CD28

protein-coding

CD28 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

NM_006139.4

Inheritance

AR

ClinVar variants

P:1U:16B:2

Top phenotype

Immunodeficiency 123 with HPV-related verrucosis

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr2:203,706,517-203,739,756

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~33.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immunodeficiency 123 with HPV-related verrucosisLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0971177

Submitter: Ambry Genetics

immunodeficiency 123 with HPV-related verrucosisMODERATE

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)

Immunodeficiency 123 with HPV-related verrucosisAR

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

Refs: 34214472Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CD28 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 15
not providedTotal: 2
Immunodeficiency 123 with HPV-related verrucosisTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
1
clinvar
16
clinvar
1
clinvar
18
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total10161119
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006139.4RefSeqNP_006130.14MANE Select
ENST00000324106.9EnsemblENSP00000324890.74MANE Select
NM_001243077.2RefSeqNP_001230006.14Standard
NM_001243078.2RefSeqNP_001230007.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.7971031280.8020.000007221437
Missense (PolyPhen)2646.6150.55777503
Synonymous-0.3915450.51.070.00000289430
Loss of Function2.1328.850.2263.72e-7117

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000260.000026rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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