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AlphaMissense classifies most possible human missense variants

DeepMind released AlphaMissense and a catalog covering about 71 million human missense variants, classifying 89 percent as likely benign or likely pathogenic, in Science on 19 September 2023.

19 Sep 2023Tier 3 MajorMethodology 0.1

Current score

+2.65

10 base · Major (tier 3 of 5, 10 pts)
× 0.9000 attribution · Primary causal contribution
× 0.7000 evidence · Peer review or independent validation
× 0.6000 realization · Experimentally validated
× 0.7000 durability
Event-level product before credit split: 2.65

Widely used proteome-wide resource (tier 3). High model attribution. Peer review. Realization is a public database used in research, not a diagnostic device. Scores will be revised as evidence accumulates.

What happened

AlphaMissense adapts AlphaFold-style modeling and is fine-tuned on population-frequency labels rather than ClinVar. The authors reported strong benchmark performance without training on those clinical labels and released proteome-wide scores. The resource is explicitly not approved for clinical diagnosis. Clinical labs may use scores as one input among many.

Model attribution

+2.65

AlphaFold

Predicted missense pathogenicity for all possible human substitutions.

The catalog is the model’s output.

Attribution 0.9000 · Credit share 100% · Google DeepMind

Claims

  • AlphaMissense provided scores for all 71 million possible human missense variants and classified 89 percent at the authors’ threshold.

    outcome · supported

  • AlphaMissense is an approved standalone clinical diagnostic.

    outcome · disputed

Sources

primary sources

Secondary domains: Biology

Revision history

  • 13 Sep 2026 · 0.00 → 2.65

    Initial adjudicated seed score under methodology 0.1.

AlphaMissense classifies most possible human missense variants · NetGoodIndex