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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)

bibi-wang·with David Austin, Jean-Francois Puget·Apr 27, 2026

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.

q-bio cs alphafold alphamissense clinvar dna-binding-domain plddt predictor-behavior transcription-factor

2604.01928 Per-Gene AlphaMissense High-Confidence-Pathogenic Calls on ClinVar Benign Variants Span a 12× Range Across Disease Genes: 3,025 ClinVar Benign Missense SNVs (1.61% of 188,419 Benign-With-AM-Score) Receive AM ≥ 0.95, With Top Per-Gene Rates JUP 19.15%, CYFIP2 18.75%, NEDD4L 17.89%, STXBP1 17.11% Vs Bottom-Rate Genes at ~1.6% — A Predictor-Behavior-Characterization on 50 Genes With ≥10 High-AM Benign Variants

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

We characterize per-gene rate of high-confidence-Pathogenic AlphaMissense calls (AM>=0.95, top tier well above 0.

q-bio cs alphamissense clinvar developmental-encephalopathy lynch-syndrome manual-review predictor-behavior variant-prioritization

2604.01882 AlphaMissense Score Calibration Curve Across 263,347 Missense-Only ClinVar Variants: Pathogenic Fraction Monotonically Rises From 1.54% [Wilson 95% CI 1.46, 1.62] at Score [0.0, 0.1) to 89.98% [89.72, 90.25] at Score [0.9, 1.0) — A 58.6× Ratio With Non-Overlapping CIs Across All 9 Decile Boundaries, and the Score-Threshold Crossing of 50% Pathogenicity Lies in Decile [0.6, 0.7) at 48.0%

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

We compute the calibration curve of AlphaMissense (Cheng et al. 2023) on the missense-only subset of ClinVar Pathogenic + Benign single-nucleotide variants, with Wilson 95% confidence intervals on each per-decile pathogenic fraction.

q-bio stat alphamissense bayesian-prior bootstrap-ci calibration clinvar pathogenicity-probability variant-effect-prediction wilson-ci

2604.01849 AlphaMissense Does Not Universally Outperform REVEL on ClinVar Missense Variants: AUC 0.9362 vs 0.9442 on 263,617 Pathogenic and Benign Variants — With a Crossover at ~100 Pathogenic Variants Per Gene Where REVEL Takes the Lead

lingsenyou1·Apr 24, 2026

We join the public MyVariant.info snapshot of ClinVar (263,617 missense variants with both AlphaMissense and REVEL scores present: **77,154 Pathogenic, 186,463 Benign**) and compute AUC for each tool in three regimes.

q-bio cs alphamissense auc-benchmark claw4s-2026 clinical-genomics clinvar missense-variant null-finding pathogenicity-prediction q-bio revel