{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:13:21Z","timestamp":1785413601796,"version":"3.56.0"},"reference-count":68,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000147","name":"Canadian Cancer Society","doi-asserted-by":"publisher","award":["705454"],"award-info":[{"award-number":["705454"]}],"id":[{"id":"10.13039\/501100000147","id-type":"DOI","asserted-by":"publisher"}]},{"award":["705454"],"award-info":[{"award-number":["705454"]}],"id":[{"id":"https:\/\/ror.org\/017343w90","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Oncology"],"abstract":"<jats:p>Background: Pathogenic germline BRCA1 and BRCA2 variants cause most hereditary breast and ovarian cancers. Widespread genetic testing has revealed thousands of variants with unknown effects on disease risk, known as variants of uncertain significance (VUS). BRCA VUS, the majority of which are missense, complicate genetic test interpretation and clinical decision-making. This study aimed to evaluate BRCA1 VUS pathogenicity with enhanced accuracy through computational, functional and structural methods. Methods: We characterized the structural distribution of BRCA1 variants. In silico tools scored known consequence variants within a specific region of BRCA1. The Molecular Feature Selection Tool (MolecularFeaST; Renwick Lab at Queen\u2019s University; Kingston, ON, Canada) performed feature selection of the most discriminative tools. MATLAB (MATLAB R2024a; Mathworks; Natick, MA, USA) Classification Learner Application trained supervised machine learning models using combinations of the most accurate tools; the best model assigned pathogenicity prediction scores to VUS. Select VUS were functionally assessed through phosphopeptide binding pull-down assays and structurally analyzed on PyMOL (v2.4.1; Schr\u00f6dinger Inc.; New York, NY, USA). Results: The RING and BRCT domains were identified as hotspots for missense pathogenic variants and VUS; BRCT was selected as the focus of the computational classifier. Nine in silico tools (CADD hg19, MetaRNN, ClinPred, VEST4, BayesDel AD, EVE, Eigen PC, gMVP and PolyPhen2) defined the BRCT-specific missense variant classifier. Twenty-two VUS (R1699P, F1704S, W1837L, W1712G, F1734S, V1804A, I1674V, V1804L, V1804I, I1807V, T1675S, I1764L, N1774I, E1698K, Q1848K, P1749S, A1669T, N1774H, L1839V, T1658I, L1705I, V1654L) demonstrated varying phosphopeptide binding ability and protein levels relative to the wildtype. Computational structural modeling contextualized VUS phosphopeptide interactions and structural implications. Conclusions: We provide in silico and functional evidence for the classification of BRCA1 BRCT VUS and highlight the utility of domain-specific computational approaches for characterizing missense variants in multi-domain genes.<\/jats:p>","DOI":"10.3390\/curroncol33060354","type":"journal-article","created":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T12:14:58Z","timestamp":1781180098000},"page":"354","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Domain-Specific Computational, Functional and Structural Methods Enable Interpretation of BRCA1 BRCT Variants of Uncertain Significance"],"prefix":"10.3390","volume":"33","author":[{"given":"Gabriella C.","family":"Torretto","sequence":"first","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"},{"name":"Division of Cancer Biology and Genetics, Sinclair Cancer Research Institute, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew D.","family":"Martin","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"},{"name":"Division of Cancer Biology and Genetics, Sinclair Cancer Research Institute, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6365-4396","authenticated-orcid":false,"given":"Kaamraan","family":"Islam","sequence":"additional","affiliation":[{"name":"Division of Cancer Biology and Genetics, Sinclair Cancer Research Institute, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole E.","family":"Archer","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"},{"name":"Division of Cancer Biology and Genetics, Sinclair Cancer Research Institute, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harriet E.","family":"Feilotter","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"},{"name":"Division of Cancer Biology and Genetics, Sinclair Cancer Research Institute, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"},{"name":"Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8909-8064","authenticated-orcid":false,"given":"Scott K.","family":"Davey","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"},{"name":"Division of Cancer Biology and Genetics, Sinclair Cancer Research Institute, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1007\/s12282-020-01148-2","article-title":"Hereditary breast and ovarian cancer (HBOC): Review of its molecular characteristics, screening, treatment, and prognosis","volume":"28","author":"Yoshida","year":"2020","journal-title":"Breast Cancer"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"341723","DOI":"10.1155\/2015\/341723","article-title":"Hereditary Ovarian Cancer: Not OnlyBRCA1 and 2 Genes","volume":"2015","author":"Toss","year":"2015","journal-title":"BioMed Res. Int."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Bouras, A., Guidara, S., Leone, M., Buisson, A., Martin-Denavit, T., Dussart, S., Lasset, C., Giraud, S., Bonnet-Dupeyron, M.-N., and Kherraf, Z.