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.

Academic Center for Thyroid Diseases Department of Internal Medicine Erasmus Medical Centre Rotterdam The Netherlands

Amsterdam Neuroscience Cellular and Molecular Mechanisms Amsterdam The Netherlands

Carol Davila University of Medicine Department of Clinical Neurosciences Paediatric Neurology Discipline 2 Bucharest Romania

Center for Multimodal Imaging and Genetics University of California San Diego La Jolla CA USA

Centre for Endocrinology William Harvey Research institute Queen Mary University of London London UK

Centre for Genomic Regulation Barcelona Spain

Centrul Medical Dr Bacos Cosma Timisoara Romania

Child Neurology Unit C O A L A 5 Buzzi Children's Hospital Milano Italy

Child Neurology Unit Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy

Childrens Hospital Los Angeles Los Angeles CA USA

Department of Child Neurology Amsterdam Leukodystrophy Center Emma Children's Hospital Amsterdam University Medical Centers Vrije Universiteit Amsterdam Amsterdam The Netherlands

Department of Child Neurology University Medical Center Groningen University of Groningen Groningen The Netherlands

Department of Clinical and Biomedical Science Università degli Studi di Milano Milano Italy

Department of Clinical Biochemistry Faculty of Chemical Sciences National University of Córdoba Córdoba Argentina

Department of Diabetes and Endocrinology Women's and Children's Hospital North Adelaide 5066 South Australia Australia

Department of Endocrinology and Diabetes Queensland Children's Hospital South Brisbane Queensland Australia

Department of Endocrinology Great Ormond Street Hospital for Children London UK

Department of Endocrinology St John's Medical College Hospital Bengaluru India

Department of General Pediatrics Neonatology and Pediatric Cardiology University Children's Hospital Medical Faculty Dusseldorf Germany

Department of Genetics Kaiser Permanente Washington Seattle WA USA

Department of Genetics University of Alabama at Birmingham Birmingham AL USA

Department of Human Genetics Donders Institute for Brain Cognition and Behaviour Radboud University Medical Center Nijmegen The Netherlands

Department of Internal and Pediatric Nursing Institute of Nursing and Midwifery Medical University of Gdańsk Gdańsk Poland

Department of Internal Medicine Division of Endocrinology Radboud University Medical Center Nijmegen The Netherlands

Department of Internal Medicine Erasmus University Medical Center Rotterdam The Netherlands

Department of Neurology Clinica Meds School of Medicine Universidad Finis Terrae Santiago Chile

Department of Neuropediatrics University Children's Hospital University of Zurich Zurich Switzerland

Department of Paediatric Cardiology Addenbrooke's Hospital Cambridge University Hospitals NHS Foundation Trust Cambridge UK

Department of Paediatric Endocrinology and Genetics Children's Hospital Toulouse University Hospital Toulouse France

Department of Paediatric Endocrinology SRCC Children's Hospital Mumbai India

Department of Paediatric Neurology Addenbrooke's Hospital Cambridge University Hospitals NHS Foundation Trust Cambridge UK

Department of Paediatric Neurology Clinical Research Facility Lancashire Teaching Hospitals NHS Trust Lancashire UK

Department of Paediatric Neurology Erasmus Medical Centre Rotterdam The Netherlands

Department of Paediatrics 2nd Faculty of Medicine Charles University University Hospital Motol Prague Czech Republic

Department of Paediatrics AOU Città della Salute e della Scienza di Torino University of Torino Turin Italy

Department of Paediatrics Christian Medical College Vellore India

Department of Paediatrics Division of Endocrinology Erasmus Medical Centre Sophia Children's Hospital Rotterdam The Netherlands

Department of Paediatrics Flevoziekenhuis Almere The Netherlands

Department of Pediatric Endocrinology and Diabetology University Hospital Angers France

Department of Pediatrics Division of Pediatric Cardiology Erasmus Medical Centre Sophia Children's Hospital Rotterdam The Netherlands

Department of Pediatrics Division of Pediatric Endocrinology University of Alabama at Birmingham Birmingham AL USA

Department of Pediatrics Doernbecher Children's Hospital Oregon Health and Sciences University Portland OR USA

Department of Pediatrics Hematology and Oncology Medical University of Gdańsk Gdańsk Poland

Department of Pediatrics University of California UC Davis Children's Hospital Sacramento CA USA

Department of Psychiatry and Psychotherapy University Medicine Greifswald Greifswald Germany

