Leveraging protein language models and a scoring function for indel characterization and transfer learning

Protein language models (PLMs) are increasingly used to assess the impact of genetic variants, achieving high accuracy and often outperforming traditional pathogenicity predictors. They enable zero-shot inference, making predictions without task-specific fine-tuning, though studying in-frame insertions and deletions (indels) remains challenging due to altered protein lengths and limited annotated datasets. Here, we present IndeLLM, a scoring approach for indel pathogenicity that accounts for sequence length differences. Our zero-shot method relies solely on sequence information, requires minimal computing resources, and achieves performance comparable to existing predictors. Building on this, we developed a Siamese network via transfer learning that outperformed all tested indel predictors (Matthews correlation coefficient = 0.77). To enhance accessibility, we provide a plug-and-play Google Colab notebook for using IndeLLM and visualizing the impact of indels on protein sequence and structure. The tool is freely available on GitHub and Google Colab.