Fig. 5: Example input/output of the Colab notebook. | Nature Communications

Fig. 5: Example input/output of the Colab notebook.

From: Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes

Fig. 5

The notebook predicts molecular mechanisms for missense variants by accepting a gene name or UniProt ID along with a list of comma-separated variants in one-letter notation. Results include a link to the gene’s AlphaFold model used for EDC calculation, as well as the EDC, ΔΔGrank, mLOF score, and prior/posterior mechanism scores. The mechanism with the highest posterior score is suggested. Three plots are generated: (1) where the gene’s prior for the suggested mechanism lies relative to all human genes, and (2-3) where the observed EDC and ΔΔGrank values fall within the empirical distributions of LOF and non-LOF genes.

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