Department of Systems Biology Harvard Medical School Boston MA USA

Department of Toxicogenomics Unit Clinical Genomics Maastricht University MHeNs School for Mental Health and Neuroscience Maastricht The Netherlands

Department of Translational Medicine Federico 2 University 80131 Naples Italy

Diagnostic Laboratory for Endocrinology Department of Internal Medicine Erasmus Medical Center Rotterdam The Netherlands

Division of Endocrinology and Diabetes Children's Hospital of Philadelphia Philadelphia PA USA

Division of Endocrinology The Hospital for Sick Children and Department of Paediatrics University of Toronto Toronto M5G 1×8 Canada

Division of Neuropediatrics and Muscular Disorders Department of Pediatrics and Adolescent Medicine University Hospital Freiburg Freiburg Germany

Division of Paediatric Radiology Erasmus Medical Centre Sophia's Children Hospital Rotterdam The Netherlands

Division of Pediatric Endocrinology and Diabetology and Children's Research Center University Children's Hospital University of Zurich Zurich Switzerland

Division of Pediatric Endocrinology Department of Pediatrics Orlando Health Arnold Palmer Hospital for Children Orlando FL USA

Division of Pediatric Endocrinology Faculty of Medicine Dokuz Eylul University İzmir Turkey

DZHK Partner Site Greifswald Greifswald Germany

East Kent Hospitals University NHS Foundation Trust Ashford UK

Emma Children's Hospital Department of Paediatric Endocrinology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands

Endocrinology and Diabetology Unit Bambino Gesù Children's Hospital IRCCS Rome Italy

Federal University of Rio Grande do Sul Porto Alegre RS Brazil

Genomics Institute Mary Bridge Children's Hospital MultiCare Health System Tacoma WA USA

Gottfried Preyer's Children Hospital Vienna Austria

Heim Pal National Pediatric Institute Budapest Hungary

Institute for Bioengineering of Catalonia The Barcelona Institute of Science and Technology Barcelona Spain

Institute of Clinical Chemistry and Department of Pediatrics Inselspital University Hospital Bern Bern Switzerland

Institute of Experimental Paediatric Endocrinology Charité Universitätsmedizin Berlin Berlin Germany

Institute of Maternal and Child Research University of Chile Santiago Chile Department of Pediatrics Clinica Las Condes Santiago Chile

John Hunter Children's Hospital Hunter Medical Research Institute University of Newcastle New Lambton Heights Australia

Marmara University School of Medicine Department of Pediatric Endocrinology Istanbul Turkey

Medanta Superspeciality Hospital Indore India

Medical Genetics Service Hospital de Clínicas de Porto Alegre Porto Alegre Brazil

National Reference Center for Rare Diseases Faculdade de Medicina de São José do Rio Preto São José do Rio Preto Brazil

Neurological Research Institute and Baylor College of Medicine Houston TX USA

Paediatric Endocrinology Diabetology and Gynaecology Department Necker Children's University Hospital Imagine Institute Affiliate Université de Paris Cité Paris France

Pediatric Center Semmelweis University Budapest Budapest Hungary

Pediatric Endocrinology Group Sabara Children's Hospital São Paulo Brazil

Pediatric Endocrinology Unit Kaplan Medical center Rehovot and the Hebrew University of Jerusalem Jerusalem Israel

Personalized Medicine area Special Education Sector at DLE Grupo Pardini Rio de Janeiro Brazil

Plymouth Hospitals NHS Trust Plymouth UK

Private paediatric Neurology practice Dr A van der Walt Durbanville South Africa

Regional Genetics Program Children's Hospital of Eastern Ontario and Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON Canada

Research Area for Innovative Therapies in Endocrinopathies Bambino Gesù Children's Hospital IRCCS Rome Italy

Royal Children's Hospital University of Melbourne Parkville Australia

Scuola Superiore Meridionale Genomics and Experimental Medicine Program University of Naples Federico 2 Naples Italy

Teaching Hospital of Universidade Federal de Pelotas Pelotas Brazil

Telethon Institute of Genetics and Medicine Pozzuoli Naples Italy

The Department of Oncology and Metabolism The University of Sheffield Western Bank Sheffield S10 2TH UK

Unit of Medical Genetics and Neurogenetics Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy

Unit of Neuromuscular and Neurodegenerative Disorders Bambino Gesu' Children's Research Hospital IRCCS Rome Italy

University Children's Hospital Regensburg University of Regensburg Campus St Hedwig Regensburg Germany

University of Lille Lille France

University of Louisville Louisville KY USA

UPMC Children's Hospital of Pittsburgh Pittsburgh PA USA

Wellcome Trust Medical Research Council Institute of Metabolic Science University of Cambridge Cambridge UK

Zobrazit více v PubMed

Rehm, H. L. et al. ClinGen-the Clinical Genome Resource. N. Engl. J. Med372, 2235–2242 (2015). PubMed PMC

Fagerberg, L., Jonasson, K., von Heijne, G., Uhlen, M. & Berglund, L. Prediction of the human membrane proteome. Proteomics10, 1141–1149 (2010). PubMed

Almeida, J. G., Preto, A. J., Koukos, P. I., Bonvin, A. & Moreira, I. S. Membrane proteins structures: A review on computational modeling tools. Biochim Biophys. Acta Biomembr.1859, 2021–2039 (2017). PubMed

Errasti-Murugarren, E., Bartoccioni, P. & Palacin, M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. Membr. (Basel)11, 155 (2021). PubMed PMC

Pires, D. E. V., Rodrigues, C. H. M. & Ascher, D. B. mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Res48, W147–W153 (2020). PubMed PMC

Heuer, H. et al. The monocarboxylate transporter 8 linked to human psychomotor retardation is highly expressed in thyroid hormone-sensitive neuron populations. Endocrinology146, 1701–1706 (2005). PubMed

Ceballos, A. et al. Importance of monocarboxylate transporter 8 for the blood-brain barrier-dependent availability of 3,5,3’-triiodo-L-thyronine. Endocrinology150, 2491–2496 (2009). PubMed PMC

Vatine, G. D. et al. Modeling Psychomotor Retardation using iPSCs from MCT8-Deficient Patients Indicates a Prominent Role for the Blood-Brain Barrier. Cell Stem Cell20, 831–843.e835 (2017). PubMed PMC

Friesema, E. C., Ganguly, S., Abdalla, A., Manning Fox, J. E., Halestrap, A. P. & Visser, T. J. Identification of monocarboxylate transporter 8 as a specific thyroid hormone transporter. J. Biol. Chem.278, 40128–40135 (2003). PubMed

Friesema, E. C., Kuiper, G. G., Jansen, J., Visser, T. J. & Kester, M. H. Thyroid hormone transport by the human monocarboxylate transporter 8 and its rate-limiting role in intracellular metabolism. Mol. Endocrinol.20, 2761–2772 (2006). PubMed

Friesema, E. C. et al. Association between mutations in a thyroid hormone transporter and severe X-linked psychomotor retardation. Lancet364, 1435–1437 (2004). PubMed

Dumitrescu, A. M., Liao, X. H., Best, T. B., Brockmann, K. & Refetoff, S. A novel syndrome combining thyroid and neurological abnormalities is associated with mutations in a monocarboxylate transporter gene. Am. J. Hum. Genet74, 168–175 (2004). PubMed PMC

Visser, W. E., Vrijmoeth, P., Visser, F. E., Arts, W. F., van Toor, H. & Visser, T. J. Identification, functional analysis, prevalence and treatment of monocarboxylate transporter 8 (MCT8) mutations in a cohort of adult patients with mental retardation. Clin. Endocrinol. (Oxf.)78, 310–315 (2013). PubMed

Groeneweg, S. et al. Disease characteristics of MCT8 deficiency: an international, retrospective, multicentre cohort study. Lancet Diab Endocrinol.8, 594–605 (2020). PubMed PMC

Groeneweg, S. et al. Effectiveness and safety of the tri-iodothyronine analogue Triac in children and adults with MCT8 deficiency: an international, single-arm, open-label, phase 2 trial. Lancet Diab Endocrinol.7, 695–706 (2019). PubMed PMC

Groeneweg, S., van den Berge, A., Meima, M. E., Peeters, R. P., Visser, T. J. & Visser, W. E. Effects of Chemical Chaperones on Thyroid Hormone Transport by MCT8 Mutants in Patient-Derived Fibroblasts. Endocrinology159, 1290–1302 (2018). PubMed

van Geest, F. S. et al. Long-Term Efficacy of T3 Analogue Triac in Children and Adults With MCT8 Deficiency: A Real-Life Retrospective Cohort Study. J. Clin. Endocrinol. Metab.107, e1136–e1147 (2022). PubMed PMC

Zhang, X. C., Zhao, Y., Heng, J. & Jiang, D. Energy coupling mechanisms of MFS transporters. Protein Sci: a Publ. Protein Soc.24, 1560–1579 (2015). PubMed PMC