-E. (2023). Overview of the Genetic Causes of Hereditary Breast and Ovarian Cancer Syndrome in a Large French Patient Cohort. Cancers, 15.","DOI":"10.3390\/cancers15133420"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1016\/j.jmoldx.2015.11.007","article-title":"Eligibility Criteria and Genetic Testing Results from a High-Risk Cohort for Hereditary Breast and Ovarian Cancer Syndrome in Southeastern Ontario","volume":"18","author":"Vidal","year":"2016","journal-title":"J. Mol. Diagn."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4148","DOI":"10.1172\/JCI78507","article-title":"Pioneering geneticist Mary-Claire King receives the 2014 Lasker~Koshland Special Achievement Award in Medical Science","volume":"124","author":"Hurst","year":"2014","journal-title":"J. Clin. Investig."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.breast.2021.12.005","article-title":"BRCA1\/2 testing for genetic susceptibility to cancer after 25 years: A scoping review and a primer on ethical implications","volume":"61","author":"Petrova","year":"2021","journal-title":"Breast"},{"key":"ref_7","unstructured":"Petrucelli, N., Daly, M.B., and Pal, T. (1998). BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. GeneReviews, University of Washington."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e025317","DOI":"10.1136\/bmjopen-2018-025317","article-title":"Real-world health services utilisation and outcomes after BRCA1 and BRCA2 testing in Ontario, Canada: The What Comes Next Cohort Study protocol","volume":"8","author":"Dossa","year":"2018","journal-title":"BMJ Open"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Bertozzi, S., Londero, A.P., Xholli, A., Azioni, G., Di Vora, R., Paudice, M., Bucimazza, I., Cedolini, C., and Cagnacci, A. (2023). Risk-Reducing Breast and Gynecological Surgery for BRCA Mutation Carriers: A Narrative Review. J. Clin. Med., 12.","DOI":"10.3390\/jcm12041422"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Ragupathi, A., Singh, M., Perez, A.M., and Zhang, D. (2023). Targeting the BRCA1\/2 deficient cancer with PARP inhibitors: Clinical outcomes and mechanistic insights. Front. Cell Dev. Biol., 11.","DOI":"10.3389\/fcell.2023.1133472"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"189","DOI":"10.5498\/wjp.v11.i5.189","article-title":"Uncertainty following an inconclusive result from the BRCA1\/2 genetic test: A review about psychological outcomes","volume":"11","author":"Bramanti","year":"2021","journal-title":"World J. Psychiatry"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41525-018-0046-7","article-title":"Clinical testing of BRCA1 and BRCA2: A worldwide snapshot of technological practices","volume":"3","author":"Toland","year":"2018","journal-title":"npj Genom. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1634\/theoncologist.2012-0452","article-title":"BRCA1\/2 Sequence Variants of Uncertain Significance: A Primer for Providers to Assist in Discussions and in Medical Management","volume":"18","author":"Lindor","year":"2013","journal-title":"Oncologist"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Jimenez-Sainz, J., and Jensen, R.B. (2021). Imprecise Medicine: BRCA2 Variants of Uncertain Significance (VUS), the Challenges and Benefits to Integrate a Functional Assay Workflow with Clinical Decision Rules. Genes, 12.","DOI":"10.3390\/genes12050780"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1111\/cas.14803","article-title":"Pathogenicity assessment of variants for breast cancer susceptibility genes based on BRCAness of tumor sample","volume":"112","author":"Yoshida","year":"2021","journal-title":"Cancer Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e201204005","DOI":"10.5936\/csbj.201204005","article-title":"Structure-Function Of The Tumor Suppressor BRCA1","volume":"1","author":"Clark","year":"2012","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4579","DOI":"10.1021\/bi2003795","article-title":"Impact of BRCA1 BRCT Domain Missense Substitutions on Phosphopeptide Recognition","volume":"50","author":"Coquelle","year":"2011","journal-title":"Biochemistry"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.pbiomolbio.2015.02.003","article-title":"Phosphopeptide interactions with BRCA1 BRCT domains: More than just a motif","volume":"117","author":"Wu","year":"2015","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1038\/s41431-024-01617-8","article-title":"Comparison of the ABC and ACMG systems for variant classification","volume":"32","author":"Houge","year":"2024","journal-title":"Eur. J. Hum. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2248","DOI":"10.1016\/j.ajhg.2021.11.001","article-title":"Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN","volume":"108","author":"Fayer","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"De Paolis, E., Paris, I., Tilocca, B., Roncada, P., Foca, L., Tiberi, G., D\u2019Angelo, T., Pavese, F., Muratore, M., and Carbognin, L. (2023). Assessing the pathogenicity of BRCA1\/2 variants of unknown significance: Relevance and challenges for breast cancer precision medicine. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.1053035"},{"key":"ref_23","first-page":"102503","article-title":"Computational identification of rare pathogenic genomic variants in esophageal cancer markers: Transcript-level analysis, sequence-based insights, and structural-functional impacts of non-synonymous SNPs","volume":"45","author":"Azmi","year":"2026","journal-title":"Biochem. Biophys. Rep."