{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T13:02:43Z","timestamp":1772024563507,"version":"3.50.1"},"reference-count":23,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,9,17]],"date-time":"2024-09-17T00:00:00Z","timestamp":1726531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministero della Salute","award":["PNC-E3-2022-23683266"],"award-info":[{"award-number":["PNC-E3-2022-23683266"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Objectives: This study aims to demonstrate the role of case-level American College of Medical Genetics (ACMG) criteria, such as familial segregation and pathology data, in providing conclusive evidence for the pathogenicity of ultrarare GLA variants causing Anderson\u2013Fabry disease when gene-level and variant-level criteria provide ambiguous or discrepant results. Case\/family description: A 52-year-old woman presented with new-onset shortness of breath, chest pain, and palpitations. Echocardiography revealed mild left ventricular wall thickening (14 mm) and mild diastolic dysfunction. She was the second of three siblings born to unrelated parents, both of whom died from malignancies. Family screening identified brothers, one affected 55-year-old with hypertension and asthma and one unaffected 47-year-old. The 15-year-old son of the proband complained of exercise-induced burning feet acral pain his electrocardiogram showed a short PR interval and signs of early hypertrophy. Results: Endomyocardial biopsies of the proband and the affected sibling demonstrated substrate accumulation (globotriaosylceramide). The anti-\u03b1-galactosidase-A immunostain showed a total loss of the enzyme in the hemizygous male and a mosaic pattern in the heterozygous female. The next-generation sequencing short-read multigene panel identified the c.547+3A&gt;G variant in the GLA gene and excluded variants in other genes; Oxford-Nanopore long-read sequencing excluded known pathogenic deep intronic variants. A Multiplex-Ligation-dependent-Probe-Amplification assay excluded copy number variations. Based on the variant-level and gene-level ACMG criteria, the variant was classified as a Variant of Uncertain Significance or Likely Benign using different bioinformatic tools. By adding case-level functional data (endomyocardial biopsy, PS3_VeryStrong) and familial data (segregation of genotype with phenotype, PP2_Moderate), the variant was classified as Likely Pathogenic\/Pathogenic. Conclusion: ACMG case-level data can unambiguously resolve uncertain interpretations of GLA variants.<\/jats:p>","DOI":"10.3390\/genes15091212","type":"journal-article","created":{"date-parts":[[2024,9,18]],"date-time":"2024-09-18T00:51:43Z","timestamp":1726620703000},"page":"1212","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Unambiguous Interpretation of the Pathogenicity of the GLA c.547+3A&gt;G Variant Causing Fabry Disease"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3289-9228","authenticated-orcid":false,"given":"Mario","family":"Urtis","sequence":"first","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia","family":"Cavaliere","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viviana","family":"Vilardo","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chiara","family":"Paganini","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandra","family":"Smirnova","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmelina","family":"Giorgianni","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7625-1103","authenticated-orcid":false,"given":"Alessandro","family":"Di Toro","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luisa","family":"Chiapparini","sequence":"additional","affiliation":[{"name":"Neuroradiology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5908-5219","authenticated-orcid":false,"given":"Carlo","family":"Pellegrini","sequence":"additional","affiliation":[{"name":"Clinical-Surgical, Diagnostic and Pediatric Sciences Department, University of Pavia, 27100 Pavia, Italy"},{"name":"Division of Cardiac Surgery, Cardiotoracovascular Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2611-4295","authenticated-orcid":false,"given":"Maurizia","family":"Grasso","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eloisa","family":"Arbustini","sequence":"additional","affiliation":[{"name":"Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1750-1172-5-30","article-title":"Fabry disease","volume":"5","author":"Germain","year":"2010","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/j.ymgme.2018.02.014","article-title":"Fabry disease revisited: Management and treatment recommendations for adult patients","volume":"123","author":"Ortiz","year":"2018","journal-title":"Mol. Genet. Metab."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Izhar, R., Borriello, M., La Russa, A., Di Paola, R., De, A., Capasso, G., Ingrosso, D., Perna, A.F., and Simeoni, M. (2023). Fabry Disease in Women: Genetic Basis, Available Biomarkers, and Clinical Manifestations. Genes, 15.","DOI":"10.3390\/genes15010037"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1016\/j.jacc.2020.12.024","article-title":"Cardiac Involvement in Fabry Disease: JACC Review Topic of the Week","volume":"77","author":"Pieroni","year":"2021","journal-title":"J. Am. Coll. Cardiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1136\/jmedgenet-2017-105080","article-title":"Fabry Disease: Prevalence of affected males and heterozygotes with pathogenic","volume":"55","author":"Doheny","year":"2018","journal-title":"J. Med. