{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T11:56:08Z","timestamp":1781610968479,"version":"3.54.5"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T00:00:00Z","timestamp":1780099200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"vor","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Med"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Despite advances in sequencing and standardized guidelines, many variants, particularly in genetically heterogeneous disorders such as hearing and vision loss, remain of uncertain significance. Multiplexed assays of variant effects (MAVEs) offer a solution to resolve these uncertainties, but their clinical integration is limited. We aimed to assess the utilization of functional evidence in hearing and vision loss genetics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We surveyed 82 hearing and ocular genetics experts, collecting quantitative and qualitative data on their practices, confidence in functional assays and perceived barriers to integrating functional evidence into clinical workflows.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we show that hearing and vision loss experts frequently encounter variants of uncertain significance and note that functional data often fails to resolve uncertainty due to limited availability or inconsistent quality. Confidence is highest in transcript assays, patient-derived cell models and computational predictors, while familiarity and trust are lower for non-mammalian models and high-throughput assays like MAVEs. Respondents highlight the need for improved data accessibility, standardized evaluation guidelines and training to support functional evidence integration.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our survey identifies both common and domain-specific challenges in applying functional evidence for variant classification in hearing and ocular genetics, emphasizing the need for frameworks that account for biological complexity, methodological limitations, and barriers to data accessibility.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1038\/s43856-026-01650-2","type":"journal-article","created":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T14:55:02Z","timestamp":1780152902000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A comparative survey of functional evidence use in hearing and vision loss genetics"],"prefix":"10.1038","volume":"6","author":[{"given":"R. Arda","family":"Inan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina T.","family":"DiStefano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sami S.","family":"Amr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Bei\u00dfbarth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2870-5099","authenticated-orcid":false,"given":"Lea M.","family":"Starita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew B.","family":"Stergachis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9134-1673","authenticated-orcid":false,"given":"Ahmad","family":"Abou Tayoun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert B.","family":"Hufnagel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6719-3447","authenticated-orcid":false,"given":"Barbara","family":"Vona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,30]]},"reference":[{"key":"1650_CR1","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/gim.2015.30","volume":"17","author":"S Richards","year":"2015","unstructured":"Richards, S. et al. 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. Genet. Med. 17, 405\u2013424 (2015).","journal-title":"Genet. Med."},{"key":"1650_CR2","doi-asserted-by":"publisher","first-page":"1517","DOI":"10.1002\/humu.23626","volume":"39","author":"AN Abou Tayoun","year":"2018","unstructured":"Abou Tayoun, A. N. et al. Recommendations for interpreting the loss of function PVS1 ACMG\/AMP variant criterion. Hum. Mutat. 39, 1517\u20131524 (2018).","journal-title":"Hum. Mutat."},{"key":"1650_CR3","volume":"12","author":"On behalf of the Clinical Genome Resource Sequence Variant Interpretation Working Group, Brnich SE, Abou Tayoun AN","year":"2020","unstructured":"On behalf of the Clinical Genome Resource Sequence Variant Interpretation Working Group, Brnich SE, Abou Tayoun AN et al. Recommendations for application of the functional evidence PS3\/BS3 criterion using the ACMG\/AMP sequence variant interpretation framework. Genome Med. 12, 1 (2020).","journal-title":"Genome Med."},{"key":"1650_CR4","doi-asserted-by":"publisher","first-page":"1687","DOI":"10.1038\/gim.2018.42","volume":"20","author":"LG Biesecker","year":"2018","unstructured":"Biesecker, L. G. & Harrison, S. M. ClinGen Sequence Variant Interpretation Working Group. The ACMG\/AMP reputable source criteria for the interpretation of sequence variants. Genet Med. 20, 1687\u20131688 (2018).","journal-title":"Genet Med."},{"key":"1650_CR5","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.ajhg.2022.10.013","volume":"109","author":"V Pejaver","year":"2022","unstructured":"Pejaver, V. et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3\/BP4 criteria.  Am. J. Hum. Genet. 109, 12 (2022).","journal-title":"Am. J. Hum. Genet."},{"key":"1650_CR6","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.ajhg.2023.06.002","volume":"110","author":"LC Walker","year":"2023","unstructured":"Walker, L. C. et al. Using the ACMG\/AMP framework to capture evidence related to predicted and observed impact on splicing: recommendations from the ClinGen SVI Splicing Subgroup.  Am. J. Hum. Genet. 110, 7 (2023).","journal-title":"Am. J. Hum. Genet."},{"key":"1650_CR7","doi-asserted-by":"publisher","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","volume":"42","author":"MJ Landrum","year":"2014","unstructured":"Landrum, M. J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucl. Acids Res. 42, D980\u2013D985 (2014).","journal-title":"Nucl. Acids Res."},{"key":"1650_CR8","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1038\/s41588-019-0528-2","volume":"51","author":"AR Martin","year":"2019","unstructured":"Martin, A. R. et al. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat. Genet. 51, 1560\u20131565 (2019).","journal-title":"Nat. Genet."},{"key":"1650_CR9","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1016\/j.ajhg.2018.08.006","volume":"103","author":"H Azaiez","year":"2018","unstructured":"Azaiez, H. et al. Genomic landscape and mutational signatures of deafness-associated genes.  Am. J. Hum. Genet. 103, 484\u2013497 (2018).","journal-title":"Am. J. Hum. Genet."},{"key":"1650_CR10","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1007\/s00439-016-1648-8","volume":"135","author":"CM Sloan-Heggen","year":"2016","unstructured":"Sloan-Heggen, C. M. et al. Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum. Genet. 135, 441\u2013450 (2016).","journal-title":"Hum. Genet."},{"key":"1650_CR11","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1007\/s00439-021-02371-3","volume":"141","author":"S Usami","year":"2022","unstructured":"Usami, S. & Nishio, S. The genetic etiology of hearing loss in Japan revealed by the social health insurance-based genetic testing of 10K patients. Hum. Genet. 141, 665\u2013681 (2022).","journal-title":"Hum. Genet."},{"key":"1650_CR12","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1038\/gim.2014.172","volume":"17","author":"MB Consugar","year":"2015","unstructured":"Consugar, M. B. et al. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet. Med. 17, 253\u2013261 (2015).","journal-title":"Genet. Med."},{"key":"1650_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-77014-4","volume":"14","author":"C Kiel","year":"2024","unstructured":"Kiel, C. et al. 18-Years of single-centre DNA testing in over 7000 index cases with inherited retinal dystrophies and optic neuropathies. Sci. Rep. 14, 25529 (2024).","journal-title":"Sci. Rep."},{"key":"1650_CR14","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03476-y","volume":"26","author":"AF Rubin","year":"2025","unstructured":"Rubin, A. F. et al. MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays. Genome Biol. 26, 13 (2025).","journal-title":"Genome Biol."},{"key":"1650_CR15","doi-asserted-by":"publisher","DOI":"10.1016\/j.gim.2023.100979","volume":"25","author":"M Solaki","year":"2023","unstructured":"Solaki, M., Wissinger, B., Kohl, S. & Reuter, P. Functional evaluation allows ACMG\/AMP-based re-classification of CNGA3 variants associated with achromatopsia. Genet. Med. 25, 100979 (2023).","journal-title":"Genet. Med."},{"key":"1650_CR16","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1101\/gr.276562.122","volume":"32","author":"H Zheng","year":"2022","unstructured":"Zheng, H. et al. Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4. Genome Res. 32, 1573\u20131584 (2022).","journal-title":"Genome Res."},{"key":"1650_CR17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ajhg.2023.11.005","volume":"111","author":"DM Fowler","year":"2024","unstructured":"Fowler, D. M. & Rehm, H. L. Will variants of uncertain significance still exist in 2030? Am. J. Hum. Genet. 111, 1 (2024).","journal-title":"Am. J. Hum. Genet."},{"key":"1650_CR18","doi-asserted-by":"publisher","first-page":"1479","DOI":"10.1016\/j.ajhg.2025.04.006","volume":"112","author":"S Allen","year":"2025","unstructured":"Allen, S. et al. Validating data from multiplex assays of variant effect: a CanVIG-UK national survey of NHS clinical scientists.  Am. J. Hum. Genet. 112, 1479\u20131488 (2025).","journal-title":"Am. J. Hum. Genet."},{"key":"1650_CR19","doi-asserted-by":"publisher","first-page":"1468","DOI":"10.1016\/j.ajhg.2025.04.009","volume":"112","author":"MS Park","year":"2025","unstructured":"Park, M. S. et al. Insights on improving accessibility and usability of functional data to unlock their potential for variant interpretation.  Am. J. Hum. Genet. 112, 1468\u20131478 (2025).","journal-title":"Am. J. Hum. Genet."},{"key":"1650_CR20","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2019.103208","volume":"95","author":"PA Harris","year":"2019","unstructured":"Harris, P. A. et al. The REDCap consortium: building an international community of software platform partners. J. Biomed. Inform. 95, 103208 (2019).","journal-title":"J. Biomed. Inform."},{"key":"1650_CR21","doi-asserted-by":"publisher","first-page":"D13","DOI":"10.1093\/nar\/gkr1184","volume":"40","author":"EW Sayers","year":"2012","unstructured":"Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40, D13\u2013D25 (2012).","journal-title":"Nucleic Acids Res."},{"key":"1650_CR22","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1038\/s41588-023-01414-x","volume":"55","author":"A Allot","year":"2023","unstructured":"Allot, A. et al. Tracking genetic variants in the biomedical literature using LitVar 2.0. Nat. Genet. 55, 901\u2013903 (2023).","journal-title":"Nat. Genet."},{"key":"1650_CR23","doi-asserted-by":"publisher","first-page":"D1038","DOI":"10.1093\/nar\/gky1151","volume":"47","author":"JS Amberger","year":"2019","unstructured":"Amberger, J. S., Bocchini, C. A., Scott, A. F. & Hamosh, A. OMIM.org: leveraging knowledge across phenotype\u2013gene relationships. Nucleic Acids Res. 47, D1038\u2013D1043 (2019).","journal-title":"Nucleic Acids Res."},{"key":"1650_CR24","doi-asserted-by":"crossref","unstructured":"Bradford, Y. M. et al. Zebrafish Information Network, the knowledgebase for Danio rerio research. Genetics. 220, iyac016 (2022).","DOI":"10.1093\/genetics\/iyac016"},{"key":"1650_CR25","doi-asserted-by":"crossref","unstructured":"\u00d6zt\u00fcrk-\u00c7olak, A. et al. FlyBase: updates to the Drosophila genes and genomes database. Genetics 227, iyad211 (2024).","DOI":"10.1093\/genetics\/iyad211"},{"key":"1650_CR26","doi-asserted-by":"crossref","unstructured":"Fisher M. et al. Xenbase: key features and resources of the Xenopus model organism knowledgebase. Genetics 224, iyad018 (2023).","DOI":"10.1093\/genetics\/iyad018"},{"key":"1650_CR27","doi-asserted-by":"publisher","first-page":"1593","DOI":"10.1002\/humu.23630","volume":"39","author":"AM Oza","year":"2018","unstructured":"Oza, A. M. et al. Expert specification of the ACMG\/AMP variant interpretation guidelines for genetic hearing loss. Hum. Mutat. 39, 1593\u20131613 (2018).","journal-title":"Hum. Mutat."},{"key":"1650_CR28","doi-asserted-by":"publisher","DOI":"10.1016\/j.preteyeres.2025.101356","volume":"106","author":"BB Thomas","year":"2025","unstructured":"Thomas, B. B. et al. Animal models for the evaluation of retinal stem cell therapies. Prog. Retin. Eye Res. 106, 101356 (2025).","journal-title":"Prog. Retin. Eye Res."},{"key":"1650_CR29","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0683-1","volume":"11","author":"DM Kanavy","year":"2019","unstructured":"Kanavy, D. M. et al. Comparative analysis of functional assay evidence use by ClinGen variant curation expert panels. Genome Med. 11, 77 (2019).","journal-title":"Genome Med."},{"key":"1650_CR30","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1093\/hmg\/ddab122","volume":"30","author":"W Lee","year":"2021","unstructured":"Lee, W. et al. Cis -acting modifiers in the ABCA4 locus contribute to the penetrance of the major disease-causing variant in Stargardt disease. Hum. Mol. Genet. 30, 1293\u20131304 (2021).","journal-title":"Hum. Mol. Genet."},{"key":"1650_CR31","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.gene.2007.01.001","volume":"393","author":"X Tang","year":"2007","unstructured":"Tang, X. et al. Very low penetrance of hearing loss in seven Han Chinese pedigrees carrying the deafness-associated 12S rRNA A1555G mutation. Gene 393, 11\u201319 (2007).","journal-title":"Gene"},{"key":"1650_CR32","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1136\/jmg-2025-110997","volume":"63","author":"W Hua","year":"2026","unstructured":"Hua, W. et al. Heterozygous TBX2 frameshift variants cause a novel syndromic hearing loss with incompletely penetrant nystagmus. J. Med. Genet. 63, 24\u201333 (2026).","journal-title":"J. Med. Genet."},{"key":"1650_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-024-02067-3","volume":"18","author":"F Jia","year":"2025","unstructured":"Jia, F., Wang, F., Li, S., Cui, Y. & Yu, Y. Transcriptome sequencing reveals regulatory genes associated with neurogenic hearing loss. BMC Med. Genom. 18, 11 (2025).","journal-title":"BMC Med. Genom."},{"key":"1650_CR34","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1038\/s12276-025-01428-x","volume":"57","author":"JA Kim","year":"2025","unstructured":"Kim, J. A. et al. Systematic genetic assessment of hearing loss using whole-genome sequencing identifies pathogenic variants. Exp. Mol. Med. 57, 775\u2013787 (2025).","journal-title":"Exp. Mol. Med."},{"key":"1650_CR35","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqae154","volume":"6","author":"H Zhang","year":"2024","unstructured":"Zhang, H., Kabir, M., Ahmed, S. & Vihinen, M. There will always be variants of uncertain significance. Analysis of VUSs. NAR Genom. Bioinform. 6, lqae154 (2024).","journal-title":"NAR Genom. Bioinform."},{"key":"1650_CR36","doi-asserted-by":"publisher","DOI":"10.1016\/j.gim.2024.101305","volume":"27","author":"A Garrett","year":"2025","unstructured":"Garrett, A. et al. Classification of variants of reduced penetrance in high-penetrance cancer susceptibility genes: framework for genetics clinicians and clinical scientists by CanVIG-UK (Cancer Variant Interpretation Group-UK). Genet. Med. 27, 101305 (2025).","journal-title":"Genet. Med."},{"key":"1650_CR37","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.1038\/s41588-018-0192-y","volume":"50","author":"SE Castel","year":"2018","unstructured":"Castel, S. E. et al. Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat. Genet. 50, 1327\u20131334 (2018).","journal-title":"Nat. Genet."},{"key":"1650_CR38","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/s41586-024-08430-9","volume":"639","author":"V Agarwal","year":"2025","unstructured":"Agarwal, V. et al. Massively parallel characterization of transcriptional regulatory elements. Nature 639, 411\u2013420 (2025).","journal-title":"Nature"},{"key":"1650_CR39","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-022-01073-3","volume":"14","author":"JM Ellingford","year":"2022","unstructured":"Ellingford, J. M. et al. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med. 14, 73 (2022).","journal-title":"Genome Med."},{"key":"1650_CR40","doi-asserted-by":"publisher","DOI":"10.1016\/j.gim.2025.101400","volume":"27","author":"G Bennett","year":"2025","unstructured":"Bennett, G. et al. Distinct rates of VUS reclassification are observed when subclassifying VUS by evidence level. Genet. Med. 27, 101400 (2025).","journal-title":"Genet. Med."},{"key":"1650_CR41","doi-asserted-by":"publisher","first-page":"2208","DOI":"10.1038\/s41436-021-01254-2","volume":"23","author":"MJ Patel","year":"2021","unstructured":"Patel, M. J. et al. Disease-specific ACMG\/AMP guidelines improve sequence variant interpretation for hearing loss. Genet. Med. 23, 2208\u20132212 (2021).","journal-title":"Genet. Med."},{"key":"1650_CR42","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1136\/jmg-2023-109750","volume":"61","author":"K Goto","year":"2024","unstructured":"Goto, K. et al. Disease-specific variant interpretation highlighted the genetic findings in 2325 Japanese patients with retinitis pigmentosa and allied diseases. J. Med. Genet. 61, 613\u2013620 (2024).","journal-title":"J. Med. Genet."}],"container-title":["Communications Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43856-026-01650-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43856-026-01650-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43856-026-01650-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T11:38:06Z","timestamp":1781609886000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43856-026-01650-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,30]]},"references-count":42,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1650"],"URL":"https:\/\/doi.org\/10.1038\/s43856-026-01650-2","relation":{},"ISSN":["2730-664X"],"issn-type":[{"value":"2730-664X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,30]]},"assertion":[{"value":"14 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A.A.T. serves on the editorial board of Communications Medicine. However, this has not influenced the editorial review or peer review process, or the decision to publish this article. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"343"}}