 ARID4B SIN3A BATF KLF5 ZNF143 ATF7 ETV6 CD40 GC20M046133
GH20J045334 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 34.3 -776.2 -776170 14.4 CLOCK MLX ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC SSRP1 GLIS1 SDC4 NCOA5 PCIF1 ZNF335 CD40 ENSG00000271984 ZSWIM1 SNX21 LOC105372630 ENSG00000233352
GH20J045967 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 39 -147.4 -147376 5.8 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF335 NCOA5 TP53RK SLC35C2 PCIF1 CD40 ZNF334 ZNF663P ZSWIM1 ENSG00000271984
GH20J046111 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 50.1 -6.9 -6874 0.8 HDGF PKNOX1 STAT5A BMI1 YBX1 IRF4 EGR1 ZNF366 ZNF207 ATF7 GC20P046113 CD40 NCOA5 PCIF1 SLC12A5 SLC12A5-AS1 ZNF663P SYS1 NEURL2 ZNF335
GH20J045880 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 26.2 -237.0 -236978 1.5 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B NEUROD1 SIN3A DMAP1 ZSWIM1 NCOA5 TP53RK CD40 WFDC3 SPATA25 PCIF1 SLC35C2 ZNF335 RPS2P7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CD40 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CD40 gene promoter:
  • c-Jun
  • ATF-2
  • AP-1
  • c-Fos

Genomic Locations for CD40 Gene

Genomic Locations for CD40 Gene
chr20:46,118,250-46,129,863
(GRCh38/hg38)
Size:
11,614 bases
Orientation:
Plus strand
chr20:44,746,906-44,758,502
(GRCh37/hg19)
Size:
11,597 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for CD40 Gene

Proteins for CD40 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P25942-TNR5_HUMAN
    Recommended name:
    Tumor necrosis factor receptor superfamily member 5
    Protein Accession:
    P25942
    Secondary Accessions:
    • E1P5S9
    • Q53GN5
    • Q5JY15
    • Q5U007
    • Q7M4Q8
    • Q86YK5
    • Q9BYU0

    Protein attributes for CD40 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for CD40 Gene

Protein Expression for CD40 Gene

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

Post-translational modifications for CD40 Gene

  • Glycosylation at posLast=180180 and Asn153
  • Modification sites at PhosphoSitePlus

Other Protein References for CD40 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for CD40

No data available for DME Specific Peptides for CD40 Gene

Domains & Families for CD40 Gene

Gene Families for CD40 Gene

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

Protein Domains for CD40 Gene

Blocks:
InterPro:
ProtoNet:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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 obsolete signal transducer activity TAS --
GO:0005031 tumor necrosis factor-activated receptor activity IBA --
GO:0005515 protein binding IEA,IPI 7527023
GO:0019899 enzyme binding IPI 12223522
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:
  • Cd40 Cd40<tm1Kik>
  • Cd40 Cd40<tm1b(KOMP)Wtsi>
  • Cd40 Cd40<tm1Geha>
  • Cd40 Cd40<tm1Arah>

Animal Model Products

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

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 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 ISS,TAS --
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

Activates:
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:0006874 cellular calcium ion homeostasis IMP 21410936
GO:0006954 inflammatory response IBA,TAS --
genes like me logo Genes that share ontologies with CD40: view

Drugs & Compounds for CD40 Gene

Products:

  1. Drug

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
rituximab Approved Pharma Therapeutic Antibodies 1808
Simvastatin Approved Pharma Competitive, Inhibitor HMG-CoA reductase inhibitor 537
nivolumab Approved Pharma Therapeutic Antibodies, Immunotherapies 604
Dacetuzumab Investigational Pharma antibody, Target 0
Lucatumumab Investigational Pharma Target 0

(48) 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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CD40 Gene

(11) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(119) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

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
CD40
ECgene alternative splicing isoforms for
CD40

Expression for CD40 Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for CD40 Gene
mRNA expression by BioGPS for CD40 GenemRNA expression by GTEx 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, MaxQB, and MOPED for CD40 Gene



NURSA nuclear receptor signaling pathways regulating expression of CD40 Gene:

CD40

SOURCE GeneReport for Unigene cluster for CD40 Gene:

Hs.472860

mRNA Expression by UniProt/SwissProt for CD40 Gene:

P25942-TNR5_HUMAN
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)
  • Thyroid gland(2)
  • Nervous system(2)

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

Germ Layers:
  • mesoderm
Systems:
  • immune
  • lymphatic
Regions:
General:
  • 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
chimpanzee
(Pan troglodytes)
 Mammalia CD40 33
  • 99.4 (n)
dog
(Canis familiaris)
 Mammalia CD40 34 33
  • 79.34 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia CD40 34 33
  • 76.65 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Cd40 16 34 33
  • 71.29 (n)
rat
(Rattus norvegicus)
 Mammalia Cd40 33
  • 70.56 (n)
oppossum
(Monodelphis domestica)
 Mammalia CD40 34
  • 55 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CD40 34 33
  • 52.58 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia CD40 34
  • 37 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia cd40 33
  • 47.77 (n)
zebrafish
(Danio rerio)
 Actinopterygii cd40 34
  • 25 (a)
 ManyToMany
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

ENSEMBL:
Gene Tree for CD40 (if available)
TreeFam:
Gene Tree for CD40 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CD40: view image

Paralogs for CD40 Gene

Paralogs for CD40 Gene

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

  • TNR5_HUMAN
  • H0YE23_HUMAN
  • Q6P2H9_HUMAN
genes like me logo Genes that share paralogs with CD40: view

Variants for CD40 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for CD40 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs11086998 likely-benign, benign, Immunodeficiency with Hyper-IgM, not specified 46,128,885(+) C/G/T 3_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs11569300 likely-benign, Immunodeficiency with Hyper-IgM 46,118,275(+) T/ 5_prime_UTR_variant, non_coding_transcript_variant
rs11569301 likely-benign, Immunodeficiency with Hyper-IgM 46,118,303(+) C/G/T 5_prime_UTR_variant, non_coding_transcript_variant
rs11569321 likely-benign, Immunodeficiency with Hyper-IgM 46,122,724(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs11569343 likely-benign, Immunodeficiency with Hyper-IgM 46,129,175(+) C/G 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

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)

Additional Variant Information for CD40 Gene

Human Gene Mutation Database (HGMD)
CD40
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD40

SNP Genotyping and Copy Number Assay Products

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

Disorders for CD40 Gene

MalaCards: The human disease database

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

- elite association - COSMIC cancer census association via MalaCards
Search CD40 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TNR5_HUMAN
  • 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.

Additional Disease Information for CD40

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 44 58
  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 44 58
  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 44 58
  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 58
  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 44 58

Products for CD40 Gene

  • Addgene plasmids for CD40