The 1-acylglycerol-3-phosphate O-acyltransferases (AGPAT) are enzymes that catalyze the conversion of lysophosphatidic acid to phosphatidic acid, which is a precursor of triacylglycerol, the main fat reservoir in mammals. In pigs, there are 5 annotated genes in the AGPAT gene family. We used whole-genome sequencing to identify genetic variants in the AGPAT gene family in pigs and then we validated their association with fat content and fatty acid composition. Among the 6,639 variants identified across the AGPAT gene family through whole-genome sequencing of 205 Duroc pigs, we preselected a missense single nucleotide polymorphism in exon 6 of AGPAT5 (rs196952262, A>G) based on minor allele frequency, association analyses, and linkage disequilibrium. The effect of this variant was validated in 1,105 pigs from the same Duroc line genotyped using a high-resolution melt protocol. The A allele showed a positive additive effect for intramuscular fat (+1.12% ± 0.21, p < 0.001, for gluteus medius and +0.89% ± 0.33, p < 0.01, for longissimus). We also observed significant effects on fatty acid composition that were, at least in part, independent of the increased intramuscular fat content. Accounting for intramuscular fat content, the A allele resulted in more monounsaturated fatty acids (+0.34% ± 0.15, p < 0.05, for longissimus) and a greater monounsaturated/polyunsaturated fatty acids ratio (+0.11 ± 0.04, p < 0.01, for gluteus medius and +0.13 ± 0.05, p < 0.05, for longissimus). Although further studies would be needed before the causality of the variant on intramuscular fat content and fatty acid composition can be confirmed, this variant can be used as a marker in assisted selection for modulating pig fat deposition and fatty acid content.