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Article

Leveraging protein language models to identify complex trait associations with previously inaccessible classes of functional rare variants.

Cell genomics - 11 Feb 2026

Jang Seon-Kyeong, Wang Zitian, Border Richard, Tuan Dinh, Wei Angela, An Ulzee, Sankararaman Sriram, Ntranos Vasilis, Flint Jonathan, Zaitlen Noah

Abstract excerpt

Protein language models (PLMs) improve variant effect predictions, but their role in gene discovery for complex traits remains unclear. We introduce an allelic series-based regression test that uses PLM-derived variant effect predictions as proxies for effect sizes, identifying ∼46% more associations than standard burden tests. Extending this to isoform-level analysis, we find 26 gene-trait pairs with stronger...

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Identifiers

PMID: 41265447
DOI: 10.1016/j.xgen.2025.101068
PMCID: PMC12903449

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