GDPD4
protein-codingglycerophosphodiester phosphodiesterase domain containing 4
Gene summary
Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in lipid metabolic process. Predicted to be active in membrane. [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 ~85.1 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 GDPD4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_182833.3. 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 | 1 | 1 | ||||
| missense | 72 | 7 | 79 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 72 | 8 | 0 | 80 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_878253.1 | 15 | MANE Select | |
| Ensembl | ENSP00000320815.4 | 15 | MANE Select | |
| Ensembl | ENSP00000365390.2 | 16 | Standard | |
| Ensembl | ENSP00000661301.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- lipid metabolic process
Molecular Function
- glycerophosphodiester phosphodiesterase activity
- metal ion binding
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000315938
- Coding exons
- 15
- Length
- 85130
- Individuals with no LoFs
- 124985
- Homozygous LoFs
- 9
- Heterozygous LoFs
- 754
- Defined
- 125748
- p
- 0.00304
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.00145 | 272 | 272 | 1.00 | 0.0000133 | 3429 |
| Missense (PolyPhen) | 74 | 82.377 | 0.89831 | 1130 | ||
| Synonymous | 0.444 | 92 | 97.6 | 0.943 | 0.00000499 | 963 |
| Loss of Function | 1.09 | 23 | 29.4 | 0.782 | 0.00000125 | 363 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0023 | 0.0022 | notable |
| Latino/Admixed American | 0.00046 | 0.00046 | rare |
| Ashkenazi Jewish | 0.0062 | 0.0061 | notable |
| East Asian | 0.031 | 0.031 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00025 | 0.00025 | rare |
| South Asian | 0.0011 | 0.0011 | notable |
| Other | 0.0031 | 0.0031 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0392
Intolerance Scores
- LoFtool
- 0.950
- RVIS EVS
- 1.73
- RVIS percentile EVS
- 96.57
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 1.87e-7
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |