This dataset contains the experimental data associated to the publication "Identification of a missense variant in the porcine AGPAT gene family associated with intramuscular fat content through whole-genome sequencing" by Molinero et al. (2022; doi: https://doi.org/10.1111/age.13258). It includes a TXT file with the genotypes obtained using real-time PCR with High-Resolution Melt and the phenotypic data necessary for the validation of the effect of single nucleotide polymorphism rs196952262 on intramuscular fat in 1,034 pigs.