Single nucleotide polymorphisms (SNPs) are the most common form of human genetic variation and can affect the protein sequence. These missense variants may affect protein stability, function or interactions with other proteins, potentially leading to disease. Protein–protein interactions (PPIs) can be strengthened or weakened by missense variants, which can cause loss of salt bridges, steric clashes or changes to post‐translational modifications, amongst other effects. Changes to PPIs can lead to rewiring of the PPI network and this can be responsible for altered phenotype. Variants at different interfaces can, in some cases, lead to different phenotypes by affecting different pathways and complexes. Understanding the effects of missense variants on PPIs and the interactome is helpful in determining how these variants can lead to disease, as shown by the improved predictive performance of our variant phenotype predictor SuSPect, which includes network features.
Key Concepts:
Missense variants can impact upon protein–protein interactions in numerous ways.
Impaired or enhanced interactions can both lead to disease.
Interactions can be affected by steric clashes, loss of salt bridges, changes to intrinsic disorder and several other mechanisms.
Variants in different parts of proteins can affect different interactions, potentially leading to different diseases.
Variants on corresponding interfaces in different proteins can lead to the same (or similar) disease.
Investigating the effects of variants in the context of interaction networks rather than in isolation can give important extra information.