The forkhead transcription factor FOXE3 is critical for vertebrate eye development. Recessive and dominant variants cause human ocular disease but the full range of phenotypes and mechanisms of action for the two classes of variants are unknown. We identified FOXE3 variants in individuals with congenital eye malformations and carried out in vitro functional analysis on selected alleles. Sixteen new recessive and dominant families, including six novel variants, were identified. Analysis of new and previously reported genetic and clinical data demonstrated a broad phenotypic range with an overlap between recessive and dominant disease. Most families with recessive alleles, composed of truncating and forkhead-domain missense variants, had severe corneal opacity (90%; sclerocornea in 47%), aphakia (83%) and microphthalmia (80%), but some had milder features including isolated cataract. The phenotype was most variable for recessive missense variants, suggesting that the functional consequences may be highly dependent on the type of amino acid substitution and its position. When assessed, aniridia or iris hypoplasia were noted in 89% and optic nerve anomalies in 60% of recessive cases, indicating that these defects are also common and may be underrecognized. In dominant pedigrees, caused by extension variants, normal eye size (96%), cataracts (99%) and variable anterior segment anomalies were seen in most, but some individuals had microphthalmia, aphakia or sclerocornea, more typical of recessive disease. Functional studies identified variable effects on the protein stability, DNA binding, nuclear localization and transcriptional activity for recessive FOXE3 variants, whereas dominant alleles showed severe impairment in all areas and dominant-negative characteristics.

Cell Biology and Human Anatomy Department UC Davis School of Medicine Davis CA 95616 USA

Department of Computer Science Czech Technical University Prague 166 36 Prague Czech Republic

Department of Ophthalmology 1st Faculty of Medicine Charles University and General University Hospital 121 08 Prague Czech Republic

Department of Pediatrics Albert Einstein Medical Center Philadelphia PA 19141 USA

Department of Pediatrics and Inherited Metabolic Disorders 1st Faculty of Medicine Charles University and General University Hospital 121 08 Prague Czech Republic

Department of Pediatrics Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin Milwaukee WI 53226 USA

Departments of Ophthalmology and Visual Sciences and Cell Biology Neurobiology and Anatomy Medical College of Wisconsin Milwaukee WI 53226 USA

Fullerton Genetics Center Mission Hospitals HCA Asheville NC 28803 USA

Pediatric Ophthalmologist Al Jalila Children's Specialty Hospital Dubai United Arab Emirates

Pediatric Ophthalmology and Ocular Genetics Flaum Eye Institute Pediatric Genetics Golisano Children's Hospital University of Rochester Rochester NY 14534 USA

Pediatric Ophthalmology and Strabismus Unit Al Shifa Trust Eye Hospital Rawalpindi Pakistan

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Rare disease gene association discovery in the 100,000 Genomes Project