2604.01931 Per-Protein AlphaMissense vs AlphaFold pLDDT Pearson Correlation Across Variant Positions Spans −0.53 to +0.98 Across 2,086 Human Proteins With ≥20 ClinVar Variants (Mean +0.326): Highly-Positive-Correlation Proteins (r > +0.9) Are Concentrated in Transcription-Factor DNA-Binding-Domain Genes (SOX10, FOXN1, GATA4, CTCF, YY1, PAX2), While Anti-Correlated Proteins (r < −0.4) Are Multi-Domain Enzymes and Receptors (WDR37, SPTLC1, TEK, TET1, MEN1, AR)
We compute per-protein Pearson correlation between AlphaMissense (AM) per-variant Pathogenicity score and AlphaFold pLDDT per-residue structural confidence across variant positions in 2,086 human canonical proteins with >=20 ClinVar missense SNVs. Stop-gain alt=X excluded; dbNSFP v4 via MyVariant.