Expanding the Phenotypic Spectrum Associated With Loss-of-Function SMARCA4 Variants to Eye Developmental Anomalies

The SMARCA4 gene encodes a catalytic subunit of the BRG1/BRM-associated factor complex, which regulates gene expression through chromatin remodeling. Heterozygous missense variants in this gene have been linked to Coffin-Siris syndrome, characterized by intellectual development disorder and various congenital anomalies (distinctive facial features, hypoplastic fifth digits, and malformations of the heart and central nervous system), but it is not typically associated with structural eye anomalies. Truncating variants in SMARCA4 have been associated with rhabdoid tumors predisposition syndrome, a group of rare and aggressive tumors occurring predominantly in infancy. Through pangenomic analyses (whole-exome or whole-genome sequencing), we identified loss-of-function variants in SMARCA4 in three unrelated individuals with microphthalmia and/or coloboma. None of these individuals had a history of rhabdoid tumors; however, a regular oncological follow-up was established following the SMARCA4 variant identification. Systemic features observed in these individuals consisted of developmental delay and brain anomalies. However, their clinical presentation does not align with classic features of Coffin-Siris syndrome. Although eye development anomalies have occasionally been reported in individuals with a pathogenic variant in SMARCA4, no clear association has been established to date. The description of these three new individuals provides further evidence supporting the role of SMARCA4 in eye development and its likely involvement in structural eye malformations.