Hailey-Hailey Disease Caused by a Novel Deep Intronic Variant in ATP2C1

Hailey-Hailey disease (OMIM#169600) is an autosomal dominantly inherited genodermatosis characterized by erosions in the flexural areas of the body. Hailey-Hailey disease is caused by variants in ATP2C1, but for ~10% of the patients, no causative variant is found in the coding region of ATP2C1. We aimed to determine the genetic cause of Hailey-Hailey disease in a family without a variant in the coding areas of ATP2C1. By genome sequencing and analysis of all exon and intron sequences of ATP2C1, we identified the variant c.532-560 T>G (NM_014382.5) in intron 7 of ATP2C1. The variant is predicted by in silico tools to create a new deep intronic donor splice site. Segregation analysis detected the variant in the three affected family members. RNA sequencing confirmed that the variant creates a new deep intronic donor splice site that gives rise to an alternative exon. The identified deep-intronic variant in ATP2C1 is the likely cause of Hailey-Hailey disease. This is to our knowledge the first report of a deep-intronic variant as the cause of Hailey-Hailey disease, which shows that the analysis of the intronic sequences of ATP2C1 could increase the genetic diagnostic yield for Hailey-Hailey disease patients.