ACAN-related short stature with an incidental ALPL variant: a case report

Hypophosphatasia (HPP) is a rare inherited metabolic bone disorder caused by pathogenic variants in the ALPL gene, with a wide clinical spectrum ranging from severe pediatric forms to mild adult-onset disease. In contrast, heterozygous variants in ACAN are a recognized cause of autosomal dominant short stature, often associated with advanced bone age and premature growth plate closure. We report a 16-yr-old girl evaluated for severe disproportionate short stature with growth arrest during early adolescence. Her medical history included benign childhood epilepsy, mild intellectual disability, and enamel abnormalities. Biochemical evaluation revealed persistently low serum and bone-specific alkaline phosphatase levels, while calcium-phosphate metabolism was otherwise normal. Genetic testing identified a heterozygous pathogenic ALPL variant (c.1426G>A; p.Glu476Lys), inherited from an asymptomatic father, consistent with autosomal dominant HPP with minimal clinical expression. Additionally, a maternally inherited ACAN variant of uncertain significance (c.511G>C; p.Ala171Pro) was detected. Based on phenotypic correlation and family segregation, the growth phenotype is more plausibly explained by ACAN-related growth plate dysfunction, while the ALPL variant likely represents an incidental or mildly expressed finding. This case highlights the importance of careful genotype-phenotype correlation and cautious interpretation of multiple genetic findings in the evaluation of severe short stature.