Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F ‐mediated inherited retinal disorders

Abstract

Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in ~260 genes. Albeit that many genes are implicated in IRD, for 30–50% of the cases, the gene defect is unknown. These cases may be explained by novel gene defects, by overlooked structural variants, by variants in intronic, promoter or more distant regulatory regions, and represent synonymous variants of known genes contributing to the dysfunction of the respective proteins. Patients with one subgroup of IRD, namely incomplete congenital stationary night blindness (icCSNB), show a very specific phenotype. The major cause of this condition is the presence of a hemizygous pathogenic variant in CACNA1F. A comprehensive study applying direct Sanger sequencing of the gene‐coding regions, exome and genome sequencing applied to a large cohort of patients with a clinical diagnosis of icCSNB revealed indeed that seven of the 189 CACNA1F‐related cases have intronic and synonymous disease‐causing variants leading to missplicing as validated by minigene approaches. These findings highlight that gene‐locus sequencing may be a very efficient method in detecting disease‐causing variants in clinically well‐characterized patients with a diagnosis of IRD, like icCSNB.

A Novel Splice-Site Variant in CACNA1F Causes a Phenotype Synonymous with Åland Island Eye Disease and Incomplete Congenital Stationary Night Blindness

“…The variant identified in this study is located in intron 36, two nucleotides away from the splice-site variant c.4294-9G>A associated with CSNB2A. Interestingly, the splice variant c.4294-9G>A was reported to be associated with CSNB2A and leads to a misplicing in an in vitro model: a part of intron 36 is retained [15]. Compared with this CSNB2A variant, the c.4294-11C>G variant may lead to intron retention until the c.4295-10 position ( Figure 3B).…”

Using an integrative machine learning approach utilising homology modelling to clinically interpret genetic variants: CACNA1F as an exemplar

“…CACNA1F-vp also misclassified 125/322 (39%) benign variants (Online Resource 2). A recent study found that disease-implicated CACNA1F variants are present in gnomAD, which might be due to overlooked/ undiagnosed cases in this dataset [53]. When we used a more stringent criterion to define benign variants (presence in the gnomAD dataset in hemizygous state in at least five individuals) we found that the misclassification rate of CACNA1F-vp was lower (16/52; 30%).…”

Optic Atrophy and Inner Retinal Thinning in CACNA1F-Related Congenital Stationary Night Blindness

“…The c.3741+2T>C substitution is located on the canonical donor splice site of intron 30, and is expected to cause exon 30 skipping. The p.(Pro1492Ser) variant affects a highly conserved residue and is predicted pathogenic by all in silico tools; further, there are other substitutions at and near position 1492 (p.(Pro1492Ala) and p.(Gly1494Arg)) that have been reported to cause iCSNB [1,42]. The mutation segregated with the disease phenotype in all tested cases (n = 18); among the four cases where segregation analysis was unavailable, two harbored previously reported mutations (case 19: p.(Pro1492Ala) [1,42] and case 21: p.(Arg1502*) [42]) and two harbored novel disease-causing variants (case 9: p.(Val611Glyfs*32) and case 17: p.(Gln1157Gln)).…”

“…The synonymous variant (c.4474C>T; p.(Gln1157Gln)) affects the last nucleotide in exon 28 and is predicted to alter the splice donor site. Recently, two other exonic synonymous variants in CACNA1F (c.646C>T; p.(Leu216Leu) and c.1719G>A; p.(Thr573Thr)) were reported to affect splicing using a minigene approach [42]. In addition, there are reported instances of pathogenic synonymous exonic variants affecting the last nucleotide of an exon leading to a splice site defect in other disorders [86,87].…”