Functional and Structural Characterization of Pathogenicity of Human Arginine-Histidine Variants

Area of Science:

• Biochemistry
• Genetics
• Structural Biology

Background:

• Missense variants involving arginine (R) and histidine (H) substitutions (R>H, H>R) preserve charge but alter pH-dependent protein behavior.
• These alterations can lead to context-dependent effects on protein function, potentially causing pathogenicity.

Purpose of the Study:

• To identify factors contributing to the pathogenicity of R>H and H>R missense variants.
• To analyze the structural, physicochemical, and functional characteristics differentiating pathogenic from benign variants.

Main Methods:

• Assembled high-confidence human R>H and H>R variants from ClinVar, categorized as pathogenic or benign.
• Analyzed variant location (core vs. surface, secondary structures), pH-optimum of activity, and protein functional classes.
• Investigated enrichment of variants in specific protein types (e.g., transcription factors, enzymes).

Main Results:

• Pathogenic R>H/H>R variants are enriched in protein cores and ordered regions, unlike benign variants found on surfaces.
• R>H pathogenic variants favor helices, while H>R pathogenic variants favor β-strands.
• Pathogenic variants are overrepresented in binding-heavy proteins and specific enzyme classes (oxidoreductases, ion channels, transporters, ligases).
• H>R pathogenic variants showed overrepresentation in the neutral/physiological pH range, impacting pH-dependent activity.

Conclusions:

• Variant location and secondary structure preference distinguish pathogenic from benign R>H/H>R variants.
• The pH-dependent behavior and protein functional class are critical factors in pathogenicity.
• Understanding these variant characteristics aids in predicting pathogenicity and disease association.