Hypophosphatasia (HPP) is caused by inactivating variants of the ALPL gene, which encodes tissue non-specific alkaline phosphatase (TNSALP). Among the six subtypes of HPP, childhood HPP presents after 6 months and before 18 yr of age, and is inherited in both autosomal dominant and autosomal recessive manners. Patients with childhood HPP have variable symptoms, including rickets-like bone changes, low bone mineral density (BMD), short stature, muscle weakness, craniosynostosis, and premature loss of deciduous teeth. Here, we describe a 7-yr-old boy with childhood HPP who showed short stature, impaired ossification of the carpal bones, and low BMD. Genetic testing identified a novel heterozygous 51-bp in-frame deletion in the ALPL gene (c.1482_1532del51), leading to the lack of 17 amino acids between Gly495 and Leu511 (p.Gly495_Leu511del). In vitro transfection experiments revealed the loss of enzymatic activity and the dominant-negative effect of the TNSALP[p.Gly495_Leu511del] variant; thus, the patient was diagnosed as having autosomal dominant HPP. The TNSALP[p.Gly495_Leu511del] variant was localized to the plasma membrane as was the wild-type TNSALP (TNSALP[WT]): however, co-immunoprecipitation experiments suggested a reduced dimerization between TNSALP[p.Gly495_Leu511del] and TNSALP[WT]. This case expands the variable clinical manifestation of childhood HPP and sheds light on the molecular bases underlying the dominant-negative effects of some TNSALP variants.