PGP
protein-codingphosphoglycolate phosphatase
Gene summary
Enables phosphoglycolate phosphatase activity and sn-glycerol 3-phosphatase activity. Involved in several processes, including glycerol biosynthetic process; negative regulation of gluconeogenesis; and toxic metabolite repair. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.2 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 PGP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001042371.3. 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 | 0 | |||||
| missense | 36 | 1 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 37 | 1 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001035830.1 | 2 | MANE Select | |
| Ensembl | ENSP00000330918.7 | 2 | MANE Select | |
| Ensembl | ENSP00000457909.1 | 1 | Standard | |
| Ensembl | ENSP00000807278.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glyoxylate and dicarboxylate metabolism - Homo sapiens (human)
- Metabolism of carbohydrates
- Metabolism
- Glycolysis
- Glucose metabolism
Biological Process
- glycerol biosynthetic process
- glycerophospholipid metabolic process
- dephosphorylation
- peptidyl-tyrosine dephosphorylation
- negative regulation of gluconeogenesis
Molecular Function
- glycerol-1-phosphatase activity
- magnesium ion binding
- protein tyrosine phosphatase activity
- phosphoglycolate phosphatase activity
- phosphatase activity
Cellular Component
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000333503
- Coding exons
- 2
- Length
- 2811
- Individuals with no LoFs
- 124719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 124723
- p
- 0.0000160
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.30 | 98 | 142 | 0.692 | 0.00000657 | 2003 |
| Missense (PolyPhen) | 30 | 65.397 | 0.45873 | 884 | ||
| Synonymous | -1.15 | 73 | 61.5 | 1.19 | 0.00000300 | 703 |
| Loss of Function | 1.56 | 2 | 6.18 | 0.324 | 2.69e-7 | 77 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Glycerol-3-phosphate phosphatase hydrolyzing glycerol-3- phosphate into glycerol. Thereby, regulates the cellular levels of glycerol-3-phosphate a metabolic intermediate of glucose, lipid and energy metabolism. Was also shown to have a 2-phosphoglycolate phosphatase activity and a tyrosine-protein phosphatase activity. However, their physiological relevance is unclear (PubMed:26755581). In vitro, has also a phosphatase activity toward ADP, ATP, GDP and GTP (By similarity). {ECO:0000250|UniProtKB:Q8CHP8, ECO:0000269|PubMed:26755581}.;
Recessive Scores
- pRec
- 0.190
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.773
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |