| Summary: | Axenfeld–Rieger anomaly (ARA) is a specific ocular disorder that is frequently associated with other systemic abnormalities. <i>PITX2</i> and <i>FOXC1</i> variants explain the majority of individuals with Axenfeld–Rieger syndrome (ARS) but leave ~30% unsolved. Here, we present pathogenic/likely pathogenic variants in nine families with ARA/ARS or similar phenotypes affecting five different genes/regions. <i>USP9X</i> and <i>JAG1</i> explained three families each. <i>USP9X</i> was recently linked with syndromic cognitive impairment that includes hearing loss, dental defects, ventriculomegaly, Dandy–Walker malformation, skeletal anomalies (hip dysplasia), and other features showing a significant overlap with <i>FOXC1</i>-ARS. Anterior segment anomalies are not currently associated with <i>USP9X</i>, yet our cases demonstrate ARA, congenital glaucoma, corneal neovascularization, and cataracts. The identification of <i>JAG1</i> variants, linked with Alagille syndrome, in three separate families with a clinical diagnosis of ARA/ARS highlights the overlapping features and high variability of these two phenotypes. Finally, intragenic variants in <i>CDK13</i>, <i>BCOR</i>, and an X chromosome deletion encompassing <i>HCCS</i> and <i>AMELX</i> (linked with ocular and dental anomalies, correspondingly) were identified in three additional cases with ARS. Accurate diagnosis has important implications for clinical management. We suggest that broad testing such as exome sequencing be applied as a second-tier test for individuals with ARS with normal results for <i>PITX2/FOXC1</i> sequencing and copy number analysis, with attention to the described genes/regions.
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