Axenfeld-Rieger syndrome associated with a megabase-scale inversion separating PITX2 from a conserved enhancer locus

Abstract

Axenfeld-Rieger Syndrome (ARS) is an autosomal dominant condition with both ocular and non-ocular manifestations. ARS is primarily caused by coding variants at the PITX2 or FOXC1 loci, yet many cases still remain undiagnosed. Here we used whole-genome sequencing to identify two non-coding structural variants associated with a typical presentation of PITX2-associated ARS: one with a 450 kb deletion removing a series of conserved enhancer elements distal to PITX2, and the second with a 12.5 Mb inversion displacing the PITX2 gene from these same enhancer elements. Neither variant disrupted the PITX2 gene itself, and therefore both were expected to reduce PITX2 expression by disrupting its proximity or access to enhancer elements. Enhancer-disrupting intergenic inversions therefore represent a unique genetic mechanism for the development of ARS, which should be carefully considered in the context of ARS and other conditions without a conclusive genetic diagnosis.

Figure 1:. Ocular and systemic features of Axenfeld Rieger Syndrome.

Photographs of all affected family members, including (from left to right) the anterior segment of the right eye, left eye, teeth, and umbilicus. Corectopia and dental hypoplasia are evident in all individuals, with redundant periumbilical skin documented in two individuals, polycoria in two individuals, and bilateral penetrating keratoplasties in one individual.

Figure 2:. A 12.54 Mb inversion and 450 kb deletion at the PITX2 locus.

(A) Schematic of chromosome 4, highlighting the g.4:98141399_110685792inv region in red. (B) Schematic of the PITX2 locus and surrounding region, demonstrating the location of the deletion and inversion variants described here (hg38, g.4:110871515_111321256del and g.4:98141399_110685792inv), along with previously reported PITX2 enhancer deletions. Adapted from Protas et al. 2017. Note that only the PITX2 gene is shown for simplicity: another 65 genes are within the inverted region indicated for Family 1. Read-level support for the g.4:110871515_111321256del (C) and g.4:98141399_110685792inv (D) variants. The absence of mapped reads at the proximal breakpoint in (C) is due to the presence of a common 4.89kb deletion in trans (4:111316365–111321256, gnomAD v4.1.0 NFE AF = 0.1243).