Functional Characterization of a Novel <i>GPC3</i> Missense Variant in Simpson–Golabi–Behmel Syndrome

Simpson-Golabi-Behmel syndrome 1 (SGBS1) is a rare X-linked recessive condition characterized by overgrowth and multiple congenital anomalies. SGBS1 is caused by damaging variants in the Glypican-3 (GPC3) gene. The GPC3 protein plays a crucial role in cellular signaling processes including cell growth, embryogenesis, and differentiation. Functional maturation of GPC3 occurs via several steps of post-translational modification (PTM) and processing to enable its transport to, and anchorage on, the plasma membrane. GPC3 positively modulates the canonical Wnt signaling pathways, while negatively regulating the Hedgehog signaling pathways. Loss-of-function is the underlying mechanism of disease for SGBS1, with a minority of reported pathogenic variants being missense substitutions. We report a family with four affected individuals in whom a novel GPC3 missense variant was identified via exome sequencing: NM_004484.3: c.695C>A; p.(Ala232Asp). The variant segregated with disease in the family, and functional studies conducted using HEK293T cells demonstrate a distinct mis-localization of the mutant GPC3 protein, thereby supporting the pathogenicity of this novel missense variant. These findings allowed for an upgraded classification of the missense variant from a variant of uncertain significance to that of likely pathogenic.