ARF1-related disorder: phenotypic and molecular spectrum

Abstract

Purpose: ARF1 was previously implicated in periventricular nodular heterotopia (PVNH) in only five individuals and systematic clinical characterisation was not available. The aim of this study is to provide a comprehensive description of the phenotypic and genotypic spectrum of ARF1-related neurodevelopmental disorder.

Methods: We collected detailed phenotypes of an international cohort of individuals (n=17) with ARF1 variants assembled through the GeneMatcher platform. Missense variants were structurally modelled, and the impact of several were functionally validated.

Results: De novo variants (10 missense, 1 frameshift, 1 splice altering resulting in 9 residues insertion) in ARF1 were identified among 17 unrelated individuals. Detailed phenotypes included intellectual disability (ID), microcephaly, seizures and PVNH. No specific facial characteristics were consistent across all cases, however microretrognathia was common. Various hearing and visual defects were recurrent, and interestingly, some inflammatory features were reported. MRI of the brain frequently showed abnormalities consistent with a neuronal migration disorder.

Conclusion: We confirm the role of ARF1 in an autosomal dominant syndrome with a phenotypic spectrum including severe ID, microcephaly, seizures and PVNH due to impaired neuronal migration.

Keywords: epilepsy; human genetics; sequence analysis, DNA.

Figure 1

Clinical overview of 21 individuals with ARF1 variants (17 individuals from this study, 3 individuals previously reported from Ge et al and one from Gana et al. Tolerance landscape from MetaDome. Plain lines point to the missense location, dashed lines point to non-missense altered residues (either to the premature terminating codon or to the nine residues insertion).

Figure 2

(A) Locations of the eight residues (yellow) altered in the two conformations of ARF1. Left, ARF1 in its inactive conformation from 1r8q; right, ARF1 in active conformation from 6cm9; blue chain: ARF1; grey chain: ARFGEF sec7 domain. Images created using Mol*. (B, C) Deleterious effect of patient ARF1 variants on nucleotide activation. Comparison of ARF1 nucleotide activation in lysates of 293 T cells transfected with either the wild-type (WT) ARF1 plasmid or that harbouring one of the five variants (p.Tyr35His, p.Thr48Ile, p.Phe51Leu, p.Arg99His, p.Lys127Glu). Lane 1, basal activated ARF1 in 293 T cells without plasmid transfection. Pulldown for GTP-activated ARF1 in cells transfected with WT (lane 2) vs patient variant-containing ARF1 plasmid (lanes 3–7). ARF1 band is visible at 21 kDa. Western blot analysis results are representative of three independent transfection and pulldown experiments. (C) Quantification of relative nucleotide activation in lysates of 293 T cells transfected with ARF1 plasmids harbouring one of five patient ARF1 variants compared with a WT ARF1 and no plasmid. Mean results are presented as the mean (±SEM) of three separate experiments. P value of the result of each variant in comparison to the WT is presented.