Sotos syndrome, characterized by intellectual disability and characteristic facial features, is caused by haploinsufficiency in the NSD1 gene. We conducted an etiological study on two siblings with Sotos features without mutations in NSD1 and detected a homozygous frameshift mutation in the APC2 gene by whole-exome sequencing, which resulted in the loss of function of cytoskeletal regulation in neurons. Apc2-deficient (Apc2−/−) mice exhibited impaired learning and memory abilities along with an abnormal head shape. Endogenous Apc2 expression was downregulated by the knockdown of Nsd1, indicating that APC2 is a downstream effector of NSD1 in neurons. Nsd1 knockdown in embryonic mouse brains impaired the migration and laminar positioning of cortical neurons, as observed in Apc2−/− mice, and this defect was rescued by the forced expression of Apc2. Thus, APC2 is a crucial target of NSD1, which provides an explanation for the intellectual disability associated with Sotos syndrome. Display omitted •The APC2 gene is homozygously mutated in two siblings with Sotos syndrome features•APC2 is downstream of NSD1, the main causative gene of Sotos syndrome•The Apc2-deficient mouse is a model for Sotos syndrome Sotos syndrome is a genetic disorder characterized by intellectual disability and distinct facial features. Almuriekhi et al. use whole-exome sequencing to identify APC2 mutations in two sibling patients with Sotos features. Apc2-deficient mice exhibit characteristic Sotos-like features. APC2 is a key target of NSD1, the primary gene responsible for Sotos syndrome.