CD28
CD28 molecule, the group of V-set domain containing|CD molecules|Ig-like cell adhesion molecule family
Basic information
Region (hg38): 2:203706517-203739756
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD28 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 6 | 1 | 2 |
Variants in CD28
This is a list of pathogenic ClinVar variants found in the CD28 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-203706740-A-G | not specified | Uncertain significance (Feb 21, 2024) | ||
| 2-203706748-G-A | Immunodeficiency 123 with HPV-related verrucosis | Pathogenic (Jul 31, 2024) | ||
| 2-203726685-G-A | Benign (Aug 23, 2018) | |||
| 2-203726696-G-C | not specified | Uncertain significance (Jun 24, 2022) | ||
| 2-203726857-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
| 2-203726887-T-G | not specified | Uncertain significance (Apr 12, 2022) | ||
| 2-203729683-C-T | not specified | Likely benign (Mar 28, 2023) | ||
| 2-203729743-C-A | not specified | Uncertain significance (Jun 05, 2023) | ||
| 2-203729789-T-C | not specified | Benign (Jan 24, 2024) | ||
| 2-203734856-C-T | not specified | Uncertain significance (Mar 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD28 | protein_coding | protein_coding | ENST00000324106 | 4 | 32438 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.358 | 0.631 | 125741 | 0 | 3 | 125744 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.797 | 103 | 128 | 0.802 | 0.00000722 | 1437 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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);Viral myocarditis - Homo sapiens (human);Systemic lupus erythematosus - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Measles - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Allograft Rejection;T-Cell Receptor and Co-stimulatory Signaling;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;Inflammatory Response Pathway;T-Cell antigen Receptor (TCR) Signaling Pathway;Disease;Signal Transduction;the co-stimulatory signal during t-cell activation;ras-independent pathway in nk cell-mediated cytotoxicity;Host Interactions of HIV factors;HIV Infection;IL12 signaling mediated by STAT4;CD28 dependent PI3K/Akt signaling;CD28 dependent Vav1 pathway;CD28 co-stimulation;Costimulation by the CD28 family;TCR;Infectious disease;Immune System;Adaptive Immune System;Nef mediated downregulation of CD28 cell surface expression;PIP3 activates AKT signaling;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;Intracellular signaling by second messengers;Diseases of signal transduction;TCR signaling in naïve CD8+ T cells;TCR signaling in naïve CD4+ T cells;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.540
Intolerance Scores
- loftool
- 0.254
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.222
- hipred
- Y
- hipred_score
- 0.560
- ghis
- 0.447
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd28
- Phenotype
- hematopoietic system phenotype; normal phenotype; neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- 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;positive regulation of phosphatidylinositol 3-kinase signaling;T cell costimulation;positive regulation of interleukin-10 production;positive regulation of interleukin-4 production;cytokine biosynthetic process;positive regulation of T cell proliferation;T cell activation;negative regulation of apoptotic process;negative thymic T cell selection;regulatory T cell differentiation;positive regulation of viral genome replication;positive regulation of interleukin-2 biosynthetic process;regulation of regulatory T cell differentiation;positive regulation of translation;positive regulation of mitotic nuclear division;positive regulation of transcription by RNA polymerase II;positive regulation of alpha-beta T cell proliferation;phosphatidylinositol phosphorylation;positive regulation of isotype switching to IgG isotypes;regulation of defense response to virus by virus;T cell receptor signaling pathway;positive regulation of protein kinase B signaling;apoptotic signaling pathway
- Cellular component
- immunological synapse;cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;protein complex involved in cell adhesion
- Molecular function
- protease binding;SH3/SH2 adaptor activity;protein binding;coreceptor activity;protein kinase binding;identical protein binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity