Vitamin B12 may increase the risk of coronary atherosclerosis by inhibiting VPS29 (Mediated Effect=0.031, 95% CI: 0.030–0.032; Mediated Proportion=13.04%, 95% CI: 12.53%-13.56%) and PSME1 (Mediated Effect=0.101, 95% CI: 0.097–0.106; Mediated Proportion=42.75%, 95% CI: 40.88%-44.61%). Here, VPS29 is linked to coronary atherosclerosis.