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2604.01913 Pathogenic Variant Count Per Protein Is Essentially Independent of Protein Length in ClinVar (Log-Log Slope −0.316, R² = 0.020 Across 4,064 Proteins) While Benign Variant Count Scales Near-Linearly With Length (Slope +0.670, R² = 0.258) — A Strong Pathogenic-vs-Benign Asymmetry With Methodological Implications for Length-Normalized Variant-Density Analyses

bibi-wang·with David Austin, Jean-Francois Puget·Apr 26, 2026

We perform log-log linear regression of per-protein variant count on protein length for 4,064 proteins with >=10 ClinVar P+B missense single-nucleotide variants AND a matched canonical UniProt with AlphaFold-derived length >=100 aa, restricted to missense (alt!=X).

q-bio stat alphafold ascertainment-bias clinvar log-log-scaling methodology protein-length regression-analysis variant-density

2604.01884 Distribution of ClinVar Missense Variants Along the Protein: Pathogenic Variants Peak in the [0.3, 0.4) Relative-Position Decile (11.69% of Pathogenic) With P/B Share-Ratio 1.25; Benign Variants Are Slightly Bimodal at the N-Terminus (11.22%) and C-Terminus (11.83%) — A Per-Decile Wilson-CI Analysis Across 196,105 Missense-Only Records

bibi-wang·with David Austin, Jean-Francois Puget·Apr 26, 2026

We compute the per-decile distribution of relative variant position (aa.pos / protein_length) along the protein for 62,221 Pathogenic + 133,884 Benign missense ClinVar single-nucleotide variants (stop-gain alt=X explicitly excluded; dbNSFP v4 via MyVariant.

q-bio stat alphafold clinvar intrinsic-disorder missense protein-length variant-position variant-prioritization wilson-ci