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We aimed to identify the molecular etiology in undiagnosed cases from the DECIPHERD study (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009167) through trio ES reanalysis guided by a computer\u2010aided facial analysis. We selected 47 patients who remained undiagnosed after initial testing and whose facial photographs were available. Genes were prioritized based on facial analysis using Face2Gene. Subsequently, we scrutinized these prioritized genes for non\u2010coding variants detectable by ES. This strategy increased the diagnostic yield by 0.6% (1\/167). We confirmed the diagnosis of Kabuki syndrome in one patient harboring a likely pathogenic variant in\n                    <jats:italic>KMT2D<\/jats:italic>\n                    . Additionally, we identified compound heterozygous variants of uncertain significance in\n                    <jats:italic>CEP290<\/jats:italic>\n                    in a second patient, suggestive of Meckel syndrome. As these variants remain functionally unconfirmed, this second case is reported as a candidate molecular diagnosis rather than an established one. This approach may represent a low\u2010cost first step to unveil additional diagnoses without recourse to more expensive genomic testing.\n                  <\/jats:p>","DOI":"10.1002\/ajmg.a.70320","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:03:01Z","timestamp":1790841781000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Computer\u2010Aided Facial Analysis and Non\u2010Coding Variants Detectable by Exome Sequencing Increase Its Diagnostic Yield: Results From the\n                    <scp>DECIPHERD<\/scp>\n                    Study"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-6040-6382","authenticated-orcid":false,"given":"Daniela","family":"B\u00f6hme","sequence":"first","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6746-0103","authenticated-orcid":false,"given":"V\u00edctor","family":"Faundes","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00e9tica y Enfermedades Metab\u00f3licas, Instituto de Nutrici\u00f3n y Tecnolog\u00eda de los Alimentos Universidad de Chile  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6817-0573","authenticated-orcid":false,"given":"Mar\u00eda Cecilia","family":"Poli","sequence":"additional","affiliation":[{"name":"Immunogenetics and Translational Immunology Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"},{"name":"Hospital Dr. Roberto del R\u00edo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8059-3202","authenticated-orcid":false,"given":"Boris","family":"Rebolledo\u2010Jaramillo","sequence":"additional","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1541-4815","authenticated-orcid":false,"given":"Catalina","family":"Lagos","sequence":"additional","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1317-3666","authenticated-orcid":false,"given":"Joan","family":"Orellana","sequence":"additional","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4153-0844","authenticated-orcid":false,"given":"Gabriela","family":"Moreno","sequence":"additional","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-9070-267X","authenticated-orcid":false,"given":"Luz Mar\u00eda","family":"Mart\u00edn","sequence":"additional","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"},{"name":"Unidad de Gesti\u00f3n Cl\u00ednica del Ni\u00f1o Hospital Padre Hurtado  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7367-5485","authenticated-orcid":false,"given":"Gonzalo","family":"Encina","sequence":"additional","affiliation":[{"name":"Biosoluciones UDD  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8569-1941","authenticated-orcid":false,"given":"Mar\u00eda Jes\u00fas","family":"Zavala","sequence":"additional","affiliation":[{"name":"Hospital Base de Valdivia  Valdivia Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4357-0295","authenticated-orcid":false,"given":"Trinidad","family":"Hasb\u00fan","sequence":"additional","affiliation":[{"name":"Departamento de Dermatolog\u00eda, Facultad de Medicina Universidad del Desarrollo, Cl\u00ednica Alemana de Santiago  Santiago Chile"},{"name":"Department of Dermatology University of Iowa Hospitals and Clinics  Iowa City Iowa USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5911-6225","authenticated-orcid":false,"given":"Camila","family":"Astudillo","sequence":"additional","affiliation":[{"name":"Hospital Dr. Roberto del R\u00edo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3404-998X","authenticated-orcid":false,"given":"Carolina","family":"Cares","sequence":"additional","affiliation":[{"name":"Unidad de Gen\u00e9tica, Hospital Dr Luis Calvo Mackenna  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0193-2704","authenticated-orcid":false,"given":"Mariana","family":"Aracena","sequence":"additional","affiliation":[{"name":"Unidad de Gen\u00e9tica, Hospital Dr Luis Calvo Mackenna  Santiago Chile"},{"name":"Secci\u00f3n de Gen\u00e9tica y Errores Cong\u00e9nitos del Metabolismo, Divisi\u00f3n de Pediatr\u00eda, Facultad de Medicina Pontificia Universidad Cat\u00f3lica de Chile  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-3524-0925","authenticated-orcid":false,"given":"Catalina","family":"Sams\u00f3","sequence":"additional","affiliation":[{"name":"Hospital