P.160The spectrum of disease-causing and normal variation in the nebulin gene

The nebulin gene (NEB) with 183 exons is one of the largest genes in human. More than 240 different disease-causing variants in NEB have been identified in some 220 families. Around 50% of nemaline myopathies (NM) are caused by mutations in NEB. Mutations in NEB also cause core-rod myopathy, distal forms of NM, distal myopathy without nemaline rods, and multiple pterygium syndrome. The majority (95%) of the disease-causing variants in NEB are recessive point mutations, mainly nonsense and splice site mutations, and small indels, causing frameshifts. The remaining 5% of mutations are large copy number variations (CNVs). In addition to the recurrent CNVs in the triplicate region and the founder mutation with world-wide occurrence, deletion of exon 55, 11 different large pathogenic duplications and deletions have been identified in NEB. Until recently, all identified mutations in NEB have been recessive. Now it is known that large in-frame deletions in NEB, leading to the expression of substantially smaller proteins, can have a dominant-negative effect, and cause dominant distal forms of NM. The genome aggregation database (gnomAD) contains exome and genome data from 141,456 unrelated individuals, excluding patients with severe pediatric disorders. The total number of different NEB variants listed in gnomAD is 10,634. Most of the variants (96%) are very rare, only present in a few heterozygotes. Intronic variants comprise 43%, missense variants 40%, synonymous variants 14%, loss-of-function variants 3%, and UTR variants 0.2% of the total variation. It is noteworthy that 12.5% of the intronic variants are in the splice regions (excluding splice donor and acceptor sites), and may affect splicing. Rare variants are the most common variant type in NEB, complicating the interpretation of pathogenicity. Therefore, the pathogenicity of especially missense and splice site variants in NEB requires verification by functional analyses at the protein and mRNA level.