This article reports a case of a 17-year-old female patient who presented with absent secondary sexual characteristics and primary amenorrhea. The patient's clinical manifestations included hearing loss, blue irides, and telecanthus, accompanied by short stature, bilateral cubitus valgus, and shield-shaped chest. Laboratory tests indicated hypogonadotropic hypogonadism with partial growth hormone deficiency, and ultrasound revealed a rudimentary uterus. Whole-exome sequencing identified a c.1029dup (p.Thr344Hisfs*58) mutation in the SOX10 gene, confirming the diagnosis of Waardenburg syndrome (WS). Sanger sequencing confirmed that this was a de novo mutation, which has not been reported in public databases. Family investigation showed that the mutation was not detected in peripheral blood samples from the patient's parents. This mutation expands the genetic mutation spectrum and clinical data of WS. In cases of unexplained hearing impairment, abnormal pigmentation, and growth retardation in children, SOX10 gene mutation should be conside-red, and genetic testing should be performed early to establish a diagnosis.