There was no prior knowledge available revealing the impact of the various genotypes studied in the current study, including heterozygous GA of HNF4A-rs4812829, (0.64; 95% CI 0.47–0.86; p < 0.01), heterozygous TC of WFS1-rs1801214 (0.60; 95% CI 0.44–0.80; p < 0.01), heterozygous GA of DUSP9-rs5945326 (0.60; 95% CI 0.39–0.92; p = 0.01), heterozygous GA of ZFAND6-rs11634397 (0.75; 95% CI 0.56–1.01; p = 0.05), and homozygous AA of FTO-rs11642841, on prediabetes susceptibility. The gene discussed is DUSP9; the disease is prediabetes syndrome.