A novel dominant negative variant of <i>ALPL</i> induces hypophosphatasia

Hypophosphatemia (HPP) is an inherited metabolic disorder characterized by defective bone and tooth mineralization, resulting from mutations in the gene encoding tissue-nonspecific alkaline phosphatase (<i>ALPL</i>). Despite the wide spectrum of clinical manifestations associated with <i>ALPL</i> mutations, the genotype-phenotype relationship remains poorly understood. In this work, we discovered a novel combination of missense mutations, p.G129E and p.Y263H. The patient with the mutations suffered from chronic musculoskeletal pain, arthralgia, and permanent dentition. Biochemical assays revealed that the Y263H mutation did not impair enzymatic function, but the G129E mutation significantly disrupted catalytic activity. Furthermore, G129E exhibited a dominant-negative effect by suppressing the function of the WT ALPL protein. Molecular dynamics simulations indicated that E129 formed novel salt bridges with R152, altering correlated motions and conformational dynamics of ALPL. These changes likely impair the formation of ALPL octamers, leading to loss of enzymatic activity. These findings establish a novel genotype-phenotype association in HPP and highlight the importance of accurate diagnosis to prevent the inappropriate use of bone resorption inhibitors in misdiagnosed patients.