A deep intronic variant inMMEcauses autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing

Abstract

AbstractBackgroundLoss-of-function variants inMME(membrane metalloendopeptidase) are a known cause of recessive Charcot-Marie-Tooth Neuropathy (CMT). A deep intronic variant,MMEc.1188+428A>G (NM_000902.5), was identified through whole genome sequencing (WGS) of two Australian families with recessive inheritance of axonal CMT using the seqr platform.MMEc.1188+428A>G was detected in a homozygous state in Family 1, and in a compound heterozygous state with a known pathogenicMMEvariant (c.467del; p.Pro156Leufs*14) in Family 2.AimsWe aimed to determine the pathogenicity of theMMEc.1188+428A>G variant through segregation and splicing analysis.MethodsThe splicing impact of the deep intronicMMEvariant c.1188+428A>G was assessed using anin vitroexon-trapping assay.ResultsThe exon-trapping assay demonstrated that theMMEc.1188+428A>G variant created a novel splice donor site resulting in the inclusion of an 83 bp pseudoexon betweenMMEexons 12 and 13. The incorporation of the pseudoexon intoMMEtranscript is predicted to lead to a coding frameshift and premature termination codon (PTC) inMMEexon 14 (p.Ala397ProfsTer47). This PTC is likely to result in nonsense mediated decay (NMD) ofMMEtranscript leading to a pathogenic loss-of-function.InterpretationTo our knowledge, this is the first report of a pathogenic deep intronicMMEvariant causing CMT. This is of significance as deep intronic variants are missed using whole exome sequencing screening methods. Individuals with CMT should be reassessed for deep intronic variants, with splicing impacts being considered in relation to the potential pathogenicity of variants.