CD80
CD80 molecule, the group of V-set domain containing|CD molecules|C2-set domain containing|B7 family
Basic information
Region (hg38): 3:119524293-119559614
Previous symbols: [ "CD28LG", "CD28LG1" ]
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 CD80 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 7 | 0 | 4 |
Variants in CD80
This is a list of pathogenic ClinVar variants found in the CD80 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-119525008-T-A | Benign (Feb 17, 2020) | |||
| 3-119525574-A-C | Benign (Feb 17, 2020) | |||
| 3-119527782-G-A | not specified | Uncertain significance (Jul 19, 2023) | ||
| 3-119527841-C-T | not specified | Uncertain significance (May 20, 2024) | ||
| 3-119529857-A-G | not specified | Uncertain significance (Jun 01, 2023) | ||
| 3-119537166-C-T | not specified | Uncertain significance (May 23, 2023) | ||
| 3-119537173-G-A | Benign (Dec 31, 2019) | |||
| 3-119537184-A-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 3-119537256-T-C | not specified | Uncertain significance (Mar 25, 2024) | ||
| 3-119537397-A-G | not specified | Uncertain significance (Nov 08, 2022) | ||
| 3-119544585-C-T | not specified | Uncertain significance (Oct 16, 2023) | ||
| 3-119544671-G-C | Benign (Dec 31, 2019) | |||
| 3-119544709-A-G | not specified | Uncertain significance (Apr 20, 2023) | ||
| 3-119544712-C-T | not specified | Likely benign (Apr 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD80 | protein_coding | protein_coding | ENST00000264246 | 5 | 35310 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0109 | 0.951 | 125724 | 0 | 11 | 125735 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.753 | 131 | 158 | 0.831 | 0.00000836 | 1890 |
| Missense in Polyphen | 33 | 48.746 | 0.67698 | 627 | ||
| Synonymous | 0.914 | 50 | 58.9 | 0.849 | 0.00000322 | 551 |
| Loss of Function | 1.80 | 5 | 11.6 | 0.429 | 4.89e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000529 | 0.0000527 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the costimulatory signal essential for T- lymphocyte activation. T-cell proliferation and cytokine production is induced by the binding of CD28, binding to CTLA-4 has opposite effects and inhibits T-cell activation. {ECO:0000269|PubMed:10583602}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Type I diabetes mellitus - 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);Toll-like receptor signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Allograft Rejection;Primary Focal Segmental Glomerulosclerosis FSGS;Interleukin-10 signaling;PI3K-AKT-mTOR - VitD3 Signalling;Inflammatory Response Pathway;Toll-like Receptor Signaling Pathway;Disease;Signal Transduction;the co-stimulatory signal during t-cell activation;IL12 signaling mediated by STAT4;CD28 dependent PI3K/Akt signaling;CD28 dependent Vav1 pathway;CD28 co-stimulation;CTLA4 inhibitory signaling;Costimulation by the CD28 family;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;TCR;Immune System;Adaptive Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;PIP3 activates AKT signaling;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;GPCR signaling-G alpha i;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
- 0.634
Intolerance Scores
- loftool
- 0.537
- rvis_EVS
- 0.62
- rvis_percentile_EVS
- 83.14
Haploinsufficiency Scores
- pHI
- 0.0895
- hipred
- N
- hipred_score
- 0.132
- ghis
- 0.480
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.554
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd80
- Phenotype
- cellular phenotype; endocrine/exocrine gland 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); immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- immune response;signal transduction;cell surface receptor signaling pathway;positive regulation of signal transduction;cytokine-mediated signaling pathway;T cell costimulation;intracellular signal transduction;positive regulation of T cell proliferation;negative regulation of T cell proliferation;positive regulation of interleukin-2 biosynthetic process;positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process;positive regulation of T-helper 1 cell differentiation;positive regulation of transcription, DNA-templated;viral entry into host cell;phosphatidylinositol phosphorylation;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of protein kinase B signaling;cellular response to lipopolysaccharide
- Cellular component
- plasma membrane;external side of plasma membrane;cell surface;integral component of membrane;protein complex involved in cell adhesion
- Molecular function
- virus receptor activity;protein binding;coreceptor activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity