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Groeneweg S, van Geest FS, Martín M, Dias M, Frazer J, Medina-Gomez C, Sterenborg RBTM, Wang H, Dolcetta-Capuzzo A, de Rooij LJ, Teumer A, Abaci A, van den Akker ELT, Ambegaonkar GP, Armour CM, Bacos I, Bakhtiani P, Barca D, Bauer AJ, van den Berg SAA, van den Berge A, Bertini E, van Beynum IM, Brunetti-Pierri N, Brunner D, Cappa M, Cappuccio G, Castellotti B, Castiglioni C, Chatterjee K, Chesover A, Christian P, Coenen-van der Spek J, de Coo IFM, Coutant R, Craiu D, Crock P, DeGoede C, Demir K, Dewey C, Dica A, Dimitri P, Dremmen MHG, Dubey R, Enderli A, Fairchild J, Gallichan J, Garibaldi L, George B, Gevers EF, Greenup E, Hackenberg A, Halász Z, Heinrich B, Hurst AC, Huynh T, Isaza AR, Klosowska A, van der Knoop MM, Konrad D, Koolen DA, Krude H, Kulkarni A, Laemmle A, LaFranchi SH, Lawson-Yuen A, Lebl J, Leeuwenburgh S, Linder-Lucht M, López Martí A, Lorea CF, Lourenço CM, Lunsing RJ, Lyons G, Malikova JK, Mancilla EE, McCormick KL, McGowan A, Mericq V, Lora FM, Moran C, Muller KE, Nicol LE, Oliver-Petit I, Paone L, Paul PG, Polak M, Porta F, Poswar FO, Reinauer C, Rozenkova K, Seckold R, Seven Menevse T, Simm P, Simon A, Singh Y, Spada M, Stals MAM, Stegenga MT, Stoupa A, et alGroeneweg S, van Geest FS, Martín M, Dias M, Frazer J, Medina-Gomez C, Sterenborg RBTM, Wang H, Dolcetta-Capuzzo A, de Rooij LJ, Teumer A, Abaci A, van den Akker ELT, Ambegaonkar GP, Armour CM, Bacos I, Bakhtiani P, Barca D, Bauer AJ, van den Berg SAA, van den Berge A, Bertini E, van Beynum IM, Brunetti-Pierri N, Brunner D, Cappa M, Cappuccio G, Castellotti B, Castiglioni C, Chatterjee K, Chesover A, Christian P, Coenen-van der Spek J, de Coo IFM, Coutant R, Craiu D, Crock P, DeGoede C, Demir K, Dewey C, Dica A, Dimitri P, Dremmen MHG, Dubey R, Enderli A, Fairchild J, Gallichan J, Garibaldi L, George B, Gevers EF, Greenup E, Hackenberg A, Halász Z, Heinrich B, Hurst AC, Huynh T, Isaza AR, Klosowska A, van der Knoop MM, Konrad D, Koolen DA, Krude H, Kulkarni A, Laemmle A, LaFranchi SH, Lawson-Yuen A, Lebl J, Leeuwenburgh S, Linder-Lucht M, López Martí A, Lorea CF, Lourenço CM, Lunsing RJ, Lyons G, Malikova JK, Mancilla EE, McCormick KL, McGowan A, Mericq V, Lora FM, Moran C, Muller KE, Nicol LE, Oliver-Petit I, Paone L, Paul PG, Polak M, Porta F, Poswar FO, Reinauer C, Rozenkova K, Seckold R, Seven Menevse T, Simm P, Simon A, Singh Y, Spada M, Stals MAM, Stegenga MT, Stoupa A, Subramanian GM, Szeifert L, Tonduti D, Turan S, Vanderniet J, van der Walt A, Wémeau JL, van Wermeskerken AM, Wierzba J, de Wit MCY, Wolf NI, Wurm M, Zibordi F, Zung A, Zwaveling-Soonawala N, Rivadeneira F, Meima ME, Marks DS, Nicola JP, Chen CH, Medici M, Visser WE. Mapping variants in thyroid hormone transporter MCT8 to disease severity by genomic, phenotypic, functional, structural and deep learning integration. Nat Commun 2025; 16:2479. [PMID: 40075072 PMCID: PMC11904026 DOI: 10.1038/s41467-025-56628-w] [Show More Authors] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 01/23/2025] [Indexed: 03/14/2025] Open
Abstract
Predicting and quantifying phenotypic consequences of genetic variants in rare disorders is a major challenge, particularly pertinent for 'actionable' genes such as thyroid hormone transporter MCT8 (encoded by the X-linked SLC16A2 gene), where loss-of-function (LoF) variants cause a rare neurodevelopmental and (treatable) metabolic disorder in males. The combination of deep phenotyping data with functional and computational tests and with outcomes in population cohorts, enabled us to: (i) identify the genetic aetiology of divergent clinical phenotypes of MCT8 deficiency with genotype-phenotype relationships present across survival and 24 out of 32 disease features; (ii) demonstrate a mild phenocopy in ~400,000 individuals with common genetic variants in MCT8; (iii) assess therapeutic effectiveness, which did not differ among LoF-categories; (iv) advance structural insights in normal and mutated MCT8 by delineating seven critical functional domains; (v) create a pathogenicity-severity MCT8 variant classifier that accurately predicted pathogenicity (AUC:0.91) and severity (AUC:0.86) for 8151 variants. Our information-dense mapping provides a generalizable approach to advance multiple dimensions of rare genetic disorders.
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Affiliation(s)
- Stefan Groeneweg
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Ferdy S van Geest
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Mariano Martín
- Department of Clinical Biochemistry (CIBICI-CONICET), Faculty of Chemical Sciences, National University of Córdoba, Córdoba, Argentina
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mafalda Dias
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jonathan Frazer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rosalie B T M Sterenborg
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hao Wang
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| | - Anna Dolcetta-Capuzzo
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Linda J de Rooij
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Alexander Teumer
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Ayhan Abaci
- Division of Pediatric Endocrinology, Faculty of Medicine, Dokuz Eylul University, İzmir, Turkey
| | - Erica L T van den Akker
- Department of Paediatrics, Division of Endocrinology, Erasmus Medical Centre -Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Gautam P Ambegaonkar
- Department of Paediatric Neurology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christine M Armour
- Regional Genetics Program, Children's Hospital of Eastern Ontario and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Iiuliu Bacos
- Centrul Medical Dr. Bacos Cosma, Timisoara, Romania
| | - Priyanka Bakhtiani
- University of Louisville, Louisville, KY, USA
- Childrens Hospital Los Angeles, Los Angeles, CA, USA
| | - Diana Barca
- Carol Davila University of Medicine, Department of Clinical Neurosciences, Paediatric Neurology Discipline II, Bucharest, Romania
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sjoerd A A van den Berg
- Diagnostic Laboratory for Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Amanda van den Berge
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital IRCCS, Rome, Italy
| | - Ingrid M van Beynum
- Department of Pediatrics, Division of Pediatric Cardiology, Erasmus Medical Centre - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80131, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Doris Brunner
- Gottfried Preyer's Children Hospital, Vienna, Austria
| | - Marco Cappa
- Research Area for Innovative Therapies in Endocrinopathies, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, 80131, Naples, Italy
- Neurological Research Institute and Baylor College of Medicine, Houston, TX, USA
| | - Barbara Castellotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Claudia Castiglioni
- Department of Neurology, Clinica Meds, School of Medicine, Universidad Finis Terrae, Santiago, Chile
| | - Krishna Chatterjee
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Alexander Chesover
- Division of Endocrinology, The Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, M5G 1×8, Canada
- Department of Endocrinology, Great Ormond Street Hospital for Children, London, UK
| | - Peter Christian
- East Kent Hospitals University NHS Foundation Trust, Ashford, UK
| | - Jet Coenen-van der Spek
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Irenaeus F M de Coo
- Department of Toxicogenomics, Unit Clinical Genomics, Maastricht University, MHeNs School for Mental Health and Neuroscience, Maastricht, The Netherlands
| | - Regis Coutant
- Department of Pediatric Endocrinology and Diabetology, University Hospital, Angers, France
| | - Dana Craiu
- Carol Davila University of Medicine, Department of Clinical Neurosciences, Paediatric Neurology Discipline II, Bucharest, Romania
| | - Patricia Crock
- John Hunter Children's Hospital, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, Australia
| | - Christian DeGoede
- Department of Paediatric Neurology, Clinical Research Facility, Lancashire Teaching Hospitals NHS Trust, Lancashire, UK
| | - Korcan Demir
- Division of Pediatric Endocrinology, Faculty of Medicine, Dokuz Eylul University, İzmir, Turkey
| | - Cheyenne Dewey
- Genomics Institute Mary Bridge Children's Hospital, MultiCare Health System, Tacoma, WA, USA
| | - Alice Dica
- Carol Davila University of Medicine, Department of Clinical Neurosciences, Paediatric Neurology Discipline II, Bucharest, Romania
| | - Paul Dimitri
- The Department of Oncology and Metabolism, The University of Sheffield, Western Bank, Sheffield, S10, 2TH, UK
| | - Marjolein H G Dremmen
- Division of Paediatric Radiology, Erasmus Medical Centre - Sophia's Children Hospital, Rotterdam, The Netherlands
| | | | - Anina Enderli
- Department of Neuropediatrics, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Jan Fairchild
- Department of Diabetes and Endocrinology, Women's and Children's Hospital, North Adelaide, 5066, South Australia, Australia
| | | | | | - Belinda George
- Department of Endocrinology, St. John's Medical College Hospital, Bengaluru, India
| | - Evelien F Gevers
- Centre for Endocrinology, William Harvey Research institute, Queen Mary University of London, London, UK
| | - Erin Greenup
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Pediatric Endocrinology, Department of Pediatrics, Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Annette Hackenberg
- Department of Neuropediatrics, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Zita Halász
- Pediatric Center, Semmelweis University Budapest, Budapest, Hungary
| | - Bianka Heinrich
- Department of Neuropediatrics, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Anna C Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tony Huynh
- Department of Endocrinology & Diabetes, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Amber R Isaza
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anna Klosowska
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Daniel Konrad
- Division of Pediatric Endocrinology and Diabetology and Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Heiko Krude
- Institute of Experimental Paediatric Endocrinology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Abhishek Kulkarni
- Department of Paediatric Endocrinology, SRCC Children's Hospital, Mumbai, India
| | - Alexander Laemmle
- Institute of Clinical Chemistry and Department of Pediatrics, Inselspital, University Hospital Bern, Bern, Switzerland
| | - Stephen H LaFranchi
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Sciences University, Portland, OR, USA
| | - Amy Lawson-Yuen
- Genomics Institute Mary Bridge Children's Hospital, MultiCare Health System, Tacoma, WA, USA
- Department of Genetics, Kaiser Permanente Washington, Seattle, WA, USA
| | - Jan Lebl
- Department of Paediatrics, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Selmar Leeuwenburgh
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Michaela Linder-Lucht
- Division of Neuropediatrics and Muscular Disorders, Department of Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Anna López Martí
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Cláudia F Lorea
- Teaching Hospital of Universidade Federal de Pelotas, Pelotas, Brazil
- Federal University of Rio Grande do Sul, Porto Alegre-RS, Brazil
| | - Charles M Lourenço
- National Reference Center for Rare Diseases, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
- Personalized Medicine area -Special Education Sector at DLE/Grupo Pardini, Rio de Janeiro, Brazil
| | - Roelineke J Lunsing
- Department of Child Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Greta Lyons
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Jana Krenek Malikova
- Department of Paediatrics, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Edna E Mancilla
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kenneth L McCormick
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anne McGowan
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Veronica Mericq
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile, Department of Pediatrics, Clinica Las Condes, Santiago, Chile
| | - Felipe Monti Lora
- Pediatric Endocrinology Group, Sabara Children's Hospital, São Paulo, Brazil
| | - Carla Moran
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Lindsey E Nicol
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Sciences University, Portland, OR, USA
