A novel deep intronic EIF2AK3 variant disrupts splicing and causes Wolcott–Rallison syndrome

Vollständiger Abstract

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Abstract Aim Deep intronic variants can disrupt splicing and cause monogenic disease but are missed by routine genetic testing. This study assessed the contribution of deep intronic variants to Wolcott–Rallison syndrome (WRS), a recessive disorder characterized by early‐onset diabetes and progressive multisystem disease caused by loss‐of‐function EIF2AK3 variants. Methods We investigated a cohort of 116 individuals referred to the Exeter Genomics Laboratory for genetic testing who had diabetes diagnosed at ≤2 years and at least one additional feature consistent with WRS: hepatic dysfunction, skeletal abnormalities or developmental delay. No genetic cause had been identified after testing all known early‐onset diabetes genes. We screened genome‐sequencing data for rare homozygous intronic EIF2AK3 variants. Candidate variants predicted to affect splicing by SpliceAI were assessed using a minigene exon‐trapping assay. Results We identified two rare homozygous intronic EIF2AK3 variants in two siblings. Only one variant, c.1651‐180G>T, was predicted to disrupt splicing in silico. The two children, born to consanguineous parents, were diagnosed with early‐onset diabetes (diagnosed at 1 year and 21 weeks), hepatic dysfunction, skeletal abnormalities, developmental delay, thyroid dysfunction, hip dysplasia and gait abnormalities. The minigene assay showed that c.1651‐180G>T creates a cryptic donor splice site within intron 9, resulting in inclusion of a 79‐nucleotide pseudoexon, causing a frameshift and premature stop codon. Using this evidence, the variant was reclassified as likely pathogenic according to ACMG/ACGS guidelines. Conclusions We report the first deep intronic EIF2AK3 variant causing WRS, highlighting the need to consider systematic intronic analysis in unresolved cases.