GDE1
protein-codingglycerophosphodiester phosphodiesterase 1
Gene summary
Predicted to enable glycerophosphodiester phosphodiesterase activity; glycerophosphoinositol glycerophosphodiesterase activity; and phosphatidylcholine lysophospholipase A1 activity. Predicted to be involved in N-acylethanolamine metabolic process; ethanolamine metabolic process; and phospholipid metabolic process. Predicted to be located in membrane. Predicted to be active in plasma membrane. [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 ~20.4 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 GDE1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016641.4. 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 | 2 | |||
| missense | 43 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 48 | 0 | 1 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057725.1 | 6 | MANE Select | |
| Ensembl | ENSP00000261386.3 | 6 | MANE Select | |
| RefSeq | NP_001310995.1 | 5 | Standard | |
| RefSeq | NP_001310996.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Phospholipid Biosynthesis
- Metabolism of lipids
- Metabolism
- Glycerophospholipid catabolism
- PI Metabolism
Biological Process
- lipid metabolic process
- phospholipid metabolic process
- glycerophospholipid catabolic process
- N-acylethanolamine metabolic process
Molecular Function
- lysophospholipase activity
- glycerophosphodiester phosphodiesterase activity
- metal ion binding
- glycerophosphoinositol glycerophosphodiesterase activity
Cellular Component
- plasma membrane
- integral component of membrane
- cytoplasmic vesicle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000353258
- Coding exons
- 6
- Length
- 20453
- Individuals with no LoFs
- 125683
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 65
- Defined
- 125748
- p
- 0.000258
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.788 | 155 | 185 | 0.837 | 0.00000891 | 2176 |
| Missense (PolyPhen) | 44 | 68.57 | 0.64168 | 784 | ||
| Synonymous | 1.34 | 58 | 72.5 | 0.800 | 0.00000368 | 628 |
| Loss of Function | 1.09 | 10 | 14.5 | 0.691 | 7.94e-7 | 156 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00033 | 0.00033 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Has glycerophosphoinositol phosphodiesterase activity. Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity). {ECO:0000250|UniProtKB:Q9JL55, ECO:0000250|UniProtKB:Q9JL56}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.659
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.75
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.788
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |