Framework for combined functional and computational assessment of variant pathogenicity in the sodium leak channel...

The sodium leak channel nonselective (NALCN) is the pore-forming channel component of the NALCN channelosome. This protein complex generates a depolarizing sodium leak in various tissues and contributes to respiratory and circadian rhythms, locomotion, and sleep. De novo and inherited variants of NALCN can lead to severe developmental syndromes referred to as CLIFAHDD and IHPRF1, respectively. Although variants of uncertain significance (VUS) have been studied in heterologous expression systems before, there is no generally accepted framework for how to assess or predict variant pathogenicity.

We functionally and computationally characterize 19 VUS detected in CLIFAHDD and IHPRF1 patients to establish a robust analysis to classify suspected disease-causing variants. Specifically, we employ multiple parameters derived from two-electrode voltage-clamp electrophysiology recordings and predicted protein stability and conservation scores.

We show that this approach is capable of distinguishing benign common variants from both gain- and loss-of-function (GoF/LoF) variants. Additionally, our work provides insight into the molecular mechanism underlying specific variants and the unusual propensity of NALCN missense variants to result in GoF phenotypes.

We anticipate that this experimental and computational framework will aid assessment of variant pathogenicity of NALCN and other components of the channelosome in the future.