Submission Details

The FOXC1 gene was first reported in relation to anterior segment dysgenesis in 1998 (PMID: 9620769). The specific disease entity, anterior segment dysgenesis 3, is one of eight such conditions distinguished by a single monogenic cause. Onset of symptoms is variable, and affected patients can be diagnosed in infancy or as late as in adulthood. Findings are primarily ocular and localized to the anterior segment, and frequently include prominent and anteriorly displaced Schwalbe’s line, iris hypoplasia, ectopia pupillae, abnormal pupil shape and iridocorneal adhesions. Glaucoma is a well-characterized phenotype that develops with approximately 50-75% penetrance, while corneal neovascularization and Peters anomaly have been observed in some affected individuals. Some affected patients exhibit additional extraocular symptoms, and are not typically diagnosed with anterior segment dysgenesis 3, but rather with Axenfeld-Rieger syndrome 3. Extraocular symptoms can include hypertelorism, midface retrusion, maxillary hypoplasia, microdontia, hearing loss, protuberant umbilical skin, heart anomalies, mild cerebellar vermis hypoplasia, and dilated perivascular spaces. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, the molecular mechanism (monoallelic loss of function) and mode of inheritance (autosomal dominant) were found to be consistent among patients with anterior segment dysgenesis 3 and Axenfeld-Rieger syndrome 3, while the phenotypic variability between them appeared to represent a spectrum of disease rather than separate disease entities. Therefore, cases caused by inherited FOXC1 variants have been lumped into a single disease entity, referred to as anterior segment dysgenesis 3 (MONDO:0024456, OMIM #601631). Ten suspected pathogenic variants were scored as part of this curation (one nonsense, three frameshift, and six missense affecting the Forkhead domain of the encoded protein), which have been collectively reported in ten probands in five publications (PMID: 9620769, PMID: 9792859, PMID: 10713890, PMID: 17210863, PMID: 11170889). More case-level evidence is available in the literature (PMID: 11170889, PMID: 16936096), but its inclusion in this curation was not necessary to reach the maximum score for genetic evidence (12 points). It is important to note that a subset of affected patients exhibit either loss or gain of FOXC1 copy number, highlighting the importance of precise FOXC1 gene dosage in anterior segment development (PMID: 11170889). Patients harboring duplications in FOXC1 exhibit a particularly severe prognosis for the development of glaucoma relative to patients with other types of FOXC1 variants (PMID: 17197537). However, these probands were not scored as part of this curation. While FOXC1 variants and copy number alterations are estimated to be present in approximately 24% of patients with anterior segment dysgenesis (PMID: 20881294), the high GC content of the locus causes sequencing challenges that may lead to under-identification of FOXC1 variants by next-generation sequencing-based panels. This gene-disease relationship has not been studied in case-control studies at the single variant level or aggregate variant level. The mechanism of pathogenicity appears to be monoallelic loss of function, characterized in some cases by truncation of the majority of the protein product and in other cases by missense variants affecting the Forkhead domain that trigger defects in DNA binding, transactivation, and/or nuclear localization (PMID: 11179011). All probands scored in this curation harbored one variant allele within the FOXC1 locus. This gene-disease association is also supported by biochemical evidence that FOXC1 functions as a transcription factor to coordinate normal development of the ocular anterior segment (PMID: 11782474, PMID: 17993506) and to promote the survival of trabecular meshwork cells (PMID: 24556684), which are known to regulate intraocular pressure and exhibit reduced cellularity in glaucoma. FOXC1 physically interacts with and colocalizes with PITX2, another transcription factor associated with anterior segment dysgenesis through an autosomal dominant mode of inheritance (PMID: 16449236). This interaction may explain why FOXC1 variants and PITX2 variants appear to act as modifiers of Axenfeld-Rieger syndrome severity when present in the same family (PMID: 21837767). FOXC1 missense variants exogenously expressed in non-patient cells exhibit disruption of nuclear localization or DNA binding in some cases, and reduced transactivation of a reporter gene in all cases (PMID: 14506133). Phenotypes of affected human patients are recapitulated by various model organisms with FOXC1 loss-of-function, including abnormalities in ocular morphology and vascularization in both zebrafish (PMID: 19458328, PMID: 32720677) and mice (PMID: 22171010). A heterozygous knockout mouse model also exhibited ectopia pupillae, irido-corneal attachments, hypoplastic iris stroma, and trabecular meshwork abnormalities (PMID: 10767326). In summary, FOXC1 is definitively associated with anterior segment dysgenesis 3. This has been repeatedly demonstrated in both research and diagnostic settings, and has been upheld over time without the emergence of contradictory evidence, leading to a Definitive classification. This classification was approved by the ClinGen Glaucoma and Neuro-Ophthalmology Gene Curation Expert Panel on November 18, 2021 (SOP Version 8).