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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Predicting how missense variants alter protein function is central to resolving the genotype-to-phenotype equation, a task now addressed by numerous computational predictors. The most accurate are increasingly opaque, however, limiting both their mechanistic value and their adoption in the clinic. Here we present QAFIsplit, a redesign of the Quantitative Assessment of Functional Impact framework that models variant effect in two interpretable stages: the mutation tolerance of a position, and the deviation introduced by a specific substitution. Framed as the prediction of a molecular endophenotype, QAFIsplit reaches state-of-the-art quantitative accuracy on independent deep mutational scanning benchmarks, surpassing black-box predictors such as AlphaMissense in most protein domains. Carried into clinical variant classification, it performs on par with established clinical tools without ever being trained on clinical labels, and complements meta-predictors without penalty. In the CAGI 7 community experiment, QAFI-based strategies were submitted blindly to four independent disease-gene challenges, backed by strong pre-submission clinical validation (AUC up to 0.99).<\/jats:p>","DOI":"10.3390\/ijms27198777","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:19:37Z","timestamp":1790777977000},"page":"8777","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Toward Advanced Quantitative Prediction of Missense Variant Effects"],"prefix":"10.3390","volume":"27","author":[{"given":"Shaopei","family":"Ye","sequence":"first","affiliation":[{"name":"Research Unit in Clinical and Translational Bioinformatics, Vall d\u2019Hebron Institute of Research (VHIR), Universitat Aut\u00f2noma de Barcelona, Bellaterra, 08193 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7398-1351","authenticated-orcid":false,"given":"Selen","family":"\u00d6zkan","sequence":"additional","affiliation":[{"name":"Research Unit in Clinical and Translational Bioinformatics, Vall d\u2019Hebron Institute of Research (VHIR), Universitat Aut\u00f2noma de Barcelona, Bellaterra, 08193 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6248-4032","authenticated-orcid":false,"given":"Aitana","family":"D\u00edaz-V\u00e1squez","sequence":"additional","affiliation":[{"name":"Research Unit in Clinical and Translational Bioinformatics, Vall d\u2019Hebron Institute of Research (VHIR), Universitat Aut\u00f2noma de Barcelona, Bellaterra, 08193 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Nat\u00e0lia","family":"Padilla","sequence":"additional","affiliation":[{"name":"Research Unit in Clinical and Translational Bioinformatics, Vall d\u2019Hebron Institute of Research (VHIR), Universitat Aut\u00f2noma de Barcelona, Bellaterra, 08193 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9738-8472","authenticated-orcid":false,"given":"Xavier","family":"de la Cruz","sequence":"additional","affiliation":[{"name":"Research Unit in Clinical and Translational Bioinformatics, Vall d\u2019Hebron Institute of Research (VHIR), Universitat Aut\u00f2noma de Barcelona, Bellaterra, 08193 Barcelona, Spain"},{"name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.cell.2019.02.003","article-title":"Genomic Medicine\u2013Progress, Pitfalls, and Promise","volume":"177","author":"Shendure","year":"2019","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Masica, D.L., and Karchin, R. 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