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1002\/humu.22150","article-title":"A guide for functional analysis of BRCA1 variants of uncertain significance","volume":"33","author":"Millot","year":"2012","journal-title":"Hum. Mutat."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1158\/0008-5472.CAN-09-2850","article-title":"Identification of breast tumor mutations in BRCA1 that abolish its function in homologous DNA recombination","volume":"70","author":"Ransburgh","year":"2010","journal-title":"Cancer Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: Public archive of relationships among sequence variation and human phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Gerolami, J., Wong, J.J.M., Zhang, R., Chen, T., Imtiaz, T., Smith, M., Jamaspishvili, T., Koti, M., Glasgow, J.I., and Mousavi, P. (2022). A Computational Approach to Identification of Candidate Biomarkers in High-Dimensional Molecular Data. Diagnostics, 12.","DOI":"10.3390\/diagnostics12081997"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_29","unstructured":"(The PyMOL Molecular Graphics System, 2017). The PyMOL Molecular Graphics System, version 3.9."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1002\/humu.21517","article-title":"dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions","volume":"32","author":"Liu","year":"2011","journal-title":"Hum. Mutat."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl Variant Effect Predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nsmb776","article-title":"Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1","volume":"11","author":"Williams","year":"2004","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4880","DOI":"10.1158\/0008-5472.CAN-09-4563","article-title":"Comprehensive Analysis of Missense Variations in the BRCT Domain of BRCA1 by Structural and Functional Assays","volume":"70","author":"Lee","year":"2010","journal-title":"Cancer Res."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Karchin, R., Monteiro, A.N.A., Tavtigian, S.V., Carvalho, M.A., and Sali, A. (2007). Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. PLoS Comput. Biol., 3.","DOI":"10.1371\/journal.pcbi.0030026"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Ismail, T., Alzneika, S., Riguene, E., Al-Maraghi, S., Alabdulrazzak, A., Al-Khal, N., Fetais, S., Thanassoulas, A., AlFarsi, H., and Nomikos, M. (2024). BRCA1 and Its Vulnerable C-Terminal BRCT Domain: Structure, Function, Genetic Mutations and Links to Diagnosis and Treatment of Breast and Ovarian Cancer. Pharmaceuticals, 17.","DOI":"10.3390\/ph17030333"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"6676","DOI":"10.1073\/pnas.93.13.6676","article-title":"Alpha-helical, but not beta-sheet, propensity of proline is determined by peptide environment","volume":"93","author":"Li","year":"1996","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"5734","DOI":"10.1080\/07391102.2023.2274517","article-title":"Inter-BRCT linker is probably the most intolerant region of the BRCA1 BRCT domain","volume":"42","author":"Yadegari","year":"2023","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Carter, H., Douville, C., Stenson, P.D., Cooper, D.N., and Karchin, R. (2013). Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-S3-S3"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/s41586-021-04043-8","article-title":"Disease variant prediction with deep generative models of evolutionary data","volume":"599","author":"Frazer","year":"2021","journal-title":"Nature"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1186\/s13073-022-01120-z","article-title":"MetaRNN: Differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning","volume":"14","author":"Li","year":"2022","journal-title":"Genome Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1038\/s42256-022-00561-w","article-title":"Predicting functional effect of missense variants using graph attention neural networks","volume":"4","author":"Zhang","year":"2022","journal-title":"Nat. Mach. Intell."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"D886","DOI":"10.1093\/nar\/gky1016","article-title":"CADD: Predicting the deleteriousness of variants throughout the human genome","volume":"47","author":"Rentzsch","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/humu.23158","article-title":"PERCH: A Unified Framework for Disease Gene Prioritization","volume":"38","author":"Feng","year":"2016","journal-title":"Hum. Mutat."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1016\/j.ajhg.2018.08.005","article-title":"ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants","volume":"103","author":"Alirezaie","year":"2018","journal-title":"Am. J. Hum. Genet."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/ng.3477","article-title":"A spectral approach integrating functional genomic annotations for coding and noncoding variants","volume":"48","author":"McCallum","year":"2016","journal-title":"Nat. Genet."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Pe\u00f1a-Guerrero, J., Fern\u00e1ndez-Rubio, C., Garc\u00eda-Sosa, A.T., and Nguewa, P.A. (2023). BRCT Domains: Structure, Functions, and Implications in Disease\u2014New Therapeutic Targets for Innovative Drug Discovery against Infections. Pharmaceutics, 15.","DOI":"10.3390\/pharmaceutics15071839"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Brown, G. (2011). Ensemble Learning. Encyclopedia of Machine Learning [Internet], Springer.","DOI":"10.1007\/978-0-387-30164-8_252"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/s41529-023-00336-7","article-title":"A machine learning approach for corrosion small datasets","volume":"7","author":"Sutojo","year":"2023","journal-title":"npj Mater. Degrad."