| | - Isabelle Oliver-Petit
- Department of Paediatric Endocrinology and Genetics, Children's Hospital, Toulouse University Hospital, Toulouse, France
| | - Laura Paone
- Endocrinology and Diabetology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Praveen G Paul
- Department of Paediatrics, Christian Medical College, Vellore, India
| | - Michel Polak
- Paediatric Endocrinology, Diabetology and Gynaecology, Department, Necker Children's University Hospital, Imagine Institute Affiliate, Université de Paris Cité, Paris, France
| | - Francesco Porta
- Department of Paediatrics, AOU Città della Salute e della Scienza di Torino, University of Torino, Turin, Italy
| | - Fabiano O Poswar
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Christina Reinauer
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty, Dusseldorf, Germany
| | - Klara Rozenkova
- Department of Paediatrics, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Rowen Seckold
- John Hunter Children's Hospital, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, Australia
| | - Tuba Seven Menevse
- Marmara University School of Medicine Department of Pediatric Endocrinology, Istanbul, Turkey
| | - Peter Simm
- Royal Children's Hospital/University of Melbourne, Parkville, Australia
| | - Anna Simon
- Department of Paediatrics, Christian Medical College, Vellore, India
| | - Yogen Singh
- Department of Paediatric Cardiology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pediatrics, University of California - UC Davis Children's Hospital, Sacramento, CA, USA
| | - Marco Spada
- Department of Paediatrics, AOU Città della Salute e della Scienza di Torino, University of Torino, Turin, Italy
| | - Milou A M Stals
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Merel T Stegenga
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Athanasia Stoupa
- Paediatric Endocrinology, Diabetology and Gynaecology, Department, Necker Children's University Hospital, Imagine Institute Affiliate, Université de Paris Cité, Paris, France
| | - Gopinath M Subramanian
- John Hunter Children's Hospital, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, Australia
| | - Lilla Szeifert
- Pediatric Center, Semmelweis University Budapest, Budapest, Hungary
| | - Davide Tonduti
- Child Neurology Unit - C.O.A.L.A. (Center for diagnosis and treatment of leukodystrophies), V. Buzzi Children's Hospital, Milano, Italy
- Department of Clinical and Biomedical Science, Università degli Studi di Milano, Milano, Italy
| | - Serap Turan
- Marmara University School of Medicine Department of Pediatric Endocrinology, Istanbul, Turkey
| | - Joel Vanderniet
- John Hunter Children's Hospital, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, Australia
| | - Adri van der Walt
- Private paediatric Neurology practice Dr A van der Walt, Durbanville, South Africa
| | | | | | - Jolanta Wierzba
- Department of Internal and Pediatric Nursing, Institute of Nursing and Midwifery, Medical University of Gdańsk, Gdańsk, Poland
| | - Marie-Claire Y de Wit
- Department of Paediatric Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Amsterdam, The Netherlands
| | - Michael Wurm
- University Children's Hospital Regensburg (KUNO), University of Regensburg, Campus St. Hedwig, Regensburg, Germany
| | - Federica Zibordi
- Child Neurology Unit, Fondazione IRCCS, Istituto Neurologico Carlo Besta, Milan, Italy
| | - Amnon Zung
- Pediatric Endocrinology Unit, Kaplan Medical center, Rehovot and the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nitash Zwaveling-Soonawala
- Emma Children's Hospital, Department of Paediatric Endocrinology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel E Meima
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Juan P Nicola
- Department of Clinical Biochemistry (CIBICI-CONICET), Faculty of Chemical Sciences, National University of Córdoba, Córdoba, Argentina
| | - Chi-Hua Chen
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| | - Marco Medici
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - W Edward Visser
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands.
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