AGPAT2

Chr 9AR

1-acylglycerol-3-phosphate O-acyltransferase 2

Also known as: 1-AGPAT2, BSCL, BSCL1, LPAAB, LPAAT-beta, LPLAT2

NCBI Gene: 10555ENSG00000169692UniProt: O15120OMIM: 603100

This gene encodes an enzyme that converts lysophosphatidic acid to phosphatidic acid in the endoplasmic reticulum, a critical step in phospholipid biosynthesis. Mutations cause congenital generalized lipodystrophy type 1 (Berardinelli-Seip syndrome), characterized by near-complete absence of adipose tissue from birth and severe insulin resistance. This condition follows autosomal recessive inheritance.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.541 OMIM phenotype
Clinical Summary— AGPAT2
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Gene-Disease Validity (ClinGen)
lipodystrophy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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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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Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
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GeneReview available — AGPAT2
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.54LOEUF
pLI 0.000
Z-score 0.20
OE 0.94 (0.59–1.54)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.72Z-score
OE missense 1.15 (1.03–1.30)
199 obs / 172.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.94 (0.59–1.54)
0≤0.351.4
Missense OE1.15 (1.03–1.30)
0≤0.61.4
Synonymous OE1.22
0≤1.21.6
LoF obs/exp: 11 / 11.7Missense obs/exp: 199 / 172.3Syn Z: -1.51

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

AGPAT2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
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
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