Unraveling the pathogenesis of ARX polyalanine tract variants using a clinical and molecular interfacing approach

Abstract

The Aristaless-related homeobox (ARX) gene is implicated in intellectual disability with the most frequent pathogenic mutations leading to expansions of the first two polyalanine tracts. Here, we describe analysis of the ARX gene outlining the approaches in the Australian and Portuguese setting, using an integrated clinical and molecular strategy. We report variants in the ARX gene detected in 19 patients belonging to 17 families. Seven pathogenic variants, being expansion mutations in both polyalanine tract 1 and tract 2, were identifyed, including a novel mutation in polyalanine tract 1 that expands the first tract to 20 alanines. This precise number of alanines is sufficient to cause pathogenicity when expanded in polyalanine tract 2. Five cases presented a probably non-pathogenic variant, including the novel HGVS: c.441_455del, classified as unlikely disease causing, consistent with reports that suggest that in frame deletions in polyalanine stretches of ARX rarely cause intellectual disability. In addition, we identified five cases with a variant of unclear pathogenic significance. Owing to the inconsistent ARX variants description, publications were reviewed and ARX variant classifications were standardized and detailed unambiguously according to recommendations of the Human Genome Variation Society. In the absence of a pathognomonic clinical feature, we propose that molecular analysis of the ARX gene should be included in routine diagnostic practice in individuals with either nonsyndromic or syndromic intellectual disability. A definitive diagnosis of ARX-related disorders is crucial for an adequate clinical follow-up and accurate genetic counseling of at-risk family members.

Keywords: ARX; Aristaless-related homeobox gene; expanded polyalanine tract; intellectual disability; pathogenic variant.

Figure 1

Clinical variability associated with expanded in polyalanine tract mutations in ARX. The panel below the graph shows the normal length of the pA1 as 16 residues and pA2 as 12 residues. The graph shows the relationship between the number of alanines and the phenotype severity in published families with pA1 (white circles) and pA2 families (black circles). Each circle represents a separate published case; some cases being a single affected individual whereas other cases are comprised of multiple affected individuals within a family. The black circle with horizontal line indicates a polyalanine tract expansion interspersed with a glycine residue (10A-G-12A) (Demos et al. 2009). The cases we are reporting in this study are shown as hatched circles. The same mutation can lead to different clinical outcomes, whereas different mutations can lead to consistent outcomes. With increasing length of residues in the pA tracts, the clinical presentation becomes more severe, with early onset seizures being a frequent but not consistent finding. Modified with permission from (Shoubridge et al. 2014).