PTGS2
prostaglandin-endoperoxide synthase 2
Basic information
Region (hg38): 1:186671791-186680922
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 PTGS2 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 | 9 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 2 | |||||
| Total | 0 | 0 | 12 | 7 | 4 |
Variants in PTGS2
This is a list of pathogenic ClinVar variants found in the PTGS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-186673926-A-G | Cholangiocarcinoma | other (Dec 10, 2022) | ||
| 1-186674384-A-G | not specified | Uncertain significance (Nov 29, 2023) | ||
| 1-186674401-A-G | Likely benign (Mar 05, 2018) | |||
| 1-186674413-G-T | Benign (Apr 24, 2018) | |||
| 1-186674426-G-C | not specified | Uncertain significance (Mar 02, 2023) | ||
| 1-186674427-C-T | not specified | Uncertain significance (May 30, 2024) | ||
| 1-186674435-G-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 1-186674435-G-C | not specified | Uncertain significance (Jun 16, 2023) | ||
| 1-186674582-G-A | not specified | Uncertain significance (Nov 30, 2022) | ||
| 1-186674671-C-T | Likely benign (Feb 13, 2018) | |||
| 1-186674745-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 1-186674755-C-G | not specified | Uncertain significance (Feb 10, 2022) | ||
| 1-186675348-C-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 1-186675890-A-G | Likely benign (Jun 22, 2018) | |||
| 1-186675946-A-G | Benign (Jul 04, 2018) | |||
| 1-186676057-T-C | Likely benign (May 26, 2018) | |||
| 1-186676537-A-G | Benign (Jul 04, 2018) | |||
| 1-186676836-A-G | Likely benign (Aug 15, 2018) | |||
| 1-186676925-T-G | Likely benign (Jul 15, 2018) | |||
| 1-186677755-T-C | not specified | Uncertain significance (Feb 02, 2022) | ||
| 1-186678252-C-T | Benign (Jun 18, 2018) | |||
| 1-186678328-G-A | Likely benign (May 13, 2018) | |||
| 1-186678338-G-C | not specified | Uncertain significance (Mar 06, 2023) | ||
| 1-186679072-C-T | not specified | Uncertain significance (Dec 09, 2023) | ||
| 1-186679113-G-A | Likely benign (Jul 16, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTGS2 | protein_coding | protein_coding | ENST00000367468 | 10 | 8637 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00403 | 125680 | 0 | 3 | 125683 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.48 | 208 | 336 | 0.619 | 0.0000174 | 3976 |
| Missense in Polyphen | 35 | 111.29 | 0.31449 | 1265 | ||
| Synonymous | -1.07 | 135 | 120 | 1.12 | 0.00000620 | 1135 |
| Loss of Function | 4.52 | 3 | 29.5 | 0.102 | 0.00000158 | 338 |
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) | 0.0000267 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Converts arachidonate to prostaglandin H2 (PGH2), a committed step in prostanoid synthesis (PubMed:26859324, PubMed:27226593). Constitutively expressed in some tissues in physiological conditions, such as the endothelium, kidney and brain, and in pathological conditions, such as in cancer. PTGS2 is responsible for production of inflammatory prostaglandins. Up- regulation of PTGS2 is also associated with increased cell adhesion, phenotypic changes, resistance to apoptosis and tumor angiogenesis. In cancer cells, PTGS2 is a key step in the production of prostaglandin E2 (PGE2), which plays important roles in modulating motility, proliferation and resistance to apoptosis. {ECO:0000269|PubMed:16373578, ECO:0000269|PubMed:26859324, ECO:0000269|PubMed:27226593}.;
- Pathway
- Regulation of lipolysis in adipocytes - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Ibuprofen Metabolism Pathway;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Etoposide Action Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Celecoxib Metabolism Pathway;Etoposide Metabolism Pathway;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Piroxicam Action Pathway;Selenium Micronutrient Network;Eicosanoid Synthesis;Spinal Cord Injury;Quercetin and Nf-kB- AP-1 Induced Cell Apoptosis;Aryl Hydrocarbon Receptor;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Overview of nanoparticle effects;Photodynamic therapy-induced HIF-1 survival signaling;Photodynamic therapy-induced NF-kB survival signaling;Hepatitis C and Hepatocellular Carcinoma;VEGFA-VEGFR2 Signaling Pathway;Gastric ulcer formation;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Chromosomal and microsatellite instability in colorectal cancer;Prostaglandin Synthesis and Regulation;Metabolism of lipids;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);Prostaglandin Leukotriene metabolism;Synthesis of 15-eicosatetraenoic acid derivatives;Arachidonic acid metabolism;Metabolism;Biosynthesis of electrophilic ?