UbiA prenyltransferase domain‐containing protein‐1 (UBIAD1) is responsible for the biosynthesis of menaquinone‐4 (MK‐4), a cofactor for extrahepatic carboxylation of vitamin K‐dependent (VKD) proteins. Genetic variations of UBIAD1 are mainly associated with Schnyder corneal dystrophy (SCD), a disease characterized by abnormal accumulation of cholesterol in the cornea. Results from in vitro studies demonstrate that SCD‐associated UBIAD1 mutations are defective in MK‐4 biosynthesis. However, SCD patients do not exhibit typical phenotypes associated with defects of MK‐4 or VKD carboxylation. Here, we coupled UBIAD1’s biosynthetic activity of MK‐4 with VKD carboxylation in HEK293 cells that stably express a chimeric VKD reporter protein. The endogenous Ubiad1 gene in these cells was knocked out by CRISPR‐Cas9‐mediated genome editing. The effect of UBIAD1 mutations on MK‐4 biosynthesis and VKD carboxylation was evaluated in Ubiad1‐deficient reporter cells by determining the production of MK‐4 or by measuring the efficiency of reporter‐protein carboxylation. Our results show that the hot‐spot mutation N102S has a moderate impact on MK‐4 biosynthesis (retained ˜ 82% activity) but does not affect VKD carboxylation. However, the G186R mutation significantly affected both MK‐4 biosynthesis and VKD carboxylation. Other mutations exhibit varying degrees of effects on MK‐4 biosynthesis and VKD carboxylation. These results are consistent with in vivo results obtained from gene knock‐in mice and SCD patients. Our findings suggest that UBIAD1’s MK‐4 biosynthetic activity does not directly correlate with the phenotypes of SCD patients. The established cell‐based assays in this study provide a powerful tool for the functional studies of UBIAD1 in a cellular milieu. UBIAD1 is an integral membrane prenyltransferase that is responsible for the biosynthesis of menaquinone‐4 (MK‐4), a cofactor for vitamin K‐dependent (VKD) carboxylation. Genetic variations of UBIAD1 are mainly associated with Schnyder Corneal Dystrophy (SCD). However, SCD patients do not exhibit typical phenotypes associated with defects of MK‐4 or VKD carboxylation. Here, we characterized the effect of UBIAD1 mutations on MK‐4 biosynthesis and VKD carboxylation in a cellular environment.