GNPAT

Chr 1AR

glyceronephosphate O-acyltransferase

Also known as: DAP-AT, DAPAT, DHAPAT, RCDP2

NCBI Gene: 8443ENSG00000116906UniProt: O15228OMIM: 602744

The protein functions as dihydroxyacetonephosphate acyltransferase, catalyzing the first step in plasmalogen biosynthesis within peroxisomal membranes. Mutations cause rhizomelic chondrodysplasia punctata type 2, a severe disorder affecting skeletal development, growth, and neurological function. Inheritance is autosomal recessive.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.421 OMIM phenotype
Clinical Summary— GNPAT
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Gene-Disease Validity (ClinGen)
glyceronephosphate O-acyltransferase deficiency · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.23) despite low pLI — interpret in context.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.42LOEUF
pLI 0.304
Z-score 4.19
OE 0.23 (0.14–0.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.67Z-score
OE missense 0.90 (0.82–0.99)
316 obs / 351.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.23 (0.14–0.42)
0≤0.351.4
Missense OE0.90 (0.82–0.99)
0≤0.61.4
Synonymous OE1.01
0≤1.21.6
LoF obs/exp: 8 / 34.6Missense obs/exp: 316 / 351.5Syn Z: -0.06

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

GNPAT · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
GNPAT promotes immunosuppression in hepatocellular carcinoma by activating the plasmalogen-PPARγ pathway to drive M2 macrophage polarization.
Hu M et al.·Front Immunol
2026Open Access
GNPAT/USP30 Stabilizes DRP1 Protein to Promote Mitochondrial Fission and Functional Damage in COPD Progression.
Cheng XG et al.·Kaohsiung J Med Sci
2025Open AccessFunctional
A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing variant in the GNPAT gene.
Boulling A et al.·Genet Sel Evol
2025Open AccessFunctional
CSE triggers ferroptosis via SIRT4-mediated GNPAT deacetylation in the pathogenesis of COPD.
Li C et al.·Respir Res
2023Open Access
Neonatal rhizomelic chondrodysplasia punctata type 2 caused by a novel homozygous variant in the GNPAT gene.
Sayed J et al.·Clin Case Rep
2023Open Access
Top 5 resultsSearch Europe PMC ↗

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