AlphaMissense
An adaptation of AlphaFold, fine-tuned on human and primate variant population frequencies, that predicts missense variant pathogenicity from structural context and evolutionary conservation.
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. 8 linked records have results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- AlphaMissense, BP4 ≤0.34 and PP3 ≥0.56 (Ramadane-Morchadi et al. 2025) Configuration · configuration · 1 evaluation · 3 results
- AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80 (Ramadane-Morchadi et al. 2025) Configuration · configuration · 1 evaluation · 3 results
- AlphaMissense, BP4 ≤0.65 and PP3 ≥0.75 (Ramadane-Morchadi et al. 2025) Configuration · configuration · 2 evaluations · 8 results
- AlphaMissense hg38, pre-computed (Pearce et al. 2026) Configuration · configuration · 1 evaluation · 1 result
- AlphaMissense (Evo 2 paper variant effect evaluations) Configuration · configuration · 10 evaluations · 20 results
- AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- AlphaMissense (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
- AlphaMissense (Bergquist et al. 2025 calibration) Configuration · configuration · 1 evaluation · 9 results
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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Evidence
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Evidence table
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1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description An adaptation of AlphaFold, fine-tuned on human and primate variant population frequencies, that predicts missense variant pathogenicity from structural context and evolutionary conservation. Individual claims | Abstract: Accurate proteome-wide missense variant effect prediction with AlphaMissense qa-descriptions-20261011-e-source-alphamissense: abstractText Version: Europe PMC core record MED/37733863 (title and abstract), Science 2023 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved with two corrections, both applied: the MutFormer source licence is CC BY 4.0 per the arXiv abstract page, and the MetaRNN source locator now names the Background passage. Checked the 27 Chen 2020 descriptions row by row against Table 1 (PMC7033911) and spot-checked AlphaMissense, MisFit, popEVE, VARITY, MetaRNN, MutFormer and gMVP against their abstracts; accurate. Licences on the other new sources match Europe PMC. Field: Claim: metadata-correction-9767662c5213c3f8f98c Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers · Original source · bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page
- Abstract: Accurate proteome-wide missense variant effect prediction with AlphaMissense · Original source · Europe PMC core record MED/37733863 (title and abstract), Science 2023
Technical metadata and extraction receipts
Stable ID: somatic-oncogenicity-20261009-method-alphamissense
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- supervised_machine_learning
- reported name
- AlphaMissense
- entity level
- method
- source locator
- Algorithm lists of the cited sources
- missing metadata
- version: reason: inapplicable; note: Family record; score sources are on configurations
Related records
- configuration of: AlphaMissense, BP4 ≤0.34 and PP3 ≥0.56 (Ramadane-Morchadi et al. 2025)
- configuration of: AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80 (Ramadane-Morchadi et al. 2025)
- configuration of: AlphaMissense, BP4 ≤0.65 and PP3 ≥0.75 (Ramadane-Morchadi et al. 2025)
- configuration of: AlphaMissense hg38, pre-computed (Pearce et al. 2026)
- configuration of: AlphaMissense (Evo 2 paper variant effect evaluations)
- subject: AlphaMissense: description
- configuration of: AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: AlphaMissense (Livesey and Marsh 2025)
- configuration of: AlphaMissense (Bergquist et al. 2025 calibration)