AbstractBackgroundTheHMGA2:c.83G>A variant was identified in Welsh ponies having pleiotropic effects on height and insulin concentration.ObjectiveDetermine whether theHMGA2:c.83G>A variant is associated with decreased height and higher basal insulin concentrations across pony breeds.AnimalsTwo hundred thirty‐six ponies across 6 breeds.MethodsCross‐sectional study. Ponies were genotyped for theHMGA2:c.83G>A variant and phenotyped for height and basal insulin concentrations. Stepwise regression was performed for model analysis using a linear regression model for height and mixed linear model for insulin with farm as a random effect. Coefficient of determination, pairwise comparison of the estimated marginal means and partial correlation coefficients (parcor) were calculated to assess the relationship betweenHMGA2genotype and height or insulin.ResultsBreed and genotype accounted for 90.5% of the variation in height across breeds, and genotype explained 21% to 44% of the variation within breeds. Breed, genotype, cresty neck score, sex, age, and farm accounted for 45.5% of the variation in insulin, with genotype accounting for 7.1%. TheHMGA2A allele frequency was 62% and correlated with both height (parcor = −0.39;P< .001) and insulin (parcor = 0.22;P= .02). Pairwise comparisons found A/A ponies were >10 cm shorter than other genotypes. Compared with G/G individuals, A/A and G/A individuals had 4.3 μIU/mL (95% confidence interval [CI]: 1.8‐10.5) and 2.7 μIU/mL (95% CI: 1.4‐5.3) higher basal insulin concentrations, respectively.Conclusions and Clinical ImportanceThese data demonstrate the pleiotropic effects of theHMGA2:c.83G>A variant and its role in identifying ponies at increased risk for insulin dysregulation.