GDPD5

Chr 11

glycerophosphodiester phosphodiesterase domain containing 5

Also known as: GDE2, PP1665

NCBI Gene: 81544ENSG00000158555UniProt: Q8WTR4

Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in positive regulation of cell cycle and positive regulation of neuron differentiation. Predicted to act upstream of or within negative regulation of Notch signaling pathway; 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. [provided by Alliance of Genome Resources, Apr 2025]

113
ClinVar variants
8
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— GDPD5
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
8 Pathogenic / Likely Pathogenic· 97 VUS of 113 total submissions

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.
0.60LOEUF
pLI 0.000
Z-score 3.31
OE 0.37 (0.24–0.60)
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.
1.70Z-score
OE missense 0.76 (0.69–0.83)
298 obs / 392.6 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.0.37 (0.24–0.60)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.76 (0.69–0.83)
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.1.07
0≤1.21.6
LoF obs/exp: 12 / 32.3Missense obs/exp: 298 / 392.6Syn Z: -0.68

ClinVar Variant Classifications

113 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic8
VUS97
Likely Benign7
Benign1
8
Pathogenic
97
VUS
7
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
8
0
8
Likely Pathogenic
0
0
0
0
0
VUS
0
95
2
0
97
Likely Benign
0
4
0
3
7
Benign
0
0
0
1
1
Total099104113

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

View in ClinVar →

Protein Context — Lollipop Plot

GDPD5 · 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
KLF7 promotes neuroblastoma differentiation through the GTPase signaling pathway by upregulating neuroblast differentiation-associated protein AHNAKs and glycerophosphodiesterase GDPD5.
Qiao S et al.·FEBS J
2024
MiR-874-3p represses the migration and invasion yet promotes the apoptosis and cisplatin sensitivity via being sponged by long intergenic non-coding RNA 00922 (LINC00922) and targeting Glycerophosphodiester Phosphodiesterase Domain Containing 5 (GDPD5) in gastric cancer cells.
Zhang X et al.·Bioengineered
2022
GDPD5, a target of miR-195-5p, is associated with metastasis and chemoresistance in colorectal cancer.
Feng C et al.·Biomed Pharmacother
2018
Unlocking the signaling potential of GPI-anchored proteins through lipolytic cleavage.
Borza R et al.·Trends Cell Biol
2025Review
IGF2BP3 Worsens Lung Cancer through Modifying Long Non-coding RNA CERS6-AS1/microRNA-1202 Axis.
Yan A et al.·Curr Med Chem
2023
Choline metabolism-based molecular diagnosis of cancer: an update.
Glunde K et al.·Expert Rev Mol Diagn
2015Review
Silencing of the glycerophosphocholine phosphodiesterase GDPD5 alters the phospholipid metabolite profile in a breast cancer model in vivo as monitored by (31) P MRS.
Wijnen JP et al.·NMR Biomed
2014Functional
Glycerophosphodiesterase GDE2 Promotes Neuroblastoma Differentiation through Glypican Release and Is a Marker of Clinical Outcome.
Matas-Rico E et al.·Cancer Cell
2016
Identification of Novel Candidate Genes and Variants for Hearing Loss and Temporal Bone Anomalies.
Santos-Cortez RLP et al.·Genes (Basel)
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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