PTGES2

prostaglandin E synthase 2, the group of Glutaredoxin domain containing

Basic information

Region (hg38): 9:128120693-128128462

Previous symbols: [ "C9orf15" ]

Links

ENSG00000148334 ∙ NCBI:80142 ∙ OMIM:608152 ∙ HGNC:17822 ∙ Uniprot:Q9H7Z7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTGES2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTGES2 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			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	1

Variants in PTGES2

This is a list of pathogenic ClinVar variants found in the PTGES2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128121152-G-A		not specified	Likely benign (Aug 16, 2022)
9-128121165-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-128121186-G-A		not specified	Uncertain significance (Dec 28, 2023)
9-128121209-G-A		not specified	Uncertain significance (Aug 02, 2021)
9-128121261-C-T		not specified	Uncertain significance (May 26, 2023)
9-128122387-C-T		not specified	Uncertain significance (Aug 05, 2024)
9-128122402-C-T		not specified	Uncertain significance (Nov 24, 2024)
9-128122456-C-T		not specified	Uncertain significance (Jul 14, 2023)
9-128122457-G-A		not specified	Uncertain significance (Aug 02, 2023)
9-128122460-C-T		not specified	Uncertain significance (May 18, 2023)
9-128122478-G-A		not specified	Uncertain significance (May 04, 2022)
9-128122959-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-128122970-G-A		not specified	Uncertain significance (Jul 13, 2022)
9-128122976-C-T		not specified	Uncertain significance (Sep 02, 2024)
9-128122992-C-A		not specified	Uncertain significance (Oct 27, 2022)
9-128122997-C-T		not specified	Uncertain significance (Mar 01, 2023)
9-128123010-C-T		not specified	Uncertain significance (Apr 13, 2023)
9-128123014-C-G			Benign (Mar 29, 2018)
9-128123015-T-C		not specified	Uncertain significance (May 31, 2023)
9-128123025-G-T		not specified	Uncertain significance (Feb 01, 2023)
9-128123066-C-T		not specified	Uncertain significance (Mar 04, 2024)
9-128123103-C-T		not specified	Uncertain significance (Feb 22, 2023)
9-128123108-G-A		not specified	Uncertain significance (Dec 10, 2024)
9-128123122-C-A		not specified	Uncertain significance (Mar 18, 2024)
9-128123733-G-C		not specified	Uncertain significance (Sep 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTGES2	protein_coding	protein_coding	ENST00000338961	7	7770

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.36e-9	0.268	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.902	165	201	0.821	0.0000123	2374
Missense in Polyphen		66	85.978	0.76764		876
Synonymous	0.109	88	89.3	0.985	0.00000601	781
Loss of Function	0.676	15	18.1	0.829	0.00000104	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000163	0.000163
South Asian	0.000294	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isomerase that catalyzes the conversion of PGH2 into the more stable prostaglandin E2 (PGE2). {ECO:0000269|PubMed:12804604, ECO:0000269|PubMed:18198127}.
• Pathway: Arachidonic acid metabolism - Homo sapiens (human);Eicosanoid Synthesis;Neutrophil degranulation;Metabolism of lipids;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);Prostaglandin Leukotriene metabolism;Arachidonic acid metabolism;Innate Immune System;Immune System;Metabolism;Fatty acid metabolism;C20 prostanoid biosynthesis;Prostaglandin formation from arachidonate;IFN-gamma pathway (Consensus)

Recessive Scores

• pRec: 0.359

Intolerance Scores

• loftool: 0.621
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.389
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptges2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cyclooxygenase pathway;electron transport chain;neutrophil degranulation;cell redox homeostasis;positive regulation of transcription, DNA-templated
• Cellular component: Golgi membrane;extracellular region;nucleus;mitochondrion;cytosol;integral component of membrane;azurophil granule lumen;perinuclear region of cytoplasm
• Molecular function: DNA binding;protein binding;electron transfer activity;protein disulfide oxidoreductase activity;lyase activity;heme binding;glutathione binding;prostaglandin-E synthase activity