PDCD1
programmed cell death 1, the group of V-set domain containing|CD molecules
Basic information
Region (hg38): 2:241849884-241858894
Previous symbols: [ "SLEB2" ]
Links
Phenotypes
GenCC
Source:
- systemic lupus erythematosus (Supportive), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Autoimmune disease with susceptibility to mycobacterium tuberculosis | AR | Allergy/Immunology/Infectious | The condition can involve susceptibility to mycobacterium tuberculosis, and awareness may enaable preventative measures and early and aggressive treatments of infections, as well as care related to autoimmune manifestations | Allergy/Immunology/Infectious | 34183838 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (12 variants)
- PDCD1-related_disorder (4 variants)
- not_provided (3 variants)
- RECLASSIFIED_-_PDCD1_POLYMORPHISM (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005018.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 10 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 10 | 4 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDCD1 | protein_coding | protein_coding | ENST00000334409 | 5 | 9028 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.417 | 0.576 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.29 | 139 | 189 | 0.735 | 0.0000127 | 1823 |
| Missense in Polyphen | 25 | 52.205 | 0.47889 | 581 | ||
| Synonymous | 0.670 | 75 | 82.8 | 0.906 | 0.00000592 | 619 |
| Loss of Function | 2.26 | 2 | 9.51 | 0.210 | 4.10e-7 | 92 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen- specific manner. Possible cell death inducer, in association with other factors. {ECO:0000269|PubMed:21276005}.;
- Disease
- DISEASE: Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269|PubMed:12402038}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);T-Cell Receptor and Co-stimulatory Signaling;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;PD-1 signaling;Costimulation by the CD28 family;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.278
Intolerance Scores
- loftool
- 0.458
- rvis_EVS
- -0.31
- rvis_percentile_EVS
- 31.93
Haploinsufficiency Scores
- pHI
- 0.142
- hipred
- N
- hipred_score
- 0.461
- ghis
- 0.590
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.456
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdcd1
- Phenotype
- respiratory system phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); neoplasm; 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; immune system phenotype; cellular phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- negative regulation of tolerance induction;apoptotic process;humoral immune response;multicellular organism development;T cell costimulation;negative regulation of apoptotic process;positive regulation of T cell apoptotic process
- Cellular component
- plasma membrane;external side of plasma membrane;integral component of membrane
- Molecular function
- protein binding