This study reveals a novel homozygous <i>HES7</i> splicing variant causing SCDO4 and reviews all the previously reported <i>HES7</i> variants and corresponding symptoms, providing a comprehensive overview of the phenotypes and genotypes of <i>HES7</i> variants.<h4>Case presentation</h4>This case report focuses on a Chinese neonate who was first hospitalized for tachypnea, cleft palate, and short trunk. The gene discussed is HES7; the disease is cleft palate.