-3 PUFA oxo-derivatives;Biosynthesis of EPA-derived SPMs;Biosynthesis of DHA-derived SPMs;Biosynthesis of DPAn-3 SPMs;Biosynthesis of DPA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;Nicotinamide salvaging;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;C20 prostanoid biosynthesis;Linoleate metabolism;Prostaglandin formation from arachidonate;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;aspirin triggered resolvin E biosynthesis;aspirin triggered resolvin D biosynthesis;aspirin-triggered lipoxin biosynthesis;C-MYB transcription factor network;Signaling mediated by p38-alpha and p38-beta;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;S1P1 pathway;Calcium signaling in the CD4+ TCR pathway;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.946
Intolerance Scores
- loftool
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.93
Haploinsufficiency Scores
- pHI
- 0.812
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.438
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.996
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptgs2
- Phenotype
- 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); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; normal 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); hematopoietic 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); endocrine/exocrine gland phenotype; neoplasm; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; cellular phenotype; homeostasis/metabolism 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); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- ptgs2a
- Affected structure
- hematopoietic stem cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- prostaglandin biosynthetic process;angiogenesis;inflammatory response;response to oxidative stress;embryo implantation;aging;learning;memory;regulation of blood pressure;negative regulation of cell population proliferation;response to fructose;response to manganese ion;response to lithium ion;positive regulation of vascular endothelial growth factor production;cytokine-mediated signaling pathway;sensory perception of pain;cyclooxygenase pathway;lipoxygenase pathway;bone mineralization;ovulation;positive regulation of prostaglandin biosynthetic process;positive regulation of fever generation;positive regulation of synaptic plasticity;negative regulation of synaptic transmission, dopaminergic;response to estradiol;response to lipopolysaccharide;positive regulation of peptidyl-serine phosphorylation;response to vitamin D;NAD biosynthesis via nicotinamide riboside salvage pathway;cellular response to heat;response to tumor necrosis factor;cellular response to UV;maintenance of permeability of blood-brain barrier;positive regulation of protein import into nucleus;hair cycle;long-chain fatty acid biosynthetic process;positive regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of nitric oxide biosynthetic process;negative regulation of cell cycle;positive regulation of vasoconstriction;negative regulation of smooth muscle contraction;positive regulation of smooth muscle contraction;decidualization;positive regulation of smooth muscle cell proliferation;regulation of inflammatory response;brown fat cell differentiation;response to glucocorticoid;negative regulation of calcium ion transport;positive regulation of synaptic transmission, glutamatergic;oxidation-reduction process;response to fatty acid;cellular response to mechanical stimulus;cellular response to lead ion;cellular response to ATP;cellular response to hypoxia;cellular response to non-ionic osmotic stress;cellular response to fluid shear stress;positive regulation of transforming growth factor beta production;positive regulation of cell migration involved in sprouting angiogenesis;positive regulation of fibroblast growth factor production;positive regulation of brown fat cell differentiation;positive regulation of platelet-derived growth factor production;negative regulation of blood vessel diameter;cellular oxidant detoxification;negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress;response to angiotensin
- Cellular component
- cytoplasm;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;caveola;organelle membrane;protein-containing complex;neuron projection
- Molecular function
- peroxidase activity;prostaglandin-endoperoxide synthase activity;protein binding;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;enzyme binding;heme binding;protein homodimerization activity;metal ion binding;arachidonate 15-lipoxygenase activity