Neurodevelopmental disorders (NDDs) pose a significant challenge to patients and their families, causing severe intellectual impairment, health complications and a diminished life expectancy. Yet, in approximately half of the affected individuals, the causal genetic variants remain elusive. Utilizing a comprehensive genetic screening strategy in a cohort of consanguineous families with multiple affected children, several gene variants associated with NDDs were identified. Among these, CLSTN1 emerged as a compelling candidate due to its high expression in the nervous system and high degree of conservation in Drosophila melanogaster. Our study aims to elucidate the function of the fly orthologue, Cals, and assess the ability of CLSTN1 and the patient-derived variant to rescue its function in vivo. We characterized the properties of human CLSTN1 and its variant using cell culture and biochemical assays showing that it can form di- or multimers. We further established a functional role of the fly orthologue Cals in dendrite and synapse formation as well as circuit function and behavior. Additionally, rescue approaches employing transgenic flies expressing human CLSTN1 or its variant upon Cals knockdown aim to assess the functional conservation of the human gene and the pathogenic potential of the variant. In summary, our findings highlight CLSTN1 as a NDD candidate gene. Further investigation is warranted to unravel its physiological function and the pathogenicity of its variant, which should contribute to our understanding of NDDs.