CD8A
protein-codingCD8 subunit alpha, the group of V-set domain containing|CD molecules
Gene summary
The CD8 antigen is a cell surface glycoprotein found on most cytotoxic T lymphocytes that mediates efficient cell-cell interactions within the immune system. The CD8 antigen acts as a coreceptor with the T-cell receptor on the T lymphocyte to recognize antigens displayed by an antigen presenting cell in the context of class I MHC molecules. The coreceptor functions as either a homodimer composed of two alpha chains or as a heterodimer composed of one alpha and one beta chain. Both alpha and beta chains share significant homology to immunoglobulin variable light chains. This gene encodes the CD8 alpha chain. Multiple transcript variants encoding different isoforms have been found for this gene. The major protein isoforms of this gene differ by the presence or absence of a transmembrane domain and thus differ in being a membrane-anchored or secreted protein. [provided by RefSeq, May 2020]
- CD8
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012161
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0012161
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0012161
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012161
Submitter: ClinGen
*CD8A* was first reported in relation to an autosomal recessive CD8 deficiency in 2001 (de la Calle-Martin O, et al., 2001, PMID:11435463). The symptomatic cases presented with recurrent respiratory infections, bronchiolitis, recurrent otitis media and pneumonia. All cases had a complete absence of CD8-positive T cells and an increase in double-negative alpha-beta T cells. The curation of *CD8A* related to autosomal recessive susceptibility to respiratory infections associated with CD8alpha chain mutation (*CD8A* deficiency) with MONDO ID 0012161 includes both case-level and experimental evidence. To date, only five individuals from three families have been reported, all homozygous for the same mutation and all from consanguineous families of Spanish or Portuguese Gipsy community. The authors hypothesized that these families might be descendants of a common founder. One of the 25 year-old probands had two younger siblings that were homozygous for the same mutation but were asymptomatic. Four familial carriers of the mutation were reportedly asymptomatic but had a lower MFI of CD8 detected on T cells by flow cytometry. The same missense variant is reported in three probands in three publications (PMIDs:11435463, 17658607 and 26563160) and these are included in this curation. A score of 1.7 points for genetic evidence has been reached. This gene-disease association is also supported by animal model and functional alteration (PMIDs: 11435463, 1673361 and 21546492). Phenotypes of mice with CD8A mutations were consistent with patients’ phenotypes, presenting an absence of CD8 expression in the surface of T cells. Like in humans, CD8B expression on the surface of lymphocytes was also absent in homozygous mutants. T cells from the mutant mice also showed a lack of specific cytotoxic activities both to allogeneic cells and viruses. In proliferation assays, the mutant murineT cells responded well to MHC class II alloantigens but not to MHC class I alloantigens. Functional alterations were also observed in patient and non-patient cells. In patient cells (PMID: 21546492) there was complete absence of CD8 expression on the surface and a higher than normal proportion of double negative (DN) T cells. When analyzed, these DN T cells had effector T cells properties for one of the patients’ cells and effector memory T cells for the other. On proliferation assays with mitogens the patient’s DN T cells proliferated less than the CD4+ cells from the patient and less than the CD8+ T cells from control. TRECs in DN T Cells were also lower in number than the CD8+ from controls and the former also exhibited a skewed repertoire of TCR Vβ. On non-patient cells transfected with WT or CD8A bearing the patient mutation, CD8 expression was ablated whereas mutations in other areas did not produce the same effect. When producing single mutants in COS-7 cells via direct mutagenesis, it was observed that WT cells mutated to either CD8ser90 or CD8arg90 abolished expression, whereas CD8ser90 (mutation in patients) reverted to CD8gly90 (WT) re-established expression, showing the importance of that amino acid to protein expression on the surface. A score of 4 points for experimental evidence has been reached, increasing the total score to 5.7 points. In summary, this curation reached a level of Limited due to the small number of published patients, bearing the same mutation. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen SCID-CID Working Group on the meeting date August 18, 2022 (SOP Version 9). CD8A’s curation and existing evidence was re-examined in October 2025 (SOP version 11) and no new cases or contradictory evidence were reported since the last curation. The total score of 5.7 points and “Limited” classification remain unchanged.
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious
Intervention: Allergy/Immunology/Infectious
Rationale: Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial
Comments: Asymptomatic individuals have been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CD8A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001768.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 63 | 3 | 66 | |||
| missense | 1 | 79 | 3 | 83 | ||
| nonsense | 1 | 1 | 2 | |||
| start loss | 0 | |||||
| frameshift | 3 | 3 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 2 | 0 | 85 | 66 | 3 | 156 |
Highest pathogenic variant AF is 0.0000012391389
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001759.3 | 6 | MANE Select | |
| Ensembl | ENSP00000283635.3 | 6 | MANE Select | |
| RefSeq | NP_001139345.1 | 6 | Standard | |
| RefSeq | NP_001369627.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Antigen processing and presentation - Homo sapiens (human)
- Primary immunodeficiency - Homo sapiens (human)
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- T cell receptor signaling pathway - Homo sapiens (human)
- Hematopoietic cell lineage - Homo sapiens (human)
Biological Process
- T cell mediated immunity
- immune response
- cell surface receptor signaling pathway
- transmembrane receptor protein tyrosine kinase signaling pathway
- antigen processing and presentation
Molecular Function
- protein binding
- coreceptor activity
- protein kinase binding
- MHC class I protein binding
Cellular Component
- extracellular region
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- T cell receptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000409511
- Coding exons
- 6
- Length
- 23791
- Individuals with no LoFs
- 125728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 20
- Defined
- 125748
- p
- 0.0000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.237 | 122 | 130 | 0.942 | 0.00000646 | 1455 |
| Missense (PolyPhen) | 40 | 39.169 | 1.0212 | 456 | ||
| Synonymous | 0.167 | 60 | 61.7 | 0.973 | 0.00000325 | 512 |
| Loss of Function | 0.469 | 8 | 9.56 | 0.836 | 4.18e-7 | 113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000067 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.00010 | 0.000092 | rare |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, functions primarily as a coreceptor for MHC class I molecule:peptide complex. The antigens presented by class I peptides are derived from cytosolic proteins while class II derived from extracellular proteins. Interacts simultaneously with the T-cell receptor (TCR) and the MHC class I proteins presented by antigen presenting cells (APCs). In turn, recruits the Src kinase LCK to the vicinity of the TCR-CD3 complex. LCK then initiates different intracellular signaling pathways by phosphorylating various substrates ultimately leading to lymphokine production, motility, adhesion and activation of cytotoxic T-lymphocytes (CTLs). This mechanism enables CTLs to recognize and eliminate infected cells and tumor cells. In NK- cells, the presence of CD8A homodimers at the cell surface provides a survival mechanism allowing conjugation and lysis of multiple target cells. CD8A homodimer molecules also promote the survival and differentiation of activated lymphocytes into memory CD8 T-cells. {ECO:0000269|PubMed:16236125, ECO:0000269|PubMed:17678538, ECO:0000269|PubMed:23657257, ECO:0000269|PubMed:26082771}.;
- Disease
- DISEASE: CD8 deficiency, familial (CD8 deficiency) [MIM:608957]: An immunologic defect characterized by absence of CD8+ cells, leading to recurrent bacterial infections. {ECO:0000269|PubMed:11435463}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.972
Intolerance Scores
- LoFtool
- 0.440
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |