AGPAT1

Chr 6

1-acylglycerol-3-phosphate O-acyltransferase 1

Also known as: 1-AGPAT1, G15, LPAAT-alpha, LPAATA, LPLAT1

NCBI Gene: 10554ENSG00000204310UniProt: Q99943

This gene encodes an enzyme that converts lysophosphatidic acid (LPA) into phosphatidic acid (PA). LPA and PA are two phospholipids involved in signal transduction and in lipid biosynthesis in cells. This enzyme localizes to the endoplasmic reticulum. This gene is located in the class III region of the human major histocompatibility complex. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

0
ClinVar variants
0
Pathogenic / LP
0.97
pLI score· haploinsufficient
0
Active trials
Clinical Summary— AGPAT1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.97). One damaged copy is likely sufficient to cause disease.
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
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.
0.31LOEUF
pLI 0.972
Z-score 3.41
OE 0.06 (0.02–0.31)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

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.
2.61Z-score
OE missense 0.45 (0.37–0.54)
80 obs / 177.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

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.0.06 (0.02–0.31)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.45 (0.37–0.54)
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.0.76
0≤1.21.6
LoF obs/exp: 1 / 15.5Missense obs/exp: 80 / 177.9Syn Z: 1.64

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

AGPAT1 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci.
Aung T et al.·Nat Genet
2017Meta-analysis
AGPAT1 as a Novel Colonic Biomarker for Discriminating Between Ulcerative Colitis With and Without Primary Sclerosing Cholangitis.
Vessby J et al.·Clin Transl Gastroenterol
2022
Temporal Effects of Disease Signature Genes and Core Mechanisms in the Hyperacute Phase of Acute Ischemic Stroke: A Bioinformatics Analysis and Experimental Validation.
Ding PL et al.·Mediators Inflamm
2025Functional
Prevalence of mutations in AGPAT2 among human lipodystrophies.
Magré J et al.·Diabetes
2003
ColoLipidGene: signature of lipid metabolism-related genes to predict prognosis in stage-II colon cancer patients.
Vargas T et al.·Oncotarget
2015Cohort
Identification of a combined apoptosis and hypoxia gene signature for predicting prognosis and immune infiltration in breast cancer.
Ren X et al.·Cancer Med
2022
Clinical significance of combining salivary mRNAs and carcinoembryonic antigen for ovarian cancer detection.
Yang J et al.·Scand J Clin Lab Invest
2021
Salivary transcriptomic biomarkers for detection of ovarian cancer: for serous papillary adenocarcinoma.
Lee YH et al.·J Mol Med (Berl)
2012
Cholestasis impairs hepatic lipid storage via AMPK and CREB signaling in hepatitis B virus surface protein transgenic mice.
Irungbam K et al.·Lab Invest
2020
3'UTR Polymorphism in ACSL1 Gene Correlates with Expression Levels and Poor Clinical Outcome in Colon Cancer Patients.
Vargas T et al.·PLoS One
2016Cohort
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.

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External Resources

Links to major genomics databases and tools