PTGS1

prostaglandin-endoperoxide synthase 1

Basic information

Region (hg38): 9:122370529-122395703

Links

ENSG00000095303 ∙ NCBI:5742 ∙ OMIM:176805 ∙ HGNC:9604 ∙ Uniprot:P23219 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• platelet-type bleeding disorder 12 (Limited), mode of inheritance: Semidominant

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTGS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTGS1 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				4	3	7
missense			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	8	4

Variants in PTGS1

This is a list of pathogenic ClinVar variants found in the PTGS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-122371212-TTCCTGC-T			Likely benign (Jul 31, 2018)
9-122371239-G-A		not specified	Uncertain significance (Apr 15, 2024)
9-122377927-G-A			Benign (Dec 08, 2020)
9-122377983-G-A		not specified	Uncertain significance (Oct 26, 2021)
9-122378008-C-T		PTGS1-related disorder	Benign (Feb 08, 2024)
9-122378466-G-A		not specified	Uncertain significance (Dec 12, 2023)
9-122378512-G-T		not specified	Uncertain significance (Mar 30, 2024)
9-122378834-T-C		Hemorrhage	Uncertain significance (-)
9-122381406-C-T		not specified	Uncertain significance (Dec 19, 2022)
9-122381442-C-A		not specified	Uncertain significance (Aug 04, 2023)
9-122381692-A-G		not specified	Uncertain significance (Dec 14, 2023)
9-122381701-G-A		not specified	Uncertain significance (Dec 01, 2022)
9-122381704-A-C		Hemorrhage • not specified	Uncertain significance (Jun 07, 2023)
9-122381715-C-T		not specified	Uncertain significance (Aug 30, 2022)
9-122381716-G-A		not specified	Uncertain significance (Dec 03, 2021)
9-122381757-G-A			Benign (Jul 06, 2018)
9-122383515-G-T		not specified	Uncertain significance (Jun 30, 2023)
9-122383532-G-A			Likely benign (May 01, 2022)
9-122383567-A-G		not specified	Uncertain significance (Sep 14, 2023)
9-122383652-G-A			Likely benign (Aug 16, 2018)
9-122383674-C-G		not specified	Uncertain significance (Jan 16, 2024)
9-122383706-C-G			Likely benign (May 01, 2022)
9-122383735-C-T		not specified	Uncertain significance (Jun 17, 2022)
9-122383740-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-122386534-C-T			Likely benign (Jul 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTGS1	protein_coding	protein_coding	ENST00000362012	11	25159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.24e-7	0.994	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.571	338	369	0.916	0.0000224	3933
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.00134	0.00134
Other	0.000163	0.000163

dbNSFP

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.
• Pathway: 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;Platelet Aggregation Inhibitor 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;Overview of nanoparticle effects;Gastric ulcer formation;Prostaglandin Synthesis and Regulation;COX reactions;mechanism of acetaminophen activity and toxicity;Phase I - Functionalization of compounds;aspirin blocks signaling pathway involved in platelet activation;eicosanoid metabolism;Metabolism of lipids;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);Prostaglandin Leukotriene metabolism;basic mechanism of action of ppara pparb(d) and pparg and effects on gene expression;Arachidonic acid metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;C20 prostanoid biosynthesis;Linoleate metabolism;Prostaglandin formation from arachidonate;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.488

Intolerance Scores

• loftool: 0.907
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.85

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.517
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptgs1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle 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); endocrine/exocrine gland phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; reproductive 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); 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; neoplasm

Zebrafish Information Network

• Gene name: ptgs1
• Affected structure: hematopoietic stem cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: prostaglandin biosynthetic process;xenobiotic metabolic process;inflammatory response;response to oxidative stress;regulation of blood pressure;cyclooxygenase pathway;regulation of cell population proliferation;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: photoreceptor outer segment;cytoplasm;endoplasmic reticulum membrane;Golgi apparatus;organelle membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: peroxidase activity;prostaglandin-endoperoxide synthase activity;heme binding;metal ion binding;dioxygenase activity