PTGS1
protein-codingprostaglandin-endoperoxide synthase 1
Gene summary
This is one of two genes encoding similar enzymes that catalyze the conversion of arachidonate to prostaglandin. The encoded protein regulates angiogenesis in endothelial cells, and is inhibited by nonsteroidal anti-inflammatory drugs such as aspirin. Based on its ability to function as both a cyclooxygenase and as a peroxidase, the encoded protein has been identified as a moonlighting protein. The protein may promote cell proliferation during tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2021]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0011588
Submitter: PanelApp Australia
Inheritance Pattern: SD
Disease ID:MONDO:0011588
Submitter: ClinGen
*PTGS1* was first reported in relation to platelet-type bleeding disorder 12 in 2018 (Bastida JM, et al., 2018, PMID: 28983057). *PTGS1* encodes a dual cyclooxygenase and peroxidase (COX-1), during platelet activation, arachidonic acid is released from membrane phospholipids and metabolized to thromboxane A2 (TXA2) through the actions of COX-1 and TXA2 synthase. An inherited defect in *PTGS1* is specifically linked to defective platelet aggregation with arachidonic acid and absence of the second wave response to epinephrine, ADP and collagen but normal response with TXA2 agonists. Several such patients with mild bleeding have been reported either with autosomal dominant or, more recently, autosomal recessive transmission of variants in *PTGS1* (reviewed in PMID: 33147934). Patients may lack protein or have a functionally defective, potentially dominant negative, but normally expressed enzyme. While the clinical and laboratory phenotype of COX-1 deficiency appear to be well established, the mode of inheritance for this pathology remains to be fully elucidated but is currently curated as semi-dominant to consider both dominant and recessive cases. Thus far, five unique variants (both missense and in-frame deletions) have been reported in five patients from three publications (PMIDs: 32299908, 28983057, 28748566). Additionally, another *PTGS1* missense variant (NM_000962:exon5:c.412T>C (p.W138R)) was identified in an affected mother and her affected son by an expert member of the Hemostasis/Thrombosis GCEP. Both individuals had normal platelet count and size and normal platelet surface glycoprotein expression. In addition, they presented with absent aggregation to AA and and reduced to low dose collagen with a normal response to endoperoxide analog suggesting a cyclooxygenase deficiency. This gene-disease relationship is supported by its biochemical function (PMID: 7947975) in platelet activation and preferential expression at high levels in selected cells, including endothelium, monocytes, platelets, renal collecting tubules, and seminal vesicles (PMID: 18657230). As well as altered function and expression in patients (PMID: 32299908). Additional functional alteration in non-patient cells showed the *PTGS1* N143S variant caused a dominant-negative effect of the COX-1 enzyme activity and reduced downstream TXB2 synthesis (PMID: 33326144) and homozygous mutant mice showed reduced platelet aggregation, which was similar to the patient phenotypes (PMID: 8521478). In summary, there is limited evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PTGS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000962.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 5 | 3 | 9 | ||
| missense | 76 | 4 | 1 | 81 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 80 | 9 | 4 | 93 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000953.2 | 11 | MANE Select | |
| Ensembl | ENSP00000354612.2 | 11 | MANE Select | |
| RefSeq | NP_001258093.1 | 10 | Standard | |
| RefSeq | NP_001258094.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ptgs1 | Danio rerio | Structure: hematopoietic stem cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Platelet activation - Homo sapiens (human)
- Regulation of lipolysis in adipocytes - Homo sapiens (human)
- Serotonergic synapse - Homo sapiens (human)
- Arachidonic acid metabolism - Homo sapiens (human)
- Celecoxib Pathway, Pharmacodynamics
Biological Process
- prostaglandin biosynthetic process
- xenobiotic metabolic process
- inflammatory response
- response to oxidative stress
- regulation of blood pressure
Molecular Function
- peroxidase activity
- prostaglandin-endoperoxide synthase activity
- heme binding
- metal ion binding
- dioxygenase activity
Cellular Component
- photoreceptor outer segment
- cytoplasm
- endoplasmic reticulum membrane
- Golgi apparatus
- organelle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000362012
- Coding exons
- 11
- Length
- 25159
- Individuals with no LoFs
- 125673
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 75
- Defined
- 125748
- p
- 0.000298
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.571 | 338 | 369 | 0.916 | 0.0000224 | 3933 |
| Missense (PolyPhen) | 119 | 164.67 | 0.72267 | 1748 | ||
| Synonymous | 0.138 | 141 | 143 | 0.985 | 0.00000821 | 1167 |
| Loss of Function | 2.47 | 15 | 29.5 | 0.508 | 0.00000154 | 311 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.0013 | 0.0013 | notable |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Converts arachidonate to prostaglandin H2 (PGH2), a committed step in prostanoid synthesis. Involved in the constitutive production of prostanoids in particular in the stomach and platelets. In gastric epithelial cells, it is a key step in the generation of prostaglandins, such as prostaglandin E2 (PGE2), which plays an important role in cytoprotection. In platelets, it is involved in the generation of thromboxane A2 (TXA2), which promotes platelet activation and aggregation, vasoconstriction and proliferation of vascular smooth muscle cells.;
Recessive Scores
- pRec
- 0.488
Intolerance Scores
- LoFtool
- 0.907
- RVIS EVS
- 0.87
- RVIS percentile EVS
- 88.85
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |