Genome and transcriptome sequencing reveal pathogenic activation of a pseudoexon in PKD1 via a de novo-common variant...

Despite improvements in and access to clinical genetic testing, many patients with classic phenotypes remain without a molecular diagnosis. Such cases may reflect variants in noncoding regions or complex alleles made up of disparate sequence variants. In this article, we report a patient with autosomal dominant polycystic kidney disease caused by a deep intronic de novo single-nucleotide substitution forming a dinucleotide variant, with an adjacent common single-nucleotide variant (formerly single-nucleotide polymorphism) inherited from an unaffected parent. Although neither variant alone was predicted to be pathogenic, together as a dinucleotide variant, they created a novel splice donor site that activated a pseudoexon within intron 16 of the PKD1 gene.

Genome sequencing was paired with transcriptome sequencing to evaluate the dinucleotide variant within intron 16 of PKD1.

Evaluation of RNA from patient cells confirmed the inclusion of a 114-bp pseudoexon and an in-frame premature termination codon into the PKD1 messenger RNA transcript. This case identified a rare scenario in which the combination of 2 independently predicted benign nucleotide substitutions immediately adjacent to one another generated a pathogenic allele.

This case highlights the diagnostic utility of genome sequencing coupled with RNA sequencing to clarify the effects of a deep intronic variant, confirming a molecular diagnosis for a patient with a clear clinical diagnosis who had undergone years of inconclusive testing. Furthermore, this case cautions that similar events may underlie unsolved cases across other genes and disorders.