We present the case of a novel homozygous nonsense (c.4846C > T [p.R1616X]) mutation in the VPS13B in a Chinese boy with the primary symptoms of Cohen syndrome. This case presented with manifestations consistent with Cohen syndrome, including developmental delay, microcephaly, typical facial features, short stature, muscle hypotonia, neutropenia, and abnormal dental development; however, the patient did not have the typical findings of obesity, myopia, progressive retinal dystrophy, or epilepsy. The patient had a homozygous nonsense mutation (NM_017890: c.4846C > T [p.R1616X]). His brother, sister, and parents are heterozygous for the mutation. This locus variation has not been previously reported in Chinese children. Different mutation sites have different phenotypes. Cohen syndrome caused by a homozygous nonsense mutation of the VPS13B c.4846C > T (p.R1616X) does not present with obesity, ophthalmic abnormalities, or epilepsy, but has abnormal dental development. This may be related to the premature termination of peptide synthesis caused by nonsense mutations at this site.