{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T01:51:36Z","timestamp":1783043496032,"version":"3.54.6"},"reference-count":37,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T00:00:00Z","timestamp":1750118400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2014Next Generation EU-Health Extended ALliance for Innovative Therapies","award":["2022B2N2BY"],"award-info":[{"award-number":["2022B2N2BY"]}]},{"name":"Italian Ministry of University and Research","award":["2022B2N2BY"],"award-info":[{"award-number":["2022B2N2BY"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Fabry disease is a rare genetic disorder caused by deficient activity of the lysosomal enzyme alpha-galactosidase A (AGAL), resulting in the accumulation of globotriaosylceramides (Gb3) in tissues and organs. This buildup leads to progressive, multi-systemic complications that severely impact quality of life and can be life-threatening. Interpreting the functional consequences of missense variants in the GLA gene remains a significant challenge, especially in rare diseases where experimental evidence is scarce. In this study, we present an integrative computational framework that combines structural, interaction, pathogenicity, and stability data from both in silico tools and experimental sources, enriched through expert curation and structural analysis. Given the clinical relevance of pharmacological chaperones in Fabry disease, we focus in particular on the structural characteristics of variants classified as \u201camenable\u201d to such treatments. Our multidimensional analysis\u2014using tools such as AlphaMissense, EVE, FoldX, and ChimeraX\u2014identifies key molecular features that distinguish amenable from non-amenable variants. We find that amenable mutations tend to preserve protein stability, while non-amenable ones are associated with structural destabilisation. By comparing AlphaMissense with alternative predictors rooted in evolutionary (EVE) and thermodynamic (FoldX) models, we explore the relative contribution of different biological paradigms to variant classification. Additionally, the investigation of outlier variants\u2014where AlphaMissense predictions diverge from clinical annotations\u2014highlights candidates for further experimental validation. These findings demonstrate how combining structural bioinformatics with machine learning\u2013based predictions can improve missense variant interpretation and support precision medicine in rare genetic disorders.<\/jats:p>","DOI":"10.3390\/ijms26125802","type":"journal-article","created":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T10:45:26Z","timestamp":1750157126000},"page":"5802","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Bioinformatics-Driven Multi-Factorial Insight into \u03b1-Galactosidase Mutations"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5579-183X","authenticated-orcid":false,"given":"Bruno","family":"Hay Mele","sequence":"first","affiliation":[{"name":"Department of Biology, University of Napoli \u201cFederico II\u201d, 80126 Napoli, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Rossetti","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Napoli \u201cFederico II\u201d, 80126 Napoli, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1594-0156","authenticated-orcid":false,"given":"Giuseppina","family":"Andreotti","sequence":"additional","affiliation":[{"name":"Institute of Biomolecular Chemistry (ICB)\u2014National Council Research of Italy, 80078 Pozzuoli, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6147-6553","authenticated-orcid":false,"given":"Maria Vittoria","family":"Cubellis","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Napoli \u201cFederico II\u201d, 80126 Napoli, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Guerriero","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Napoli \u201cFederico II\u201d, 80126 Napoli, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3136-2138","authenticated-orcid":false,"given":"Maria","family":"Monticelli","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Napoli \u201cFederico II\u201d, 80126 Napoli, Italy"},{"name":"Institute of Biomolecular Chemistry (ICB)\u2014National Council Research of Italy, 80078 Pozzuoli, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1126\/science.167.3922.1268","article-title":"Fabry\u2019s Disease: Alpha-Galactosidase Deficiency","volume":"167","author":"Kint","year":"1970","journal-title":"Science"},{"key":"ref_2","unstructured":"Adam, M.P., Feldman, J., Mirzaa, G.M., Pagon, R.A., Wallace, S.E., and Amemiya, A. 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