A Novel Intronic Variant Causes Aberrant Splicing of PCDH15 in a Family With Usher Syndrome Type 1F

Variants of the proto-cadherin 15 (PCDH15) gene are related to Usher syndrome type 1F (USH1F). The purpose of this study was to determine the genetic etiology of a USH1F family in China and to perform a minigene assay for the PCDH15 gene to explore the effect of variation on splicing and determine the pathogenicity of the identified variant.

Targeted next-generation sequencing of 127 hearing loss-related genes was performed for a 26-year-old proband to identify the candidate variants. Then, multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing were performed for all family members to confirm the variants. Further, to verify the pathogenicity of the intronic variant, a minigene splicing assay was performed.

Compound heterozygous PCDH15 EX1_2DEL and c.3717+5G>A variants were identified in the proband. MLPA and Sanger sequencing confirmed these two variants and showed the same genotype of a paternally inherited c.3717+5G>A and a maternally inherited EX1_2DEL variation in both the proband and his affected sister. The minigene assay verified the pathogenicity of c.3717+5G>A and indicated that this variant possibly caused abnormal splicing, resulting in jump of exon 27 and retention of 51 bp at the 5' end of intron 27, leading to the formation of abnormal proteins.

This study reports a novel pathogenic variant c.3717+5G>A of PCDH15 in a proband for the first time. These findings offer evidence for the genetic counseling of USH1F. Minigene splicing assays are considered to be one of the most powerful methods for determining whether intron mutations lead to abnormal splicing.