GDPD3
protein-codingglycerophosphodiester phosphodiesterase domain containing 3
Gene summary
Enables phosphoric diester hydrolase activity. Involved in N-acylethanolamine metabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.7 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 GDPD3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024307.3. 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 | 47 | 6 | 53 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 49 | 6 | 0 | 55 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_077283.2 | 10 | MANE Select | |
| Ensembl | ENSP00000384363.3 | 10 | MANE Select | |
| Ensembl | ENSP00000455508.2 | 2 | Standard | |
| Ensembl | ENSP00000454472.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gdpd3a | Danio rerio | Structure: pigment cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ether lipid metabolism - Homo sapiens (human)
- Metabolism of lipids
- Metabolism
- Glycerophospholipid catabolism
- PI Metabolism
Biological Process
- phospholipid metabolic process
- phosphatidylcholine catabolic process
- glycerophospholipid catabolic process
Molecular Function
- lysophospholipase activity
- phosphoric diester hydrolase activity
- metal ion binding
Cellular Component
- endoplasmic reticulum membrane
- integral component of membrane
- perinuclear region of cytoplasm
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000406256
- Coding exons
- 10
- Length
- 9047
- Individuals with no LoFs
- 125590
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 158
- Defined
- 125748
- p
- 0.000628
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.289 | 187 | 198 | 0.942 | 0.0000126 | 2050 |
| Missense (PolyPhen) | 63 | 71.901 | 0.87621 | 804 | ||
| Synonymous | 0.983 | 67 | 78.0 | 0.858 | 0.00000456 | 643 |
| Loss of Function | -0.238 | 22 | 20.8 | 1.06 | 0.00000132 | 203 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00038 | 0.00037 | rare |
| Latino/Admixed American | 0.00075 | 0.00075 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00076 | 0.00076 | rare |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00076 | 0.00076 | rare |
| South Asian | 0.00066 | 0.00059 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF) and lysophosphatidylcholine (lyso-PC), and to a lesser extent for lysophosphatidylethanolamine (lyso-PE). Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine. {ECO:0000250|UniProtKB:Q99LY2}.;
Intolerance Scores
- LoFtool
- 0.699
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 57.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |