GDPD5
protein-codingglycerophosphodiester phosphodiesterase domain containing 5
Gene summary
Predicted to enable glycerophosphodiester phosphodiesterase activity and glycerophospholipase activity. Predicted to be involved in several processes, including negative regulation of Notch signaling pathway; negative regulation of amyloid precursor protein biosynthetic process; and positive regulation of neuron differentiation. Predicted to act upstream of or within neuron differentiation and regulation of timing of cell differentiation. Predicted to be located in axon; neuronal cell body; and perinuclear endoplasmic reticulum. Predicted to be active in plasma membrane raft. [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 ~91.3 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 GDPD5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030792.8. 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 | 3 | 1 | 5 | ||
| missense | 99 | 4 | 103 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 103 | 7 | 1 | 111 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_110419.5 | 15 | MANE Select | |
| Ensembl | ENSP00000337972.3 | 15 | MANE Select | |
| RefSeq | NP_001338096.1 | 11 | Standard | |
| RefSeq | NP_001338097.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gdpd5a | Danio rerio | Structure: whole organism Quality: decreased length abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Glycerophospholipid catabolism
- PI Metabolism
- Phospholipid metabolism
Biological Process
- lipid metabolic process
- spinal cord motor neuron differentiation
- cerebral cortex neuron differentiation
- neuron projection development
- positive regulation of neuron differentiation
Molecular Function
- phosphatidylinositol phospholipase C activity
- protein binding
- glycerophosphodiester phosphodiesterase activity
- glycerophosphocholine phosphodiesterase activity
Cellular Component
- integral component of membrane
- growth cone
- neuronal cell body
- perinuclear endoplasmic reticulum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000336898
- Coding exons
- 15
- Length
- 91264
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 24
- Defined
- 125748
- p
- 0.000103
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 298 | 393 | 0.759 | 0.0000259 | 3885 |
| Missense (PolyPhen) | 100 | 143.62 | 0.69626 | 1527 | ||
| Synonymous | -0.679 | 179 | 168 | 1.07 | 0.0000115 | 1245 |
| Loss of Function | 3.31 | 12 | 32.3 | 0.372 | 0.00000139 | 335 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00010 | 0.000097 | rare |
| South Asian | 0.00040 | 0.00036 | rare |
| Other | 0.00035 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Promotes neurite formation. Cooperates with PRDX1 to drive postmitotic motor neuron differentiation. The glycerophosphodiester phosphodiesterase activity may be required for its role in neuronal differentiation. May contribute to the osmotic regulation of cellular glycerophosphocholine.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- LoFtool
- 0.593
- RVIS EVS
- -1.28
- RVIS percentile EVS
- 5.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.143
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |