PLAAT3

Chr 11AR

phospholipase A and acyltransferase 3

Also known as: AdPLA, FPLD9, H-REV107, H-REV107-1, HRASLS3, HREV107, HREV107-1, HREV107-3

NCBI Gene: 11145ENSG00000176485UniProt: P53816

Enables N-acyltransferase activity; lipid binding activity; and phospholipase activity. Involved in N-acylphosphatidylethanolamine metabolic process. Predicted to be located in several cellular components, including lysosome; nuclear envelope; and peroxisome. Predicted to be active in cytoplasm. Biomarker of seminoma. [provided by Alliance of Genome Resources, Jul 2025]

Primary Disease Associations & Inheritance

Lipodystrophy, familial partial, type 9MIM #620683
AR
52
ClinVar variants
11
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— PLAAT3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 40 VUS of 52 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.
1.86LOEUF
pLI 0.000
Z-score -0.49
OE 1.21 (0.69–1.86)
Tolerant

Highly tolerant — LoF variants common in population

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.
0.18Z-score
OE missense 0.95 (0.81–1.13)
97 obs / 102.1 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.1.21 (0.69–1.86)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.95 (0.81–1.13)
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.1.10
0≤1.21.6
LoF obs/exp: 8 / 6.6Missense obs/exp: 97 / 102.1Syn Z: -0.48

ClinVar Variant Classifications

52 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic8
Likely Pathogenic3
VUS40
Likely Benign1
8
Pathogenic
3
Likely Pathogenic
40
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
0
6
0
8
Likely Pathogenic
0
0
3
0
3
VUS
0
37
3
0
40
Likely Benign
0
0
0
1
1
Benign
0
0
0
0
0
Total23712152

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

View in ClinVar →

Protein Context — Lollipop Plot

PLAAT3 · protein map & ClinVar variants

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

Gene2Phenotype Curations

PLAAT3-related lipodystrophy syndrome with neurological features

limited
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗
frameshift variantstop gained

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Lipodystrophy, familial partial, type 9

MIM #620683

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The PLAAT family as phospholipid-related enzymes.
Uyama T et al.·Prog Lipid Res
2025Review
Silencing effects of mutant RAS signalling on transcriptomes.
Sers C et al.·Adv Biol Regul
2023
Harnessing lysosomal genetics: development of a risk stratification panel and unveiling of DPP7 as a biomarker for colon adenocarcinoma.
Luo Z et al.·J Genet Genomics
2025
A study on the mechanism of action of Syringin in the treatment of type 2 diabetes by integrating metabolomics, network pharmacology, molecular docking technology and experimental validation.
Wan C et al.·Int Immunopharmacol
2025Functional
GWAS loci associated with Chagas cardiomyopathy influences DNA methylation levels.
Casares-Marfil D et al.·PLoS Negl Trop Dis
2021
Shortcutting the diagnostic odyssey: the multidisciplinary Program for Undiagnosed Rare Diseases in adults (UD-PrOZA).
Schuermans N et al.·Orphanet J Rare Dis
2022
Proceedings of the annual meeting of the European Consortium of Lipodystrophies (ECLip), Pisa, Italy, 28-29 September 2023.
Ceccarini G et al.·Ann Endocrinol (Paris)
2024
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