OBJECTIVES: To investigate the molecular mechanism underlying Leber hereditary optic neuropathy (LHON) caused by the m.3472T>C (p.Phe56Leu) mutation. METHODS: From a cohort of 1397 LHON patients, three large pedigrees (WZL122, WZ676, WZ706) carrying the m.3472T>C mutation were identified and selected for this study. Immortalized lymphoblastoid cell lines were established from peripheral blood samples obtained from two affected individuals carrying the homoplasmic m.3472T>C mutation (derived from one Han Chinese LHON pedigree) and two genetically unrelated, matched healthy controls. The MitoTool software was used to analyze the complete mitochondrial DNA sequence to determine the haplogroup background, and the conservation of the mtDNA mutation site was evaluated using the MitoMap database. The secondary structure of the ND1 protein was predicted and analyzed using online prediction software. The three-dimensional structure and molecular interaction changes of wild-type and mutant ND1 proteins were visualized and analyzed using PyMOL. Western blotting was performed to determine the expression levels of key proteins. Cellular ATP levels were measured using a chemiluminescence assay. Mitochondrial membrane potential and intracellular reactive oxygen species (ROS) levels were assessed by flow cytometry. RESULTS: mtDNA haplotype analysis showed that the subjects all belonged to the East Asian mitochondrial haplogroup D4. The m.3472T>C mutation results in the substitution of a highly conserved phenylalanine with leucine (p.Phe56Leu) in the ND1 subunit of mitochondrial complex Ⅰ, which may alter the structure and function of ND1. In lymphoblastoid cell lines carrying the m.3472T>C mutation, manifestations of mutant ND1 instability were observed, including reduced ND1 protein levels, diminished mitochondrial ATP production, decreased mitochondrial membrane potential, and increased mitochondrial ROS production. Concurrently, the expression levels of the antioxidant enzymes catalase and SOD2 were elevated (all P<0.01). These findings collectively suggest impaired complex Ⅰ function. CONCLUSIONS The m.3472T>C mutation contributes to the pathogenesis of LHON by disrupting the structural stability of the ND1 subunit in complex Ⅰ, leading to mitochondrial dysfunction.