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Site-saturation mutagenesis of 500 human protein domains

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Beltran, Antoni, Jiang, Xiang’er, Shen, Yue, Lehner, Ben·2025·Nature
DOI 10.1038/s41586-024-08370-4PMC PMC11754108
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Abstract

Missense variants that change the amino acid sequences of proteins cause one-third of human genetic diseases 1 . Tens of millions of missense variants exist in the current human population, and the vast majority of these have unknown functional consequences. Here we present a large-scale experimental analysis of human missense variants across many different proteins. Using DNA synthesis and cellular selection experiments we quantify the effect of more than 500,000 variants on the abundance of more than 500 human protein domains. This dataset reveals that 60% of pathogenic missense variants reduce protein stability. The contribution of stability to protein fitness varies across proteins and diseases and is particularly important in recessive disorders. We combine stability measurements with protein language models to annotate functional sites across proteins. Mutational effects on stability are largely conserved in homologous domains, enabling accurate stability prediction across entire protein families using energy models. Our data demonstrate the feasibility of assaying human protein variants at scale and provides a large consistent reference dataset for clinical variant interpretation and training and benchmarking of computational methods.

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Cited by

Sorted by citations

Authors
Beltran, A., Jiang, X., Shen, Y., & Lehner, B.
Affiliations
  • Barcelona Institute of Science and Technology (ES)
  • BGI Group (China) (CN)
  • Institució Catalana de Recerca i Estudis Avançats (ES)
Corresponding author
Lehner, Ben
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2025-01-08
Volume
637
Issue
8047
Pages
885-894
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-024-08370-4
PMC
PMC11754108
OpenAlex
W4406167408
Cited by
126
References
8
Citations by year
2026: 72 · 2025: 48 · 2024: 6
FWCI
62.89
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Centres de Recerca de Catalunya
  • European Commission (HORIZON2020, 101030961)
  • National Natural Science Foundation of China (32322047, BM2023009)
  • AXA Research Fund
  • Generalitat de Catalunya (2017-SGR)
  • Ministerio de Ciencia e Innovación
  • Fondation Bettencourt Schueller
  • Agència de Gestió d'Ajuts Universitaris i de Recerca (2017SGR)
  • H2020 European Research Council (883742)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
missense mutations, protein stability, saturation mutagenesis, protein domains, recessive disorders, variant annotation, protein language models, stability prediction, homologous protein families, variant interpretation, clinical variant interpretation
MeSH terms
Protein Domains, Humans, Models, Molecular, Proteins, Mutagenesis, Mutation, Missense, Protein Stability

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