Frazer, J. et al. Disease variant prediction with deep generative models of evolutionary data. Nature599, 91–95 (2021). PubMed

Haendel, M. et al. How many rare diseases are there? Nat. Rev. Drug Discov.19, 77–78 (2020). PubMed PMC

Rehm, H. L. Time to make rare disease diagnosis accessible to all. Nat. Med28, 241–242 (2022). PubMed PMC

McNeill, A. Good genotype-phenotype relationships in rare disease are hard to find. Eur. J. Hum. Genet30, 251 (2022). PubMed PMC

Kersseboom, S. et al. In vitro and mouse studies supporting therapeutic utility of triiodothyroacetic acid in MCT8 deficiency. Mol. Endocrinol.28, 1961–1970 (2014). PubMed PMC

Zada, D., Tovin, A., Lerer-Goldshtein, T. & Appelbaum, L. Pharmacological treatment and BBB-targeted genetic therapy for MCT8-dependent hypomyelination in zebrafish. Dis. Model Mech.9, 1339–1348 (2016). PubMed PMC

Braun, D. & Schweizer, U. The Chemical Chaperone Phenylbutyrate Rescues MCT8 Mutations Associated With Milder Phenotypes in Patients With Allan-Herndon-Dudley Syndrome. Endocrinology158, 678–691 (2017). PubMed

van Hasselt, P. M. et al. Monocarboxylate transporter 1 deficiency and ketone utilization. N. Engl. J. Med371, 1900–1907 (2014). PubMed

Kloeckener-Gruissem, B. et al. Mutation of solute carrier SLC16A12 associates with a syndrome combining juvenile cataract with microcornea and renal glucosuria. Am. J. Hum. Genet82, 772–779 (2008). PubMed PMC

Frints, S. G. et al. MCT8 mutation analysis and identification of the first female with Allan-Herndon-Dudley syndrome due to loss of MCT8 expression. Eur. J. Hum. Genet16, 1029–1037 (2008). PubMed

Quesada-Espinosa, J. F. et al. First female with Allan-Herndon-Dudley syndrome and partial deletion of X-inactivation center. Neurogenetics22, 343–346 (2021). PubMed

Olivati, C. et al. Allan-Herndon-Dudley syndrome in a female patient and related mechanisms. Mol. Genet Metab. Rep.31, 100879 (2022). PubMed PMC

Iwayama, H. et al. Measurement of Reverse Triiodothyronine Level and the Triiodothyronine to Reverse Triiodothyronine Ratio in Dried Blood Spot Samples at Birth May Facilitate Early Detection of Monocarboxylate Transporter 8 Deficiency. Thyroid31, 1316–1321 (2021). PubMed PMC

Russell, D. J., Rosenbaum, P. L., Cadman, D. T., Gowland, C., Hardy, S. & Jarvis, S. The gross motor function measure: a means to evaluate the effects of physical therapy. Dev. Med Child Neurol.31, 341–352 (1989). PubMed

Sparrow, S. S., Balla, D. A. & Cicchetti, D. V. Vineland-II Adaptive Behavior Scales: Survey Forms Manual. (AGS Publishing 2005).

Bayley, N. Bayley scales of infant and toddler development–Third edition. (Pearson Education, Inc., 2006).

Flynn, J. T. et al. Clinical Practice Guideline for Screening and Management of High Blood Pressure in Children and Adolescents. Pediatrics140, e20171904 (2017). PubMed

Whelton, P. K. et al. 2017 ACC/AHA/AAPA/ABC/ACPM/AGS/APhA/ASH/ASPC/NMA/PCNA Guideline for the Prevention, Detection, Evaluation, and Management of High Blood Pressure in Adults: Executive Summary: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines. Circulation138, e426–e483 (2018). PubMed

Fleming, S. et al. Normal ranges of heart rate and respiratory rate in children from birth to 18 years of age: a systematic review of observational studies. Lancet377, 1011–1018 (2011). PubMed PMC

Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature581, 434–443 (2020). PubMed PMC

Groeneweg, S., et al. Insights into the mechanism of MCT8 oligomerization. J. Endocr. Soc. 4, bvaa080 (2020) PubMed PMC

van Geest, F. S. et al. Clinical and Functional Consequences of C-Terminal Variants in MCT8: A Case Series. J. Clin. Endocrinol. Metab.106, 539–553 (2021). PubMed PMC

Masnada, S. et al. Novel mutations in SLC16A2 associated with a less severe phenotype of MCT8 deficiency. Metab. Brain Dis.34, 1565–1575 (2019). PubMed

