Macrodactyly is a congenital abnormality characterized by overgrowth of single or multiple digits, frequently accompanied by pathological changes in bone, soft tissue, and nerve tissue, and is caused mostly by somatic variants. Previous studies have demonstrated that macrodactyly is predominantly caused by pathogenic variants in the PIK3CA gene, yet the underlying molecular mechanism remains unclear. In this study, we analyzed 13 patients clinically diagnosed with isolated macrodactyly. Through whole-exome and Sanger sequencing, we identified one pediatric patient carrying a novel mosaic de novo in-frame deletion mutation (c.307_312del/p.Glu103_Pro104del) in the PIK3CA gene, which was not detected in either parent. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, we classified this mutation as a variant of uncertain significance (PM4+PM2_Supporting+PM6_Supporting). Protein structure prediction analysis indicated that this in-frame deletion altered the protein’s local conformation and surface electrostatic potential. Furthermore, the wild-type and mutant expression vectors were constructed, including the well-established pathogenic mutation c.353G>A/p.Gly118Asp in PIK3CA gene as a control. We transfected these vectors into HEK293T cells for functional analyses, respectively. The results showed that although this mutation did not significantly affect PIK3CA mRNA or protein expression levels, it promoted the phosphorylation of downstream AKT protein at both Thr308 and Ser473. Therefore, the mutation may express the localized overgrowth phenotype by activating the PI3K/AKT signaling pathway. This study not only expands the genetic variant spectrum of macrodactyly, but also further clarifies the role of the PI3K/AKT pathway in the PIK3CA-related overgrowth.