PTGR1
protein-codingprostaglandin reductase 1
Gene summary
This gene encodes an enzyme that is involved in the inactivation of the chemotactic factor, leukotriene B4. The encoded protein specifically catalyzes the NADP+ dependent conversion of leukotriene B4 to 12-oxo-leukotriene B4. A pseudogene of this gene is found on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]
- LTB4DH
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PTGR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001146108.2. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 45 | 4 | 49 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 55 | 4 | 0 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001139580.1 | 9 | MANE Select | |
| Ensembl | ENSP00000385763.2 | 9 | MANE Select | |
| RefSeq | NP_001139581.1 | 9 | Standard | |
| RefSeq | NP_036344.2 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- Metabolism of lipids
- Synthesis of Leukotrienes (LT) and Eoxins (EX)
- Arachidonic acid metabolism
Biological Process
- leukotriene metabolic process
- prostaglandin metabolic process
- oxidation-reduction process
- response to antineoplastic agent
Molecular Function
- 2-alkenal reductase [NAD(P)] activity
- 13-prostaglandin reductase activity
- 15-oxoprostaglandin 13-oxidase activity
Cellular Component
- cytoplasm
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000407693
- Coding exons
- 9
- Length
- 50134
- Individuals with no LoFs
- 125517
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 231
- Defined
- 125748
- p
- 0.000919
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.412 | 164 | 180 | 0.914 | 0.00000913 | 2123 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.0017 | 0.0017 | notable |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.00088 | 0.00088 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.0989
Intolerance Scores
- LoFtool
- 0.955
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 61.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0766
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |