Among the many reported etiologic genes for hereditary motor-sensory neuropathy, the GNB4 variant has been rarely reported, with only one case reported in a Japanese family. We present the case of a 14-year-old girl with hereditary motor-sensory neuropathy who was diagnosed as having a GNB4 variant after proper examination. Her chief complaints were repeated falls and learning difficulties. She had been diagnosed with tethered spinal cord syndrome due to a terminal filum lipoma at the age of 8 years and had undergone untethering surgery, but her tendency to fall and poor academic performance had not improved. No notable findings were observed in the cerebral neurological examination, but the patient had weakness of the anterior cervical muscles and decreased sensation in the S1 area. Blood tests and MRI of the head and spinal cord showed no abnormalities. Nerve conduction studies revealed decreased nerve conduction velocity with lower extremity predominance. Genetic analysis showed no duplication or deletion of PMP22, but a heterozygous variant was found in GNB4 gene (NM_021629.4 : c.229G>A, p.Gly77Arg) by the etiological gene analysis for Charcot-Marie-Tooth disease. This is a de novo variant that has not been included in any database ; the same variant was not found in the parents. Her intelligence quotient scores by the WISC-IV were in the borderline range. There was variability in each item, with especially low scores in perceptual reasoning. Although few studies have reported on GNB4 variants and no association with neurodevelopmental disorders, it is necessary to compile more cases because GNB4 variants may be related to the symptoms of the central nervous system.