Virtual screening to identify pathogenic functional mutations in the exon of ACTN3 gene, which codes for masseter muscle, thereby affecting mandibular morphology

Abstract

Aim: To determine if In silico methods can be used to identify pathogenic non-synonymous variants in the ACTN3 (alpha actinin 3) alpha actinin gene that encodes for alpha actinin 3 three protein employing computational tools. Materials and Methods: In silico methods of detecting pathogenic variants were initiated by identifying 854 reported non-synonymous mutations in the ACTN3 gene from the Ensembl database. The non-synonymous variants of ACTN3-201 (transcript ID: ENST00000502692.5) were derived from the Ensembl database. Variants found to be pathogenic were curated using SIFT tool (The Sorting Intolerant From Tolerant), PolyPhen2 (Polymorphism Phenotyping v2), and PROVEAN (Protein Variation Effect Analyzer). The panel of curated variants was analyzed for protein stability based on substituting existing amino acid residue with a variant encoded amino acid using IMutant 3.0. Results: Among 854 variants reported in the ACTN3 gene, 26 were found to be harmful, and possibly pathogenic. The SIFT tool identified 15 variants to be highly intolerant, PolyPhen2 identified two other variants as possibly damaging, and PROVEAN predicted two variants to be highly harmful. Finally, IMutant 3.0 showed that one (single nucleotide polymorphism) resulted in decreased stability of the ACTN3 protein. Conclusions: Applying in silico approaches can help researchers identify variants exhibiting putative association with the disease phenotype.

Keywords

• alpha-actinin
• malocclusion
• mutation
• non-synonymous
• polymorphism