A leaky deep intronic splice variant in CLRN1 is associated
with non-syndromic retinitis pigmentosa

Introduction: Inherited retinal diseases (IRDs) are clinically complex and genetically heterogeneous visual impairment disorders with varying penetrance and severity. Disease-causing variants in at least 289 nuclear and mitochondrial genes have been implicated in their pathogenesis. Methods: Genomic DNA was isolated from peripheral blood lymphocytes. Exome sequencing was performed on an Illumina platform, and splicing analysis was performed using a pET01 minigene plasmid in Hela cells. Results: In the current study, we performed exome sequencing on a 51 year-old Ashkenazi Jewish patient with non-syndromic retinitis pigmentosa (RP) and identified compound heterozygous variants in the CLRN1 gene: a known pathogenic missense [p.(N48K)] and a novel deep intronic variant, c.254- 643G>T. A minigene splicing assay was performed, aiming to study the effect of the c.254- 643G>T variant on CLRN1 pre-mRNA splicing, and this revealed the inclusion of a pseudo-exon that was also reported to be included in the transcript due to an adjacent variant, c.254-649T>G. However, unlike the reported c.254-649T>G variant, c.254-643G>T showed aberrant splicing in a leaky manner, implying that the identified variant is not totally penetrant. Conclusion: The non-syndromic phenotype observed in this index case may be attributed to the leaky nature of this variant, which causes some normal transcripts to be produced. To conclude, we report on a novel deep intronic variant in CLRN1 causing non-syndromic RP due to the leaky nature of the identified variant.