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; glycerophospholipase activity; and lipid binding activity. Involved in N-acylphosphatidylethanolamine metabolic process. Located in cytosol. Biomarker of seminoma. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtLipodystrophy, familial partial, 9

Clinical highlights

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.86

LOEUF

LOF

Mechanism· G2P

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

Background carrier burden — how many people carry a rare variant somewhere in PLAAT3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 210

226 rare PASS variants

Rare truncating (LoF)

1 in 540

44 rare PASS variants

Rare synonymous (reference)

1 in 270

82 rare PASS variants

Rare missense and truncating variants are carried at similar rates in PLAAT3; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 380	1 in 1,100
South Asian	~43k	1 in 220	1 in 1,200
Remaining (unassigned)	~30k	1 in 170	1 in 5,000
European (Finnish)	~27k	1 in 300	none seen
Admixed American	~22k	1 in 150	1 in 500
African / African American	~21k	1 in 140	1 in 840
East Asian	~20k	1 in 270	1 in 1,000
Ashkenazi Jewish	~13k	1 in 870	none seen
Middle Eastern	~2,884	1 in 180	1 in 310

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 3 of 4 coding exons well covered in gnomAD exomes; exon 2 marginal. Genomes: all 4.? see exons ↓