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Gene

CD3D

CD3 delta subunit of T-cell receptor complex

Summary

Cytogenetic location
11q23.3
Coordinates
Chromosome 11: 118,339,075–118,342,705 (GRCh38)
Exons
5 exons across 3.6 kb
Protein
171 amino acids
Inheritance
Autosomal recessive
Also known as
CD3DELTA, CD3-DELTA
Previous symbols
T3D
MANE Select transcript
ENST00000300692.9NM_000732.6
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

  • Severe Combined Immunodeficiency

    • Autosomal recessive

      Severe combined immunodeficiency (SCID) comprises a group of rare monogenic primary immunodeficiency disorders characterized by a lack of functional peripheral T lymphocytes resulting in early-onset severe respiratory infections and failure to thrive. They are classified according to immunological phenotype into SCID with absence of T cells but presence of B cells (T-B+ SCID) or SCID with absence of both (T-B- SCID). Both of these groups include several forms, with or without natural killer (NK) cells.

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

Broader groupings

  • Other Inborn Errors of Immunity

    • 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

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CD3D is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 11, with a bracket where CD3D sits. CD3D and 24 genes near it on chromosome 11, from 117,840,890 to 118,840,889.Chromosome 1111q23.3p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q25118 Mb118.2 Mb118.4 Mb118.6 Mb118.8 MbFXYD6-FXYD2: 117,820,163–117,876,667, reverse strandFXYD6-FXYD2FXYD6: 117,833,023–117,877,675, reverse strandFXYD6TMPRSS13: 117,900,641–117,929,459, reverse strandTMPRSS13IL10RA: 117,986,370–118,003,037, forward strandIL10RASMIM35: 118,003,634–118,088,299, reverse strandSMIM35TMPRSS4: 118,076,986–118,125,510, forward strandTMPRSS4SCN4B: 118,133,377–118,152,906, reverse strandSCN4BSCN2B: 118,162,806–118,176,653, reverse strandSCN2BJAML: 118,193,725–118,226,323, reverse strandJAMLMPZL3: 118,226,690–118,252,375, reverse strandMPZL3MPZL2: 118,253,416–118,264,536, reverse strandMPZL2CD3E: 118,304,701–118,316,175, forward strandCD3ECD3D: 118,339,075–118,342,705, reverse strandCD3DCD3G: 118,344,338–118,355,161, forward strandCD3GUBE4A: 118,359,578–118,399,211, forward strandUBE4AATP5MG: 118,401,345–118,433,278, forward strandATP5MG: 118,401,602–118,482,737, forward strandKMT2A: 118,436,456–118,526,832, forward strandKMT2ATTC36: 118,527,314–118,531,197, forward strandTTC36TMEM25: 118,530,636–118,548,273, forward strandTMEM25IFT46: 118,544,381–118,572,970, reverse strandIFT46ARCN1: 118,572,384–118,603,033, forward strandARCN1PHLDB1: 118,606,396–118,658,038, forward strandPHLDB1TREH: 118,657,265–118,679,694, reverse strandTREHDDX6: 118,747,763–118,791,226, reverse strandDDX6Diagram of CD3D: 5 exons on the reverse strand of chromosome 11Exon 3: 1 known disease-causing siteExon 2: 5 known disease-causing sitesExon 1: 5 known disease-causing sitesExon 5: 118,339,075–118,339,227, 153 basesExon 4: 118,339,451–118,339,494, 44 basesExon 3: 118,339,775–118,339,906, 132 basesExon 2: 118,340,375–118,340,593, 219 basesExon 1: 118,342,553–118,342,705, 153 bases543215′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 0.7 kb of the gene's 3.6 kb; 516 of those bases code for the protein.

How a genome test reads CD3D

17

positions in CD3D 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 3.6 kb of CD3D, introns included, not only the 0.7 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.). CD3D gene: CD3 delta subunit of T-cell receptor complex. Retrieved 17 October 2026, from https://dantelabs.com/genes/cd3d

Vancouver

Dante Labs. CD3D gene: CD3 delta subunit of T-cell receptor complex [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cd3d

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