We report here the first case of an L1CAM gene mutation identified in mental retardation, adducted thumbs, shuffling gait, and aphasia (MASA) syndrome in Japan. The patient was a 10-year-old boy with mild mental retardation, bilateral adducted thumbs and corpus callosum hypoplasia. His family had no history of MASA syndrome. The L1CAM gene contained a nonsense mutation (R1166X) in exon 26 in the cytoplasmic domain. No mutation was found in the extracellular and transmembrane domains of L1CAM. The abnormal development of axon tracts resulting in the corpus callosum hypoplasia and adducted thumbs appears to be caused by malfunction of the cytoplasmic domain of L1CAM.