AGPAT5

Chr 8

1-acylglycerol-3-phosphate O-acyltransferase 5

Also known as: 1AGPAT5, LPAATE, LPLAT5

NCBI Gene: 55326ENSG00000155189UniProt: Q9NUQ2

The AGPAT5 protein converts lysophosphatidic acid to phosphatidic acid in the second step of de novo phospholipid biosynthesis. Mutations cause autosomal recessive congenital cataracts, facial dysmorphism, and neuropathy (CCFDN), a disorder affecting the eyes, peripheral nervous system, and facial features. This gene shows low constraint against loss-of-function variants (pLI 0.000007, LOEUF 0.979), consistent with its recessive inheritance pattern.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
4
Pubs (1 yr)
110
P/LP submissions
0%
P/LP missense
0.98
LOEUF
DN
Mechanism· predicted
Clinical Summary— AGPAT5
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
109 unique Pathogenic / Likely Pathogenic· 83 VUS of 210 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.98LOEUF
pLI 0.000
Z-score 1.63
OE 0.59 (0.37–0.98)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-1.66Z-score
OE missense 1.33 (1.21–1.48)
262 obs / 196.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.59 (0.37–0.98)
0≤0.351.4
Missense OE1.33 (1.21–1.48)
0≤0.61.4
Synonymous OE1.51
0≤1.21.6
LoF obs/exp: 11 / 18.6Missense obs/exp: 262 / 196.4Syn Z: -3.52
DN
0.6454th %ile
GOF
0.5856th %ile
LOF
0.2871th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

210 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic104
Likely Pathogenic5
VUS83
Likely Benign5
Benign3
104
Pathogenic
5
Likely Pathogenic
83
VUS
5
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
103
0
104
Likely Pathogenic
0
0
5
0
5
VUS
0
69
14
0
83
Likely Benign
0
1
3
1
5
Benign
0
1
2
0
3
Total1711271200

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

View in ClinVar →

Protein Context — Lollipop Plot

AGPAT5 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Identification of a missense variant in the porcine AGPAT gene family associated with intramuscular fat content through whole-genome sequencing
Molinero E et al.·Anim Genet
2022
Integrative Analysis of Gene Networks Associated with Adipose and Muscle Traits in Hanwoo Steers
Hwang S et al.·Animals (Basel)
2025
A Prognostic Lysine Crotonylation Signature Shapes the Immune Microenvironment in Hepatocellular Carcinoma.
Su W et al.·Curr Med Chem
2025
Construction and Validation of a Novel Butyrylation-Related Gene Signature Related to Prognosis, Clinical Implications, and Immune Microenvironment Characterization of Hepatocellular Carcinoma.
Su W et al.·ACS Omega
2025
[Molecular Mechanisms of Intervention With Lishukang Capsule in a Rat Model of High-Altitude Pulmonary Edema].
Zhang D et al.·Sichuan Da Xue Xue Bao Yi Xue Ban
2025Functional
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Liver-specific deletion of Agpat5 protects against liquid sucrose-induced hyperinsulinemia and glucose intolerance.
Michorowska S et al.·Biochem Biophys Res Commun
2024Open Access
Low Expression of AGPAT5 Is Associated With Clinical Stage and Poor Prognosis in Colorectal Cancer and Contributes to Tumour Progression.
Zang J et al.·Clin Med Insights Oncol
2022Open Access
Lipid biosynthesis enzyme Agpat5 in AgRP-neurons is required for insulin-induced hypoglycemia sensing and glucagon secretion.
Strembitska A et al.·Nat Commun
2022Open Access
The rs196952262 Polymorphism of the AGPAT5 Gene is Associated with Meat Quality in Berkshire Pigs.
Park WB et al.·Korean J Food Sci Anim Resour
2017Open Access
Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria.
Prasad SS et al.·J Lipid Res
2011
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