PTGES3
prostaglandin E synthase 3
Basic information
Region (hg38): 12:56663341-56688408
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 PTGES3 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 | 0 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 1 | 0 | 1 |
Variants in PTGES3
This is a list of pathogenic ClinVar variants found in the PTGES3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-56666237-A-C | not specified | Uncertain significance (Jan 07, 2022) | ||
| 12-56670300-A-G | not specified | Uncertain significance (May 06, 2024) | ||
| 12-56686880-CAT-C | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTGES3 | protein_coding | protein_coding | ENST00000262033 | 8 | 25033 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.985 | 0.0146 | 119200 | 0 | 2 | 119202 | 0.00000839 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.27 | 49 | 81.2 | 0.604 | 0.00000394 | 1099 |
| Missense in Polyphen | 7 | 19.152 | 0.3655 | 300 | ||
| Synonymous | 0.194 | 25 | 26.3 | 0.952 | 0.00000144 | 241 |
| Loss of Function | 3.32 | 0 | 12.8 | 0.00 | 7.01e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000339 | 0.0000339 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000959 | 0.00000903 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytosolic prostaglandin synthase that catalyzes the oxidoreduction of prostaglandin endoperoxide H2 (PGH2) to prostaglandin E2 (PGE2) (PubMed:10922363). Molecular chaperone that localizes to genomic response elements in a hormone-dependent manner and disrupts receptor-mediated transcriptional activation, by promoting disassembly of transcriptional regulatory complexes (PubMed:11274138, PubMed:12077419). Facilitates HIF alpha proteins hydroxylation via interaction with EGLN1/PHD2, leading to recruit EGLN1/PHD2 to the HSP90 pathway (PubMed:24711448). {ECO:0000269|PubMed:10922363, ECO:0000269|PubMed:11274138, ECO:0000269|PubMed:12077419, ECO:0000269|PubMed:24711448}.;
- Pathway
- Arachidonic acid metabolism - Homo sapiens (human);Aryl Hydrocarbon Receptor Pathway;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Signal Transduction;HSF1 activation;Attenuation phase;HSF1-dependent transactivation;Aryl hydrocarbon receptor signalling;Phase I - Functionalization of compounds;Metabolism of lipids;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);HSP90 chaperone cycle for steroid hormone receptors (SHR);Cellular responses to stress;Arachidonic acid metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;C20 prostanoid biosynthesis;Cellular responses to external stimuli;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;Cellular response to heat stress;Signaling by Nuclear Receptors;ESR-mediated signaling;Regulation of Telomerase
(Consensus)
Recessive Scores
- pRec
- 0.281
Intolerance Scores
- loftool
- 0.400
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 66.57
Haploinsufficiency Scores
- pHI
- 0.966
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.694
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptges3
- 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); respiratory system phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region 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);
Gene ontology
- Biological process
- telomere maintenance;prostaglandin biosynthetic process;protein folding;xenobiotic metabolic process;telomere maintenance via telomerase;signal transduction;cyclooxygenase pathway;positive regulation of phosphorylation;protein stabilization;chaperone cofactor-dependent protein refolding;chaperone-mediated protein complex assembly;positive regulation of telomerase activity;regulation of cellular response to heat;telomerase holoenzyme complex assembly
- Cellular component
- chromosome, telomeric region;nucleus;nucleoplasm;telomerase holoenzyme complex;cytoplasm;cytosol;protein-containing complex;chaperone complex
- Molecular function
- telomerase activity;protein binding;prostaglandin-E synthase activity;unfolded protein binding;chaperone binding;Hsp90 protein binding;DNA polymerase binding