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1016\/j.jacc.2016.05.090","article-title":"Genetic Screening of Anderson-Fabry Disease in Probands Referred from Multispecialty Clinics","volume":"68","author":"Favalli","year":"2016","journal-title":"J. Am. Coll. Cardiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1016\/j.jacc.2007.06.062","article-title":"Prevalence of fabry disease in a cohort of 508 unrelated patients with hypertrophic cardiomyopathy","volume":"50","author":"Monserrat","year":"2007","journal-title":"J. Am. Coll. Cardiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1016\/j.jstrokecerebrovasdis.2013.08.010","article-title":"Prevalence of Fabry disease in stroke patients\u2014A systematic review and meta-analysis","volume":"23","author":"Shi","year":"2014","journal-title":"J. Stroke Cerebrovasc. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1007\/s40620-019-00663-6","article-title":"Identifying Fabry patients in dialysis population: Prevalence of GLA mutations by renal clinic screening, 1995\u20132019","volume":"33","author":"Capuano","year":"2020","journal-title":"J. Nephrol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1111\/1346-8138.16237","article-title":"Beneficial screening of Fabry disease in patients with hypohidrosis","volume":"49","author":"Fukunaga","year":"2022","journal-title":"J. Dermatol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.rce.2022.10.002","article-title":"Results of the screening program for Fabry disease in patients with cornea verticillata at the University Hospital of Navarre","volume":"223","author":"Fanlo","year":"2023","journal-title":"Rev. Clin. Esp."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e000943","DOI":"10.1136\/bmjophth-2021-000943","article-title":"Drug-induced corneal deposits: An up-to-date review","volume":"7","author":"Sahyoun","year":"2022","journal-title":"BMJ Open Ophthalmol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/j.dld.2018.02.011","article-title":"Non-specific gastrointestinal features: Could it be Fabry disease?","volume":"50","author":"Hilz","year":"2018","journal-title":"Dig. Liver Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1186\/s13023-020-01436-2","article-title":"Pathologic substrate of gastropathy in Anderson-Fabry disease","volume":"15","author":"Narula","year":"2020","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_15","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_16","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.1093\/eurheartj\/ehab895","article-title":"Interpretation and actionability of genetic variants in cardiomyopathies: A position statement from the European Society of Cardiology Council on cardiovascular genomics","volume":"43","author":"Arbustini","year":"2022","journal-title":"Eur. Heart J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1734","DOI":"10.1002\/humu.24088","article-title":"Fitting a naturally scaled point system to the ACMG\/AMP variant classification guidelines","volume":"41","author":"Tavtigian","year":"2020","journal-title":"Hum. Mutat."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1089\/1066527041410418","article-title":"Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals","volume":"11","author":"Yeo","year":"2004","journal-title":"J. Comput. Biol."},{"key":"ref_19","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","year":"2019","journal-title":"Cell"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1007\/s10157-023-02361-x","article-title":"All reported non-canonical splice site variants in GLA cause aberrant splicing","volume":"27","author":"Okada","year":"2023","journal-title":"Clin. Exp. Nephrol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"35","DOI":"10.2147\/TACG.S146022","article-title":"Multiple phenotypic domains of Fabry disease and their relevance for establishing genotype-phenotype correlations","volume":"12","author":"Oliveira","year":"2019","journal-title":"Appl. Clin. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13023-024-03028-w","article-title":"A review and recommendations for oral chaperone therapy in adult patients with Fabry disease","volume":"19","author":"Nowicki","year":"2024","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_23","unstructured":"(2024, August 14). Available online: http:\/\/fabry-database.org\/mutants\/."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/15\/9\/1212\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:57:40Z","timestamp":1760111860000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/15\/9\/1212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,17]]},"references-count":23,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2024,9]]}},"alternative-id":["genes15091212"],"URL":"https:\/\/doi.org\/10.3390\/genes15091212","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,17]]}}}