Clinical features and functional analysis of novel SCN9A variants causing congenital insensitivity to pain

Pain perception is a fundamental protective mechanism that enables us to detect noxious stimuli. With a focus on finding treatments for pain, the molecular mechanisms and key players involved in pain perception are currently under intense study. Congenital insensitivity to pain is one of the rarest and most unusual pain disorders. One of the reasons of pure congenital absence of pain are pathogenic variants in the SCN9A gene, which encodes the α-subunit of the Na v 1.7 voltage-gated sodium channel. To date, most of the described variants in SCN9A associated with congenital insensitivity to pain are biallelic frameshifting variants, and the extent to which splice-affecting variants contribute to this rare phenotype remains largely unknown. Here, we describe 4 novel variants in previously unreported patients with congenital insensitivity to pain, all carrying noncoding variants in a homozygous or compound-heterozygous state in the SCN9A gene. Functional analyses demonstrated that all variants affect mRNA splicing, leading to both out-of-frame and in-frame isoforms. In 1 case, a deep-intronic variant detected through whole-genome sequencing led to the inclusion of a pseudoexon in intron 9. Genotype-phenotype analysis did not reveal significant differences in phenotype severity among the patients, suggesting that in-frame shortening of the Na v 1.7 protein completely disrupts its function. These findings broaden the understanding of SCN9A -related pain insensitivity and uncover the molecular mechanisms of novel noncoding variants in the SCN9A gene, which is crucial for the development of future tailored therapeutic approaches.