Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome

Abstract

Background: Joubert syndrome (JS) is a neurodevelopmental ciliopathy characterised by a distinctive mid-hindbrain malformation, the 'molar tooth sign'. Over 40 JS-associated genes are known, accounting for two-thirds of cases.

Methods: While most variants are novel or extremely rare, we report on 11 recurring variants in seven genes, including three known 'founder variants' in the Ashkenazi Jewish, Hutterite and Finnish populations. We evaluated variant frequencies in ~550 European patients with JS and compared them with controls (>15 000 Italian plus gnomAD), and with an independent cohort of ~600 JS probands from the USA.

Results: All variants were markedly enriched in the European JS cohort compared with controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazim founder variant (TMEM216 c.218G>T) was significantly enriched in American compared with European patients with JS, while MKS1 c.1476T>G was about 10 times more frequent among European JS. Frequencies of other variants were comparable in the two cohorts. Genotyping of several markers identified four novel European founder haplotypes.Two recurrent variants (MKS1 c.1476T>G and KIAA0586 c.428delG), have been detected in homozygosity in unaffected individuals, suggesting they could act as hypomorphic variants. However, while fibroblasts from a MKS1 c.1476T>G healthy homozygote showed impaired ability to form primary cilia and mildly reduced ciliary length, ciliary parameters were normal in cells from a KIAA0586 c.428delG healthy homozygote.

Conclusion: This study contributes to understand the complex genetic landscape of JS, explain its variable prevalence in distinct geographical areas and characterise two recurrent hypomorphic variants.

Keywords: Cerebellar Diseases; Founder Effect; Gene Frequency; Genetic Carrier Screening; Genotype.

Figure 1

Allele frequencies of 11 recurrent JS variants. Allelic frequencies of recurrent variants in the European JS cohort (blue), the US JS cohort (orange) and four distinct non-JS control cohorts (grey shades). JS, Joubert syndrome; NIG, Network of Italian Genomes.

Figure 2

Schematics of the four novel founder haplotypes identified in this study. (A) Shared haplotypes across families, genomic size and estimated age of founder variants; (B) Example of dating plot (for founder variant MKS1 c.1476T>G); (C) Geographical origin of families carrying the four variants.

Figure 3

Functional assessment of MKS1 c.1476T>G and KIAA0586 c.428delG variants. Count of ciliated cells and ciliary length in four healthy controls, patients and healthy subjects carrying either variant in the homozygous or in the compound heterozygous state, as stated. (A) Representative images of immunofluorescence experiments showing primary cilia marked with γ-tubulin and acetylated-α-tubulin antibody in serum starved fibroblasts; (B–C) Box plots showing the percentage of ciliated fibroblasts (B) and ciliary length (C) in tested fibroblasts. Black circles: healthy controls; Orange: JS affected subjects; Blue: healthy subjects; Triangles: carriers of MKS1 c.1476T>G variant; Squares: carriers of KIAA0586 c.428delG variant. *p<0.01; **p<0.001; ***p<0.0001. JS, Joubert syndrome