PTGR1

prostaglandin reductase 1

Basic information

Region (hg38): 9:111549721-111599893

Previous symbols: [ "LTB4DH" ]

Links

ENSG00000106853 ∙ NCBI:22949 ∙ OMIM:601274 ∙ HGNC:18429 ∙ Uniprot:Q14914 ∙ 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 PTGR1 gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTGR1 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			15	3		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	15	3	1

Variants in PTGR1

This is a list of pathogenic ClinVar variants found in the PTGR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-111563194-A-T		not specified	Uncertain significance (Oct 31, 2023)
9-111563210-A-G		not specified	Likely benign (Dec 14, 2023)
9-111570117-T-C		not specified	Uncertain significance (Dec 06, 2022)
9-111570119-A-G		not specified	Uncertain significance (Feb 23, 2023)
9-111570132-G-A			Likely benign (May 21, 2018)
9-111570150-G-A		not specified	Uncertain significance (May 26, 2023)
9-111570156-C-T		not specified	Uncertain significance (Oct 05, 2021)
9-111570173-C-T		not specified	Likely benign (Jul 13, 2021)
9-111574740-G-T		not specified	Uncertain significance (Sep 16, 2021)
9-111574743-G-A		not specified	Uncertain significance (Feb 05, 2024)
9-111574755-T-C		not specified	Uncertain significance (Dec 22, 2023)
9-111574782-T-C		not specified	Uncertain significance (Jan 26, 2022)
9-111574812-C-T		not specified	Likely benign (Dec 02, 2022)
9-111578812-T-C		not specified	Uncertain significance (Dec 26, 2023)
9-111578830-G-A		not specified	Uncertain significance (Apr 10, 2023)
9-111578867-T-C		not specified	Uncertain significance (May 09, 2022)
9-111578879-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-111578882-C-T		not specified	Uncertain significance (Mar 27, 2023)
9-111578941-A-G		not specified	Uncertain significance (Dec 06, 2022)
9-111578960-A-G			Benign (Dec 05, 2017)
9-111583487-C-A		not specified	Uncertain significance (Aug 12, 2021)
9-111586028-G-C		not specified	Uncertain significance (Jan 23, 2023)
9-111586088-A-G		not specified	Uncertain significance (Jun 06, 2023)
9-111586093-G-C		not specified	Uncertain significance (Dec 18, 2023)
9-111586095-G-A		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTGR1	protein_coding	protein_coding	ENST00000407693	9	50134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.54e-8	0.341	125517	0	231	125748	0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.412	164	180	0.914	0.00000913	2123
Missense in Polyphen		41	46.604	0.87975		560
Synonymous	0.364	62	65.8	0.943	0.00000351	650
Loss of Function	0.669	13	15.9	0.819	6.66e-7	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000541	0.000539
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00171	0.00171
European (Non-Finnish)	0.00133	0.00132
Middle Eastern	0.00	0.00
South Asian	0.000882	0.000882
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as 15-oxo-prostaglandin 13-reductase and acts on 15-oxo-PGE1, 15-oxo-PGE2 and 15-oxo-PGE2-alpha. Has no activity towards PGE1, PGE2 and PGE2-alpha (By similarity). Catalyzes the conversion of leukotriene B4 into its biologically less active metabolite, 12-oxo-leukotriene B4. This is an initial and key step of metabolic inactivation of leukotriene B4. {ECO:0000250}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Glycine Serine metabolism;Synthesis of Lipoxins (LX);Metabolism;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;sphingosine and sphingosine-1-phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.955
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.0900
• hipred: N
• hipred_score: 0.380
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptgr1

Gene ontology

• Biological process: leukotriene metabolic process;prostaglandin metabolic process;oxidation-reduction process;response to antineoplastic agent
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: 2-alkenal reductase [NAD(P)] activity;13-prostaglandin reductase activity;15-oxoprostaglandin 13-oxidase activity