To analyze the clinical phenotype and genetic characteristics of Zhu-Tokita-TakenouchiKim (ZTTK) syndrome caused by SON gene mutation. Methods The clinical data of ZTTK syndrome from one proband were collected, and the suspected ZTTK syndrome was diagnosed by the next generation sequencing technology and Sanger sequencing. Results A 3 -year-old boy presented with psychomotor developmental delay, intellectual disability, ECG abnormality and hypoplasia of the corpus calloum. Gene tests found a de novo heterozygous mutation of c. 5753 - 5756 del, (p.Val 1918 Glufs* 87 ) in the SON gene. According to the ACMG guidelines, the mutation was classified as pathogenic. Conclusions The patient’s clinical phenotype was consistent with ZTTK syndrome. The heterozygous mutation of c. 5753 - 5756 del, p.Val1918 Glufs* 87 in SON was pathogenic, which enriches the SON gene variant spectrum in Chinese children.