LPCAT1

Chr 5

lysophosphatidylcholine acyltransferase 1

Also known as: AGPAT10, AGPAT9, AYTL2, LPCAT-1, LPLAT8, PFAAP3, lpcat, lysoPAFAT

NCBI Gene: 79888ENSG00000153395UniProt: Q8NF37

This gene encodes a member of the 1-acyl-sn-glycerol-3-phosphate acyltransferase family of proteins. The encoded enzyme plays a role in phospholipid metabolism, specifically in the conversion of lysophosphatidylcholine to phosphatidylcholine in the presence of acyl-CoA. This process is important in the synthesis of lung surfactant and platelet-activating factor (PAF). Elevated expression of this gene may contribute to the progression of oral squamous cell, prostate, breast, and other human cancers. [provided by RefSeq, Sep 2016]

0
ClinVar variants
0
Pathogenic / LP
0.14
pLI score
0
Active trials
Clinical Summary— LPCAT1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.25) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
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.
0.48LOEUF
pLI 0.137
Z-score 3.62
OE 0.25 (0.14–0.48)
Moderately constrained

More LoF-intolerant than ~75% 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.
1.61Z-score
OE missense 0.75 (0.68–0.84)
254 obs / 337.3 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.0.25 (0.14–0.48)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.75 (0.68–0.84)
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.1.11
0≤1.21.6
LoF obs/exp: 7 / 27.5Missense obs/exp: 254 / 337.3Syn Z: -1.07

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

LPCAT1 · 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
LPCAT1-mediated membrane phospholipid remodelling promotes ferroptosis evasion and tumour growth.
Li Z et al.·Nat Cell Biol
2024Functional
The validation and clinical significance of LPCAT1 down-regulation in acute myeloid leukemia.
Chen Q et al.·Mol Biol Rep
2023
LPCAT1 enhances the invasion and migration in gastric cancer: Based on computational biology methods and in vitro experiments.
Chen ZX et al.·Cancer Med
2023
A Feedback Loop Between Fatty Acid Metabolism and Epigenetics in Clear Cell Renal Carcinoma.
Ye Z et al.·Adv Sci (Weinh)
2025
LPCAT1 acts as an independent prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma.
Li L et al.·Eur J Med Res
2022
LPCAT1 functions as an oncogene in cervical cancer through mediating JAK2/STAT3 signaling.
Gao F et al.·Exp Cell Res
2022
[Prognostic Significance of LPCAT1 in Adult Acute Myeloid Leukemia Patients with FAB Subtype M2].
Liu Y et al.·Zhongguo Shi Yan Xue Ye Xue Za Zhi
2023Cohort
LPCAT1 promotes brain metastasis of lung adenocarcinoma by up-regulating PI3K/AKT/MYC pathway.
Wei C et al.·J Exp Clin Cancer Res
2019
Lysophosphatidylcholine acyltransferase 1 promotes epithelial-mesenchymal transition of hepatocellular carcinoma via the Wnt/β-catenin signaling pathway.
Shen L et al.·Ann Hepatol
2022
Association of LPCAT1-rs8352 genetic variant with susceptibility and severity of pediatric bronchial asthma: a case-control study.
Mohany KM et al.·BMC Pediatr
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Oncogenic LPCAT1 Accelerates Intrahepatic Cholangiocarcinoma Development Through PI3K/Akt Signaling-Dependent Cell Cycle Regulation.
Jiang E et al.·J Gastroenterol Hepatol
2026
ATF2-LPCAT1-mediated PKM2 acetylation links cholesterol stress to macrophage metabolic reprogramming and functional remodeling.
Cao H et al.·Biochem Biophys Res Commun
2026Functional
LPCAT1 as a prognostic biomarker and risk indicator for hepatocellular carcinoma: insights into genes related to lipid metabolism.
Zhai H et al.·Front Oncol
2026🔓 Open Access
Lysolecithin reprogramming via LPCAT1 modulation restores endothelial function and prevents diabetes-associated dysmetabolism.
Sommella EM et al.·Cardiovasc Diabetol
2026🔓 Open Access
SOX2 induces LPCAT1 expression to promote cholesterol metabolic reprogramming-mediated invasion and metastasis in osteosarcoma.
Zhu L et al.·Front Mol Biosci
2025🔓 Open Access
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