CD28
protein-codingCD28 molecule, the group of V-set domain containing|CD molecules|Ig-like cell adhesion molecule family
Gene summary
The protein encoded by this gene is essential for T-cell proliferation and survival, cytokine production, and T-helper type-2 development. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0971177
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0971177
Submitter: ClinGen
CD28 was first reported in relation to autosomal recessive immunodeficiency 123 with HPV-related verrucosis in 2021 (Beziat et al., 34214472). Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. At least one missense variant that affects mRNA splicing has been reported in a consanguineous family where it segregated with disease in three affected family members (PMID: 34214472). They had severe human papillomavirus (HPV)-driven skin papillomatosis ranging from HPV-4-associated skin warts in two patients to HPV-2- associated ‘‘tree man syndrome’’ in one patient. Additional symptoms include increased levels of Epstein-Barr virus (EBV) and cytomegalovirus (CMV) viremia, and a defect in mounting antibody responses to vaccines. Heterozygous carriers were unaffected. The mechanism of pathogenicity appears to be loss of function. This gene-disease relationship is supported by animal models, expression studies, in vitro functional assays, and rescue in patient cells. CD28 deficient mice are susceptible to MmuPV1 (Mouse papillomavirus type 1). Keratinocytes from affected patients have absent CD28 expression and their T-cells have no detectable p65 phosphorylation in response to CD28 or CD3/CD28 cross-linking. A lentiviral vector expressing the WT CD28 cDNA restored p65 phosphorylation in response to CD28 or CD3/CD28 cross-linking in patient T cells (PMID: 34214472). In summary, there is moderate evidence to support this gene-disease relationship. 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 GCEP on the meeting date October 17, 2024 (SOP Version 11)].
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious
Intervention: Allergy/Immunology/Infectious
Rationale: The condition can involve susceptibility to HPV-related verrucosis, and awareness may allow preventative measures and early and aggressive treatment of infections
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CD28 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006139.4. 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 | 1 | 1 | ||||
| missense | 1 | 16 | 1 | 18 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 16 | 1 | 1 | 19 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006130.1 | 4 | MANE Select | |
| Ensembl | ENSP00000324890.7 | 4 | MANE Select | |
| RefSeq | NP_001230006.1 | 4 | Standard | |
| RefSeq | NP_001230007.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- Type I diabetes mellitus - Homo sapiens (human)
- T cell receptor signaling pathway - Homo sapiens (human)
- Allograft rejection - Homo sapiens (human)
- Graft-versus-host disease - Homo sapiens (human)
Biological Process
- positive regulation of inflammatory response to antigenic stimulus
- humoral immune response
- cell surface receptor signaling pathway
- positive regulation of gene expression
- negative regulation of gene expression
Molecular Function
- protease binding
- SH3/SH2 adaptor activity
- protein binding
- coreceptor activity
- protein kinase binding
Cellular Component
- immunological synapse
- cytosol
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000324106
- Coding exons
- 4
- Length
- 32438
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125744
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.797 | 103 | 128 | 0.802 | 0.00000722 | 1437 |
| Missense (PolyPhen) | 26 | 46.615 | 0.55777 | 503 | ||
| Synonymous | -0.391 | 54 | 50.5 | 1.07 | 0.00000289 | 430 |
| Loss of Function | 2.13 | 2 | 8.85 | 0.226 | 3.72e-7 | 117 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in T-cell activation, the induction of cell proliferation and cytokine production and promotion of T-cell survival. Enhances the production of IL4 and IL10 in T-cells in conjunction with TCR/CD3 ligation and CD40L costimulation (PubMed:8617933). Isoform 3 enhances CD40L-mediated activation of NF-kappa-B and kinases MAPK8 and PAK2 in T-cells (PubMed:15067037). {ECO:0000269|PubMed:15067037, ECO:0000269|PubMed:8617933}.;
Recessive Scores
- pRec
- 0.540
Intolerance Scores
- LoFtool
- 0.254
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |