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Updated: Dec 24, 2025

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Integrating structural and evolutionary data to interpret variation and pathogenicity in adapter protein complex 4.

John E Gadbery1, Abin Abraham2, Carli D Needle1

  • 1Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.

Protein Science : a Publication of the Protein Society
|April 15, 2020
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Summary

Genetic variations in adapter protein complex 4 (AP-4) cause neurological disorders. This study identifies key AP-4 regions, particularly subunit interfaces, vulnerable to pathogenic mutations, aiding disease interpretation.

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Area of Science:

  • Molecular Biology
  • Neurogenetics
  • Structural Biology

Background:

  • Genetic variations in adapter protein complex 4 (AP-4) are linked to severe neurological phenotypes.
  • The structural basis for AP-4 dysfunction due to genetic variation remains poorly understood.

Purpose of the Study:

  • To investigate the structural and evolutionary patterns of AP-4 to predict regions susceptible to pathogenic variation.
  • To provide a framework for interpreting the functional impact of novel AP-4 variants.

Main Methods:

  • Analysis of AP-4 genetic evolution and conservation patterns.
  • Mapping known AP-4 variants onto a homology model.
  • Prediction of pathogenic variation likelihood based on structural location.

Main Results:

  • Identified significant clustering of pathogenic variants at the β4-N-μ4 subunit interface.
  • Observed variant accumulation throughout the C-μ4 subunit.
  • Established a structure-function correlation for AP-4 genetic variation.

Conclusions:

  • Genetic and evolutionary forces shape AP-4 structure and function.
  • The identified variant hotspots provide insights into AP-4-related neurological diseases.
  • This study serves as a foundation for understanding uncharacterized AP-4 variants.