PLAAT3

Chr 11

phospholipase A and acyltransferase 3

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

NCBI Gene: 11145 ENSG00000176485 UniProt: P53816

The protein exhibits phospholipase A1/A2 and N-acyltransferase activities, catalyzing the release of fatty acids from glycerophospholipids and the transfer of fatty acyl groups to form N-acylphosphatidylethanolamine, which serves as a precursor for bioactive lipid mediators. Mutations cause familial partial lipodystrophy type 9, inherited in an autosomal recessive pattern. The gene shows low constraint against loss-of-function variants (pLI near 0), consistent with recessive inheritance where heterozygous carriers are typically unaffected.

ResearchSummary from RefSeq, OMIM, UniProt

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]

ResearchGenerating clinical summary…

LOFmechanismLOEUF 1.86

Clinical Summary— PLAAT3

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

4 unique Pathogenic / Likely Pathogenic· 38 VUS of 51 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

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?

0.18Z-score

OE missense 0.95 (0.81–1.13)

97 obs / 102.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.21 (0.69–1.86)

0≤0.351.4

Missense OE?0.95 (0.81–1.13)

0≤0.61.4

Synonymous OE?1.10

0≤1.21.6

LoF obs/exp: 8 / 6.6Missense obs/exp: 97 / 102.1Syn Z: -0.48

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

limitedPLAAT3-related lipodystrophy syndrome with neurological featuresLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.84top 10%

GOF

0.79top 25%

LOF

0.1697th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

51 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic3

Likely Pathogenic1

VUS38

Likely Benign1

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	3	0	0	0	3
Likely Pathogenic	1	0	0	0	1
VUS	0	37	1	0	38
Likely Benign	0	0	0	1	1
Benign	0	0	0	0	0
Total	4	37	1	1	43

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

View in ClinVar →

9 pathogenic / likely-pathogenic (of 12) ClinVar copy-number / structural variants overlap PLAAT3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →