Missense mutations in intrinsically disordered protein regions link pathogenicity and phase separation

Area of Science:

• Biochemistry and Molecular Biology
• Genetics and Genomics
• Computational Biology

Background:

• Missense genetic variations, particularly in intrinsically disordered regions (IDRs), pose challenges in predicting their impact on protein function.
• Intrinsically disordered regions are known to undergo liquid- ગુજરાત liquid phase separation, a process implicated in various cellular functions and diseases.
• It is hypothesized that mutations disrupting phase separation may preferentially contribute to disease pathogenesis.

Purpose of the Study:

• To investigate the correlation between disease association and the phase separation propensity of intrinsically disordered regions (IDRs).
• To determine if mutations within phase-separating IDRs exhibit a higher pathogenic mutation rate compared to non-phase-separating IDRs.
• To analyze the impact of specific amino acid substitutions and post-translational modifications on pathogenicity within phase-separating IDRs.

Main Methods:

• Utilized computational predictions for phase-separating (PS) IDRs.
• Analyzed databases of disease-associated proteins and mutations.
• Mapped the prevalence of PS IDRs across various diseases.
• Calculated and compared pathogenic mutation rates in PS versus non-PS IDRs.
• Examined the pathogenicity of specific amino acid substitutions (arginine, aromatic, serine, threonine, alanine) and phosphorylation sites.

Main Results:

• Disease-associated proteins show a higher prevalence of predicted phase separation behavior compared to typical human proteins.
• A significant enrichment of phase separation is observed in proteins linked to a wide range of diseases.
• The pathogenic mutation rate in predicted PS IDRs is threefold higher than in IDRs not predicted to phase separate.
• Specific amino acid substitutions (arginine, aromatic) are more pathogenic in PS IDRs, while others (serine, threonine, alanine) are benign.
• Half of mutations of uncertain clinical significance in PS IDRs are predicted to be pathogenic.
• Phosphorylation sites are enriched in PS IDRs, but mutations at these sites are mostly benign.
• Pathogenicity is highest for mutations in predicted PS IDRs that are also part of short linear motifs.

Conclusions:

• Phase separation of intrinsically disordered regions (IDRs) is strongly associated with disease pathogenesis.
• Mutations affecting phase separation in IDRs are significantly more likely to be pathogenic, highlighting their critical role in disease.
• The study provides a framework for assessing the pathogenicity of mutations with uncertain clinical significance, particularly those within phase-separating IDRs.