In conclusion, our finding showed a statistically significant gene–diet interaction between the CARTPT rs2239670 and compliance with healthy and good quality diet rich in antioxidants in relation to obesity and related metabolic phenotypes; high intake of NEAC by minor allele carriers attenuated genetic association with BMI and FM%; however, high compliance with these indices could not affect genetic predisposition to blood sugar abnormalities. The gene discussed is CARTPT; the disease is obesity due to melanocortin 4 receptor deficiency.