PTGS1

protein-coding

prostaglandin-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

NM_000962.4

Inheritance

AR, SD

ClinVar variants

U:80B:13

Top phenotype

Hemorrhage

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr9:122,370,530-122,395,703

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~25.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

platelet-type bleeding disorder 12MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0011588

Submitter: PanelApp Australia

platelet-type bleeding disorder 12LIMITED

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

4 Conditions Cataloged
not specifiedTotal: 75
not providedTotal: 15
HemorrhageTotal: 3
PTGS1-related disorderTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
5
clinvar
3
clinvar
9
missense
76
clinvar
4
clinvar
1
clinvar
81
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total00809493
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000962.4RefSeqNP_000953.211MANE Select
ENST00000362012.7EnsemblENSP00000354612.211MANE Select
NM_001271164.2RefSeqNP_001258093.110Standard
NM_001271165.2RefSeqNP_001258094.18Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ptgs1Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5713383690.9160.00002243933
Missense (PolyPhen)119164.670.722671748
Synonymous0.1381411430.9850.000008211167
Loss of Function2.471529.50.5080.00000154311

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.000220.00022rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000190.00018rare
South Asian0.00130.0013notable
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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