New insights into the pathogenicity of non-synonymous variants through multi-level analysis

Precise classification of non-synonymous single nucleotide variants (SNVs) is a fundamental goal of clinical genetics. Next-generation sequencing technology is effective for establishing the basis of genetic diseases. However, identification of variants that are causal for genetic diseases remains a challenge. We analyzed human non-synonymous SNVs from a multilevel perspective to characterize pathogenicity. We showed that computational tools, though each having its own strength and weakness, tend to be overly dependent on the degree of conservation. For the mutations at non-degenerate sites, the amino acid sites of pathogenic substitutions show a distinct distribution in the classes of protein domains compared with the sites of benign substitutions. Overlooked disease susceptibility of genes explains in part the failures of computational tools. The more pathogenic sites observed, the more likely the gene is expressed in a high abundance or in a high tissue-specific manner, and have a high node degree of protein-protein interaction. The destroyed functions due to some false-negative mutations may arise because of a reprieve from the epigenetic repressed state which shouldn’t happen in multiple biological conditions, instead of the defective protein. Our work adds more to our knowledge of non-synonymous SNVs’ pathogenicity, thus will benefit the field of clinical genetics.