Visser, W. E. et al. Novel pathogenic mechanism suggested by ex vivo analysis of MCT8 (SLC16A2) mutations. Hum. Mutat.30, 29–38 (2009). PubMed

Friesema, E. C., Jansen, J., Jachtenberg, J. W., Visser, W. E., Kester, M. H. & Visser, T. J. Effective cellular uptake and efflux of thyroid hormone by human monocarboxylate transporter 10. Mol. Endocrinol.22, 1357–1369 (2008). PubMed PMC

Maranduba, C. M. et al. Decreased cellular uptake and metabolism in Allan-Herndon-Dudley syndrome (AHDS) due to a novel mutation in the MCT8 thyroid hormone transporter. J. Med Genet43, 457–460 (2006). PubMed PMC

Groeneweg, S. et al. The role of Arg445 and Asp498 in the human thyroid hormone transporter MCT8. Endocrinology155, 618–626 (2014). PubMed

Johannes, J., Braun, D., Kinne, A., Rathmann, D., Kohrle, J. & Schweizer, U. Few Amino Acid Exchanges Expand the Substrate Spectrum of Monocarboxylate Transporter 10. Mol. Endocrinol.30, 796–808 (2016). PubMed PMC

Groeneweg, S., Lima de Souza, E. C., Meima, M. E., Peeters, R. P., Visser, W. E. & Visser, T. J. Outward-Open Model of Thyroid Hormone Transporter Monocarboxylate Transporter 8 Provides Novel Structural and Functional Insights. Endocrinology158, 3292–3306 (2017). PubMed

Teumer, A. et al. Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation. Nat. Commun.9, 4455 (2018). PubMed PMC

Sidorenko, J. et al. The effect of X-linked dosage compensation on complex trait variation. Nat. Commun.10, 3009 (2019). PubMed PMC

Bycroft, C. et al. The UK Biobank resource with deep phenotyping and genomic data. Nature562, 203–209 (2018). PubMed PMC

Zhou, W. et al. Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. Nat. Genet50, 1335–1341 (2018). PubMed PMC

Makowski, C. et al. Discovery of genomic loci of the human cerebral cortex using genetically informed brain atlases. Science375, 522–528 (2022). PubMed PMC

Jiang, L. et al. A resource-efficient tool for mixed model association analysis of large-scale data. Nat. Genet51, 1749–1755 (2019). PubMed

Bakshi, A. et al. Fast set-based association analysis using summary data from GWAS identifies novel gene loci for human complex traits. Sci. Rep.6, 32894 (2016). PubMed PMC

Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res38, W529–533 (2010). PubMed PMC

Veidenberg, A., Medlar, A. & Loytynoja, A. Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization. Mol. Biol. Evol.33, 1126–1130 (2016). PubMed

Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol.7, 539 (2011). PubMed PMC

Hooft, R. W., Vriend, G., Sander, C. & Abola, E. E. Errors in protein structures. Nature381, 272 (1996). PubMed

Morris, G. M. et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem.19, 1639–1662 (1998).

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature596, 583–589 (2021). PubMed PMC

Wejaphikul, K. et al. Role of leucine 341 in thyroid hormone receptor beta revealed by a novel mutation causing thyroid hormone resistance. Thyroid10.1089/thy.2018.0146 (2018). PubMed

Laimer, J., Hofer, H., Fritz, M., Wegenkittl, S. & Lackner, P. MAESTRO-multi agent stability prediction upon point mutations. BMC Bioinforma.16, 116 (2015). PubMed PMC

Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F. & Serrano, L. The FoldX web server: an online force field. Nucleic Acids Res33, W382–388 (2005). PubMed PMC

Martin, M. & Nicola, J. P. Impact of the Mutational Landscape of the Sodium/Iodide Symporter in Congenital Hypothyroidism. Thyroid31, 1776–1785 (2021). PubMed

Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T. & Kanehisa, M. AAindex: amino acid index database, progress report 2008. Nucleic Acids Res36, D202–205 (2008). PubMed PMC

Delgado, J., Radusky, L. G., Cianferoni, D. & Serrano, L. FoldX 5.0: working with RNA, small molecules and a new graphical interface. Bioinformatics35, 4168–4169 (2019). PubMed PMC

Pedregosa, F. V. G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M. & Duchesnay, E. Scikit-learn: machine learning in python. J. Mach. Learn Res12, 2825–2830 (2011).

Waskom, M. L. Seaborn: Statistical data visualization. J. Open Source Softw.6, 3021 (2021).