Congenital insensitivity to pain: a novel mutation affecting a U12-type intron causes multiple aberrant splicing of SCN9A

ABSTRACT: Mutations in the alpha subunit of voltage-gated sodium channel 1.7 (NaV1.7), encoded by SCN9A gene, play an important role in the regulation of nociception, and can lead to a wide range of clinical outcomes, ranging from extreme pain syndromes to congenital inability to experience pain. To expand the phenotypic and genotypic spectrum of SCN9A-related channelopathies we describe the proband, a daughter born from consanguineous parents, that had pain insensitivity, diminished temperature sensation, foot burns, and severe loss of nociceptive nerve fibers in the epidermis. Next-generation sequencing of SCN9A (NM_002977.3) revealed a novel homozygous substitution (c.377+7T>G) in the donor splice-site of intron 3. As the RNA functional testing is challenging, the in silico analysis are the first approach to predict possible alterations. In this case, the computational analysis was unable to identify the splicing consensus and couldn't provide any prediction for splicing defects. The affected intron indeed belongs to the U12-type, a family of introns characterised by non-canonical consensus at splice-sites, accounting only for 0.35% of all human introns, and are not included in most of the training-sets for splicing prediction. Functional study on proband RNA shown different aberrant transcripts, where exon 3 was missing and an intron fragment was included. Quantification study using real-time PCR showed a significant reduction of the NaV1.7 canonical transcript. Collectively, these data widen the spectrum of SCN9A-related insensitivity to pain, by describing a mutation causing NaV1.7 deficiency, underlying the nociceptor dysfunction, and highlights the importance of molecular investigation of U12-introns mutations despite the silent prediction.