The transcription factor, MafB, plays important role in the differentiation and functional maintenance of various cells and tissues, such as the inner ear, kidney podocyte, parathyroid gland, pancreatic islet, and macrophages. The rare heterozygous substitution (p.Leu239Pro) of the DNA binding domain in MAFB is the cause of Focal Segmental Glomerulosclerosis associated with Duane Retraction Syndrome, which is characterized by impaired horizontal eye movement due to cranial nerve maldevelopment in humans. In this research, we generated mice carrying MafB p.Leu239Pro (Mafbmt/mt) and retrieved their tissues for analysis. As a result, we found that the phenotype of Mafbmt/mt mouse was similar to that of the conventional Mafb deficient mouse. This finding suggests that the Leucine residue at 239 in the DNA binding domain plays a key role in MafB function and could contribute to the diagnosis or development of treatment for patients carrying the MafB p.Leu239Pro missense variant. •Mafbmt/mt mice displayed abnormal development of the inner ear and kidney podocyte, similar to the MAFB mutant patients.•Mafbmt/mt mice had decreased serum PTH level, abnormal number of α- and β-cell in the pancreas, and abnormal F4/80+ macrophages.•The phenotype of Mafbmt/mt and Mafb deficient mice was similar, indicating MafB DNA binding domain critical for its function.