Dr. V\u00edctor R\u00edos Ruiz  Los Angeles Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6211-0270","authenticated-orcid":false,"given":"Fernanda","family":"Espinosa","sequence":"additional","affiliation":[{"name":"Centro Avanzado de Neurociencias Aplicado a la Neurorrehabilitaci\u00f3n e Investigaci\u00f3n  Talca Chile"},{"name":"Facultad de Psicolog\u00eda Universidad de la Laguna  San Crist\u00f3bal de la Laguna Espa\u00f1a"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8868-7430","authenticated-orcid":false,"given":"Marcela","family":"D\u00edaz","sequence":"additional","affiliation":[{"name":"Departamento de Pediatr\u00eda y Cirug\u00eda Infantil Campus Centro, Facultad de Medicina Universidad de Chile  Santiago Chile"},{"name":"Servicio de Neonatolog\u00eda Cl\u00ednica Alemana de Santiago  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-2228-3420","authenticated-orcid":false,"given":"Evelyn","family":"Silva","sequence":"additional","affiliation":[{"name":"Hospital Regional de Talca Dr. C\u00e9sar Garavagno Burotto  Talca Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0120-5684","authenticated-orcid":false,"given":"Gabriela M.","family":"Repetto","sequence":"additional","affiliation":[{"name":"Rare Diseases Program, Center for Genetics and Genomics, Institute for Science and Innovation in Medicine, Facultad de Medicina Cl\u00ednica Alemana Universidad del Desarrollo  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"issue":"6","key":"e_1_2_11_2_1","doi-asserted-by":"crossref","first-page":"101402","DOI":"10.1016\/j.gim.2025.101402","article-title":"Calibration of 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A.","year":"2024","journal-title":"Genes"},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","first-page":"eaau9113","DOI":"10.1126\/scitranslmed.aau9113","article-title":"AMELIE Speeds Mendelian Diagnosis by Matching Patient Phenotype and Genotype to Primary Literature","volume":"12","author":"Birgmeier J.","year":"2020","journal-title":"Science Translational Medicine"},{"issue":"10","key":"e_1_2_11_6_1","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1002\/humu.21337","article-title":"CEP290, a Gene With Many Faces: Mutation Overview and Presentation of CEP290base","volume":"31","author":"Coppieters F.","year":"2010","journal-title":"Human Mutation"},{"issue":"7","key":"e_1_2_11_7_1","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1093\/brain\/awaa152","article-title":"Synonymous Variants in Holoprosencephaly Alter Codon Usage and Impact the Sonic Hedgehog Protein","volume":"143","author":"Tayrac M.","year":"2020","journal-title":"Brain"},{"issue":"1","key":"e_1_2_11_8_1","doi-asserted-by":"crossref","first-page":"6869","DOI":"10.1038\/s41598-023-33374-x","article-title":"Population\u2010Specific Facial Traits and Diagnosis Accuracy of Genetic and Rare Diseases in an Admixed Colombian Population","volume":"13","author":"Echeverry\u2010Quiceno L. M.","year":"2023","journal-title":"Scientific Reports"},{"issue":"2","key":"e_1_2_11_9_1","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1038\/s10038-018-0536-6","article-title":"A Comparative Analysis of KMT2D Missense Variants in Kabuki Syndrome, Cancers and the General Population","volume":"64","author":"Faundes V.","year":"2019","journal-title":"Journal of Human Genetics"},{"issue":"6","key":"e_1_2_11_10_1","first-page":"682","article-title":"DECIPHER: Supporting the Interpretation and Sharing of Rare Disease Phenotype\u2010Linked Variant Data to Advance Diagnosis and Research","volume":"43","author":"Foreman J.","year":"2022","journal-title":"Human Mutation"},{"issue":"1","key":"e_1_2_11_11_1","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41591-018-0279-0","article-title":"Identifying Facial Phenotypes of Genetic Disorders Using Deep Learning","volume":"25","author":"Gurovich Y.","year":"2019","journal-title":"Nature Medicine"},{"issue":"1","key":"e_1_2_11_12_1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41525-024-00455-3","article-title":"Exome Sequencing of 18,994 Ethnically Diverse Patients With Suspected Rare Mendelian Disorders","volume":"10","author":"Han H.","year":"2025","journal-title":"NPJ Genomic Medicine"},{"issue":"3","key":"e_1_2_11_13_1","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/s41588-021-01010-x","article-title":"GestaltMatcher Facilitates Rare Disease Matching Using Facial Phenotype Descriptors","volume":"54","author":"Hsieh T.\u2010C.","year":"2022","journal-title":"Nature Genetics"},{"issue":"12","key":"e_1_2_11_14_1","doi-asserted-by":"crossref","first-page":"2807","DOI":"10.1038\/s41436-019-0566-2","article-title":"PEDIA: Prioritization of Exome Data by Image Analysis","volume":"21","author":"Hsieh T.\u2010C.","year":"2019","journal-title":"Genetics in Medicine"},{"key":"e_1_2_11_15_1","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1002\/humu.24380","article-title":"Phenotype\u2010Driven Approaches to Enhance Variant Prioritization and Diagnosis of Rare Disease","volume":"43","author":"Jacobsen J. O. B.","year":"2022","journal-title":"Human Mutation"},{"issue":"3","key":"e_1_2_11_16_1","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","article-title":"Predicting Splicing From Primary Sequence With Deep Learning","volume":"176","author":"Jaganathan K.","year":"2019","journal-title":"Cell"},{"key":"e_1_2_11_17_1","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1038\/s41525-020-00140-1","article-title":"Partially Automated Whole\u2010Genome Sequencing Reanalysis of Previously Undiagnosed Pediatric Patients Can Efficiently Yield New Diagnoses","volume":"5","author":"James K. N.","year":"2020","journal-title":"NPJ Genomic Medicine"},{"issue":"22","key":"e_1_2_11_18_1","doi-asserted-by":"crossref","first-page":"13534","DOI":"10.1093\/nar\/gku1206","article-title":"In Silico Prediction of Splice\u2010Altering Single Nucleotide Variants in the Human Genome","volume":"42","author":"Jian X.","year":"2014","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"e_1_2_11_19_1","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1515\/medgen-2023-2014","article-title":"The Future Role of Facial Image Analysis in ACMG Classification Guidelines","volume":"35","author":"Lesmann H.","year":"2023","journal-title":"Medizinische Genetik"},{"issue":"11","key":"e_1_2_11_20_1","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1038\/s41436-021-01242-6","article-title":"Exome and Genome Sequencing for Pediatric Patients With Congenital Anomalies or Intellectual Disability: An Evidence\u2010Based Clinical Guideline of the American College of Medical Genetics and Genomics (ACMG)","volume":"23","author":"Manickam K.","year":"2021","journal-title":"Genetics in Medicine"},{"issue":"1","key":"e_1_2_11_21_1","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13073-025-01464-2","article-title":"Systematic Identification of Disease\u2010Causing Promoter and Untranslated Region Variants in 8040 Undiagnosed Individuals With Rare Disease","volume":"17","author":"Martin\u2010Geary A. 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V.","year":"2024","journal-title":"Journal of Medical Internet Research"},{"issue":"4","key":"e_1_2_11_26_1","doi-asserted-by":"crossref","first-page":"101666","DOI":"10.1016\/j.gim.2025.101666","article-title":"RNA Sequencing Offers New Diagnostic Opportunities in Neurodevelopmental Disorders: A Systematic Review","volume":"28","author":"Rosenblum J.","year":"2026","journal-title":"Genetics in Medicine"},{"issue":"1","key":"e_1_2_11_27_1","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-025-03476-y","article-title":"MaveDB 2024: A Curated Community Database With Over Seven Million Variant Effects From Multiplexed Functional Assays","volume":"26","author":"Rubin A. F.","year":"2025","journal-title":"Genome Biology"},{"key":"e_1_2_11_28_1","unstructured":"The Association for Clinical Genomic Science.2024.ACGS Best Practice Guidelines for Variant Classification in Rare Disease. v1.2 ed."},{"key":"e_1_2_11_29_1","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/s41525-024-00456-2","article-title":"Efficient Reinterpretation of Rare Disease Cases Using Exomiser","volume":"9","author":"Vestito L.","year":"2024","journal-title":"NPJ Genomic Medicine"},{"issue":"7","key":"e_1_2_11_30_1","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1016\/j.ajhg.2023.06.002","article-title":"Using the ACMG\/AMP Framework to Capture Evidence Related to Predicted and Observed Impact on Splicing: Recommendations From the ClinGen SVI Splicing Subgroup","volume":"110","author":"Walker L. C.","year":"2023","journal-title":"American Journal of Human Genetics"},{"issue":"1","key":"e_1_2_11_31_1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/s41525-024-00396-x","article-title":"Evidence Review and Considerations for Use of First Line Genome Sequencing to Diagnose Rare Genetic Disorders. Npj","volume":"9","author":"Wigby K. M.","year":"2024","journal-title":"Genomic Medicine"},{"issue":"8","key":"e_1_2_11_32_1","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1016\/j.ajhg.2023.06.009","article-title":"Beyond the Exome: What's Next in Diagnostic Testing for Mendelian Conditions","volume":"110","author":"Wojcik M. H.","year":"2023","journal-title":"American Journal of Human Genetics"},{"issue":"12","key":"e_1_2_11_33_1","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1038\/s10038-019-0673-6","article-title":"Using Facial Analysis Technology in a Typical Genetic Clinic: Experience From 30 Individuals From a Single Institution","volume":"64","author":"Zarate Y. A.","year":"2019","journal-title":"Journal of Human Genetics"}],"container-title":["American Journal of Medical Genetics Part A"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ajmg.a.70320","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/ajmg.a.70320","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ajmg.a.70320","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:03:08Z","timestamp":1790841788000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/ajmg.a.70320"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":32,"alternative-id":["10.1002\/ajmg.a.70320"],"URL":"https:\/\/doi.org\/10.1002\/ajmg.a.70320","archive":["Portico"],"relation":{},"ISSN":["1552-4825","1552-4833"],"issn-type":[{"value":"1552-4825","type":"print"},{"value":"1552-4833","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,1]]},"assertion":[{"value":"2026-02-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-01","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"ajmg.a.70320"}}