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Gene

CD40

CD40 molecule

Summary

Cytogenetic location
20q13.12
Coordinates
Chromosome 20: 46,118,314–46,129,858 (GRCh38)
Exons
9 exons across 11.5 kb
Protein
277 amino acids
Also known as
p50, Bp50
Previous symbols
TNFRSF5
MANE Select transcript
ENST00000372285.8NM_001250.6
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Hyper-IgM Syndromes

    • Hyper-IgM syndrome

      Defective antibody class switching caused by changes in CD40LG (X-linked), CD40, AICDA or UNG.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Immunoglobulin replacement is standard; CD40L and CD40 deficiency also need Pneumocystis prophylaxis, safe drinking water to prevent cryptosporidium and consideration of stem cell transplantation.

Broader groupings

  • Other Inborn Errors of Immunity

    • Inborn error of immunity

      One of 114 genes linked to it

      Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

How CD40 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 20, with a bracket where CD40 sits. CD40 and 30 genes near it on chromosome 20, from 45,624,086 to 46,624,085.Chromosome 2020q13.12p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3345.8 Mb46 Mb46.2 Mb46.4 Mb46.6 MbWFDC9: 45,607,939–45,631,284, reverse strandWFDC9WFDC10A: 45,629,733–45,631,196, forward strandWFDC10AWFDC11: 45,648,563–45,670,270, reverse strandWFDC11WFDC10B: 45,684,651–45,705,019, reverse strandWFDC10BWFDC13: 45,702,038–45,708,817, forward strandWFDC13SPINT4: 45,722,347–45,725,830, forward strandSPINT4WFDC3: 45,747,944–45,791,932, reverse strandWFDC3DNTTIP1: 45,791,937–45,811,427, forward strandUBE2C: 45,812,561–45,816,965, forward strandUBE2CTNNC2: 45,823,214–45,833,745, reverse strandTNNC2SNX21: 45,833,633–45,843,276, forward strandSNX21ACOT8: 45,841,709–45,857,435, reverse strandACOT8ZSWIM3: 45,857,591–45,879,131, forward strandZSWIM1: 45,881,201–45,885,266, forward strandSPATA25: 45,886,491–45,887,626, reverse strandNEURL2: 45,888,002–45,891,220, reverse strandNEURL2CTSA: 45,890,144–45,898,949, forward strandCTSAPLTP: 45,897,535–45,912,235, reverse strandPLTPPCIF1: 45,934,673–45,948,023, forward strandPCIF1ZNF335: 45,948,653–45,972,358, reverse strandZNF335MMP9: 46,008,869–46,016,561, forward strandMMP9SLC12A5: 46,021,675–46,060,150, forward strandSLC12A5NCOA5: 46,060,984–46,089,973, reverse strandNCOA5CD40: 46,118,314–46,129,858, forward strandCD40CDH22: 46,173,737–46,309,009, reverse strandCDH22SLC35H1: 46,345,980–46,364,460, reverse strandSLC35H1ELMO2: 46,366,045–46,432,985, reverse strandELMO2ZNF840P: 46,459,441–46,495,558, forward strandZNF840PZNF334: 46,499,630–46,513,596, reverse strandZNF334OCSTAMP: 46,540,946–46,550,654, reverse strandOCSTAMPSLC13A3: 46,557,823–46,684,467, reverse strandSLC13A3Diagram of CD40: 9 exons on the forward strand of chromosome 20Exon 3: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 1: 46,118,314–46,118,394, 81 basesExon 2: 46,121,820–46,121,898, 79 basesExon 3: 46,122,233–46,122,358, 126 basesExon 4: 46,122,610–46,122,756, 147 basesExon 5: 46,123,126–46,123,219, 94 basesExon 6: 46,126,640–46,126,701, 62 basesExon 7: 46,128,138–46,128,224, 87 basesExon 8: 46,128,330–46,128,358, 29 basesExon 9: 46,128,882–46,129,858, 977 bases1246895′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.7 kb of the gene's 11.5 kb; 834 of those bases code for the protein.

How a genome test reads CD40

4

positions in CD40 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 11.5 kb of CD40, introns included, not only the 1.7 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CD40 gene: CD40 molecule. Retrieved 17 October 2026, from https://dantelabs.com/genes/cd40

Vancouver

Dante Labs. CD40 gene: CD40 molecule [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cd40

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