BackgroundHeterozygous loss-of-function mutations in the chromodomain helicase DNA-binding protein 7 (CHD7) gene cause CHARGE syndrome characterized by various congenital anomalies. A majority of patients with CHARGE syndrome present with congenital hypogonadotropic hypogonadism (HH), and combined pituitary hormone deficiency (CPHD) can also be present. WhereasCHD7mutations have been identified in some patients with isolated HH without a diagnosis of CHARGE syndrome, it remains unclear whetherCHD7mutations can be identified in patients with CPHD who do not fulfill the criteria for CHARGE syndrome.Case presentationA 33-year-old woman was admitted to our hospital. She had primary amenorrhea and was at Tanner stage 2 for both pubic hair and breast development. She was diagnosed with CPHD (HH, growth hormone deficiency, and central hypothyroidism), and a heterozygous rare missense mutation (c.6745G > A, p.Asp2249Asn) in theCHD7gene was identified. Our conservation analysis and numerous in silico analyses suggested that this mutation had pathogenic potential. She had mild intellectual disability, a minor feature of CHARGE syndrome, but did not fulfill the criteria for CHARGE syndrome.ConclusionsWe report a rare case of CPHD harboringCHD7mutation without CHARGE syndrome. This case provides valuable insights into phenotypes caused byCHD7mutations.CHD7mutations can have a continuous phenotypic spectrum depending on the severity of hypopituitarism and CHARGE features. Therefore, we would like to propose a novel concept of CHD7-associated syndrome.