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Updated: Jun 18, 2026

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Compensated pathogenic deviations: analysis of structural effects.

Anja Baresić¹, Lisa E M Hopcroft, Hubert H Rogers

¹Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK.

Journal of Molecular Biology

|November 11, 2009

Summary

This summary is machine-generated.

Compensated pathogenic deviations (CPDs) are disease-causing mutations in humans that are benign in other species. These mutations are often milder and located on protein surfaces, with nearby compensatory mutations helping to explain their lack of pathogenicity.

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Published on: November 22, 2024

Area of Science:

Evolutionary biology
Molecular biology
Genetics

Background:

Pathogenic deviations (PDs) are human missense mutations causing disease.
Compensated pathogenic deviations (CPDs) are PDs found as wild-type in functionally equivalent proteins of other species.
CPDs suggest compensatory mutations mitigate pathogenicity.

Purpose of the Study:

Investigate structural features of CPDs.
Identify compensatory mutations in CPDs.
Understand protein evolution through fitness landscape traversal.

Main Methods:

Curated PD and CPD datasets from OMIM database.
Analyzed 245 human proteins with known structures (2328 mutations).
Searched for spatially close compensatory mutations and used SAAPdb for structural effect analysis.

Main Results:

Identified 453 CPDs (from 85 structures) in non-human species.
CPDs exhibit milder structural effects than uncompensated PDs.
CPDs are frequently located on protein surfaces.
Residues surrounding CPDs show higher mutation rates, supporting local compensation.

Conclusions:

Compensated pathogenic deviations are structurally distinct from uncompensated ones.
Local mutations likely explain the lack of pathogenicity in CPDs.
Findings advance understanding of protein evolution and mutation tolerance.