GDPD1

Chr 17

glycerophosphodiester phosphodiesterase domain containing 1

Also known as: GDE4

NCBI Gene: 284161UniProt: Q8N9F7

This gene encodes a member of the glycerophosphodiester phosphodiesterase family of enzymes that catalyze the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol. The encoded protein is localized to the cytoplasm and concentrates near the perinuclear region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

0
Active trials
45
ClinVar variants
11
Pathogenic / LP
1.6
Missense Z
0.69
LOEUF
4
Pubs (2 yr)
Clinical Summary— GDPD1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 30 VUS of 45 total submissions
Some data sources returned errors (1)

ensembl: Error: Ensembl fetch failed: 500 for https://rest.ensembl.org/lookup/symbol/homo_sapiens/GDPD1?content-type=application/json&expand=1

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.69LOEUF
pLI 0.003
Z-score 2.62
OE 0.38 (0.22–0.69)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.56Z-score
OE missense 0.65 (0.56–0.77)
106 obs / 162.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.38 (0.22–0.69)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.65 (0.56–0.77)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.00
0≤1.21.6
LoF obs/exp: 8 / 20.9Missense obs/exp: 106 / 162.0Syn Z: 0.02

ClinVar Variant Classifications

45 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic10
Likely Pathogenic1
VUS30
Likely Benign3
Benign1
10
Pathogenic
1
Likely Pathogenic
30
VUS
3
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
10
0
10
Likely Pathogenic
0
0
1
0
1
VUS
0
22
8
0
30
Likely Benign
0
0
3
0
3
Benign
0
0
1
0
1
Total02223045

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

GDPD1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Glycerophosphodiester phosphodiesterase 1 mediates G3P accumulation for Eureka lemon resistance to citrus yellow vein clearing virus
Liao P et al.·Hortic Res
2024
Identification of novel 3D-genome altering and complex structural variants underlying retinitis pigmentosa type 17 through a multistep and high-throughput approach
de Bruijn SE et al.·Front Genet
2024
Alteration of N6-methyladenosine Modification Profiles in the Neutrophilic RNA Following Ischemic Stroke.
Fan J et al.·Neuroscience
2024
The non-tandem CCCH zinc finger protein AtC3H26 modulates salt stress response and phosphate starvation response through its ribonuclease activity in Arabidopsis
Seok HY et al.·BMC Plant Biol
2025
ABHD4 regulates adipocyte differentiation in vitro but does not affect adipose tissue lipid metabolism in mice
Seramur ME et al.·J Lipid Res
2023
Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7
Kitakaze K et al.·J Lipid Res
2021
Non-Invasive and Real-Time Monitoring of the Breast Cancer Metastasis Degree via Metabolomics
Zhu W et al.·Cancers (Basel)
2022
Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds
DeMers LC et al.·Front Plant Sci
2021
Top 8 full-text resultsSearch PubTator3 ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients