CD274
CD274 molecule, the group of V-set domain containing|CD molecules|C2-set domain containing|Receptor ligands|B7 family
Basic information
Region (hg38): 9:5450503-5470566
Previous symbols: [ "PDCD1LG1" ]
Links
Phenotypes
GenCC
Source:
- neonatal diabetes mellitus (Limited), mode of inheritance: AR
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 CD274 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 | 2 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 3 | 1 | 4 |
Variants in CD274
This is a list of pathogenic ClinVar variants found in the CD274 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-5457224-A-G | Benign (Jul 16, 2018) | |||
| 9-5457389-C-A | Benign (Apr 27, 2018) | |||
| 9-5462875-C-A | not specified | Uncertain significance (May 14, 2024) | ||
| 9-5462876-C-G | Likely benign (Jul 01, 2022) | |||
| 9-5462987-A-C | not specified | Uncertain significance (Dec 02, 2022) | ||
| 9-5463088-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 9-5466808-A-G | not specified | Uncertain significance (Aug 16, 2022) | ||
| 9-5467955-G-A | Benign (Feb 17, 2020) | |||
| 9-5470497-A-G | Benign (Feb 17, 2020) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD274 | protein_coding | protein_coding | ENST00000381577 | 6 | 20064 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0192 | 0.964 | 125698 | 0 | 5 | 125703 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.898 | 123 | 154 | 0.797 | 0.00000753 | 1918 |
| Missense in Polyphen | 29 | 47.712 | 0.60781 | 625 | ||
| Synonymous | -1.39 | 71 | 57.6 | 1.23 | 0.00000286 | 541 |
| Loss of Function | 2.08 | 5 | 13.1 | 0.381 | 6.39e-7 | 164 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000153 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a critical role in induction and maintenance of immune tolerance to self. As a ligand for the inhibitory receptor PDCD1/CD279, modulates the activation threshold of T-cells and limits T-cell effector response (PubMed:11015443). The PDCD1/CD279-mediated inhibitory pathway is exploited by tumors to attenuate anti-tumor immunity and facilitate tumor survival (PubMed:28813417, PubMed:28813410). Through a yet unknown activating receptor, may costimulate T-cell subsets that predominantly produce interleukin-10 (IL10) (PubMed:10581077). {ECO:0000269|PubMed:10581077, ECO:0000269|PubMed:11015443, ECO:0000269|PubMed:28813410, ECO:0000269|PubMed:28813417}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);PD-1 signaling;Costimulation by the CD28 family;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.220
Intolerance Scores
- loftool
- 0.547
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 75.12
Haploinsufficiency Scores
- pHI
- 0.0324
- hipred
- N
- hipred_score
- 0.258
- ghis
- 0.420
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.450
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd274
- Phenotype
- hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- positive regulation of tolerance induction to tumor cell;immune response;signal transduction;cell surface receptor signaling pathway;positive regulation of cell migration;T cell costimulation;negative regulation of interferon-gamma production;negative regulation of interleukin-10 production;response to cytokine;positive regulation of T cell proliferation;negative regulation of T cell proliferation;regulation of activated T cell proliferation;negative regulation of activated T cell proliferation;regulation of T cell apoptotic process;cellular response to lipopolysaccharide;toxin transport;negative regulation of tumor necrosis factor superfamily cytokine production;regulation of activated CD4-positive, alpha-beta T cell apoptotic process;positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process;negative regulation of CD4-positive, alpha-beta T cell proliferation;positive regulation of interleukin-10 secretion;negative regulation of CD8-positive, alpha-beta T cell activation
- Cellular component
- plasma membrane;external side of plasma membrane;cell surface;integral component of membrane;early endosome membrane;recycling endosome membrane;extracellular exosome
- Molecular function
- protein binding