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.

Microphthalmia with brain and digital anomalies (MCOPS6, MIM# 607932) is an autosomal dominant disorder caused by loss-of-function variants or large deletions involving BMP4, which encodes bone morphogenetic protein 4, a member of the TGF-β protein superfamily. BMP4 has a number of roles in embryonic development including neurogenesis, lens induction, development of cartilage and bone, urogenital development, limb and digit patterning, hair follicle regeneration, as well as tooth formation. In addition to syndromic microphthalmia, BMP4 variants have been implicated in non-syndromic cleft lip with or without cleft palate and congenital healed cleft lip indicating different allelic presentations. MCOPS6 subjects may also lack some of the major phenotypic hallmarks of the disorder, including microphthalmia, indicating variable expressivity. As only a handful of individuals with MCOPS6 have been described, we review the clinical findings in previously reported cases with either deletions or loss-of-function variants in BMP4. We describe three new cases, including two subjects with novel deletions and one subject with a likely pathogenic de novo nonsense variant [c.1052C>G, p.(S351*)] in BMP4. One of the subjects had dual molecular diagnoses including a co-occurring microdeletion at 17q21.31 associated with Koolen de Vries syndrome, which has a partially overlapping disease phenotype. None of these individuals had clinically apparent microphthalmia or anopthalmia, which have been reported in a majority of previously described cases. One subject had exophthalmia and strabismus, while another had bilateral Peters anomaly and sclerocornea, thus expanding the phenotype associated with BMP4 loss-of-function variants.