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Kiyak, E.O., Ghasemkhani, B., and Birant, D. (2023). High-Level K-Nearest Neighbors (HLKNN): A Supervised Machine Learning Model for Classification Analysis. Electronics, 12.","DOI":"10.3390\/electronics12183828"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"eadg7492","DOI":"10.1126\/science.adg7492","article-title":"Accurate proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","author":"Cheng","year":"2023","journal-title":"Science"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e2400908","DOI":"10.1200\/PO-24-00908","article-title":"AlphaMissense for Identifying Pathogenic Missense Mutations in DNA Damage Repair Genes in Cancer","volume":"9","author":"Yazaki","year":"2025","journal-title":"JCO Precis Oncol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1038\/s41588-023-01465-0","article-title":"Genome-wide prediction of disease variant effects with a deep protein language model","volume":"55","author":"Brandes","year":"2023","journal-title":"Nat. Genet."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s13059-023-03024-6","article-title":"Cross-protein transfer learning substantially improves disease variant prediction","volume":"24","author":"Jagota","year":"2023","journal-title":"Genome Biol."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Wei, Q., and Dunbrack, R.L. (2013). The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0067863"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.csbj.2023.12.031","article-title":"Structural and functional prediction, evaluation, and validation in the post-sequencing era","volume":"23","author":"Li","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"W547","DOI":"10.1093\/nar\/gkaf394","article-title":"UniProt Consortium. The UniProt website API: Facilitating programmatic access to protein knowledge","volume":"53","author":"Ahmad","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1177\/1947601910392988","article-title":"Tandem BRCT Domains: DNA\u2019s Praetorian Guard","volume":"1","author":"Mesquita","year":"2010","journal-title":"Genes Cancer"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"53007","DOI":"10.1074\/jbc.M310182200","article-title":"Detection of Protein Folding Defects Caused by BRCA1-BRCT Truncation and Missense Mutations","volume":"278","author":"Williams","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"44772","DOI":"10.1021\/acsomega.2c04782","article-title":"In Silico and Structure-Based Assessment of Similar Variants Discovered in Tandem Repeats of BRCT Domains of BRCA1 and BARD1 To Characterize the Folding Pattern","volume":"7","author":"Barua","year":"2022","journal-title":"ACS Omega"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1002\/(SICI)1098-1004(1999)14:3<186::AID-HUMU2>3.0.CO;2-J","article-title":"Protein misfolding and degradation in genetic diseases","volume":"14","author":"Bross","year":"1999","journal-title":"Hum. Mutat."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1038\/s41698-024-00741-4","article-title":"Reduced penetrance BRCA1 and BRCA2 pathogenic variants in clinical germline genetic testing","volume":"8","author":"Pal","year":"2024","journal-title":"npj Precis. Oncol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e4690","DOI":"10.21769\/BioProtoc.4690","article-title":"Cycloheximide (CHX) Chase Assay to Examine Protein Half-life","volume":"13","author":"Miao","year":"2023","journal-title":"Bio-Protocol"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e2443","DOI":"10.21769\/BioProtoc.2443","article-title":"Assessment of Modulation of Protein Stability Using Pulse-chase Method","volume":"7","author":"Elgendy","year":"2017","journal-title":"Bio-Protocol"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"28.9.1","DOI":"10.1002\/0471140864.ps2809s79","article-title":"Analysis of protein stability and ligand interactions by thermal shift assay","volume":"79","author":"Huynh","year":"2015","journal-title":"Curr. Protoc. Protein Sci."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Madern, M.F., Haselbach, D., and Tanenbaum, M.E. (2026). In vivo kinetics of protein degradation by individual proteasomes. bioRxiv.","DOI":"10.2139\/ssrn.6330107"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.ajhg.2022.01.019","article-title":"The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays","volume":"109","author":"Adamovich","year":"2022","journal-title":"Am. J. Hum. Genet."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/s41586-018-0461-z","article-title":"Accurate classification of BRCA1 variants with saturation genome editing","volume":"562","author":"Findlay","year":"2018","journal-title":"Nature"}],"container-title":["Current Oncology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1718-7729\/33\/6\/354\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T04:41:48Z","timestamp":1781325708000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1718-7729\/33\/6\/354"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,11]]},"references-count":68,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["curroncol33060354"],"URL":"https:\/\/doi.org\/10.3390\/curroncol33060354","relation":{},"ISSN":["1718-7729"],"issn-type":[{"value":"1718-7729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,11]]}}}