Variants in the ciliopathy gene SCLT1 are associated with non-syndromic and syndromic retinal degeneration of variable severity

Inherited retinal degenerations (IRDs) are a group of clinically and genetically heterogeneous blinding disorders. In this study, we describe five families clearly or which were presumed to be diagnosed with autosomal recessive non-syndromic IRD and one with mild syndromic IRD, in which affected probands carried rare bi-allelic variants in SCLT1, a gene previously associated with multiple autosomal recessive ciliopathies. Eight of the ten variants identified were novel; five variants affected splicing, including the known missense p.(Lys544Arg), detected in compound heterozygosity in three East Asian probands, and the novel, hypomorphic, deep-intronic variant c.290+2732A>G, leading to the inclusion of a 45-bp cryptic exon containing a premature termination codon. Analysis of the genomic data also revealed a large in-frame tandem duplication spanning exons 3-10, which was subsequently validated. Although no clear correlation was found between the severity of the SCLT1-associated phenotypes and the identified causal variants, this report expands the current knowledge of SCLT1-associated disease by enriching its mutational landscape and clearly supports its association with autosomal recessive non-syndromic IRD.