ATP7B Variant c.1934T>G p.Met645Arg Causes Wilson Disease by Promoting Exon 6 Skipping

Wilson Disease is a recessive disorder caused by pathogenic loss-of-function variants in the ATP7B gene. It is characterized by disrupted copper homeostasis resulting in liver disease and/or neurological abnormalities. Variant NM_000053.3:c.1934T>G (Met645Arg) has been reported in compound heterozygosity in several Wilson Disease patients and is highly prevalent among individuals of Spanish descent. Accordingly, it is recognized as pathogenic by leading molecular diagnostic centers. However, functional studies investigating the amino acid change have failed to demonstrate a significant protein alteration, leading at least one ClinVar submitter to question its pathogenicity. Here we demonstrate that c.1934T>G results in almost complete exon 6 skipping, both in a mini-gene system and in CRISPR/Cas9 edited HepG2 cells. Exon 6 is out-of-frame and its skipping is expected to cause loss of function. The elucidation of the mechanistic effect for this variant resolves any doubt about its pathogenicity and enables the development of genetic medicines for splicing modulation.