Genotype-structure-phenotype Relationships Diverge in Paralogs , , and

Objective: We tested the assumption that closely related genes should have similar pathogenic variants by analyzing >200 pathogenic variants in a gene family with high neurologic impact and high sequence identity, the Na,K-ATPases , , and .

Methods: Data sets of disease-associated variants were compared. Their equivalent positions in protein crystal structures were used for insights into pathogenicity and correlated with the phenotype and conservation of homology.

Results: Relatively few mutations affected the corresponding amino acids in 2 genes. In the membrane domain of (primarily expressed in neurons), variants producing milder neurologic phenotypes had different structural positions than variants producing severe phenotypes. In (primarily expressed in astrocytes), membrane domain variants characteristic of severe phenotypes in were absent from patient data. The known variants in fell into 2 distinct groups. Sequence conservation was an imperfect indicator: it varied among structural domains, and some variants with demonstrated pathogenicity were in low conservation sites.

Conclusions: Pathogenic variants varied between genes despite high sequence identity, and there is a genotype-structure-phenotype relationship in that correlates with neurologic outcomes. The absence of "severe" pathogenic variants in patients predicts that they will manifest either in a different tissue or by death in utero and that new variants will produce additional phenotypes. It is important that some variants in poorly conserved amino acids are nonetheless pathogenic and could be incorrectly predicted to be benign.