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del Caño-Ochoa F, Ng BG, Rubio-del-Campo A, Mahajan S, Wilson MP, Vilar M, Rymen D, Sánchez-Pintos P, Kenny J, Martos ML, Campos T, Wortmann SB, Freeze HH, Ramón-Maiques S. Beyond genetics: Deciphering the impact of missense variants in CAD deficiency. J Inherit Metab Dis 2023; 46:1170-1185. [PMID: 37540500 PMCID: PMC10838372 DOI: 10.1002/jimd.12667] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
CAD is a large, 2225 amino acid multienzymatic protein required for de novo pyrimidine biosynthesis. Pathological CAD variants cause a developmental and epileptic encephalopathy which is highly responsive to uridine supplements. CAD deficiency is difficult to diagnose because symptoms are nonspecific, there is no biomarker, and the protein has over 1000 known variants. To improve diagnosis, we assessed the pathogenicity of 20 unreported missense CAD variants using a growth complementation assay that identified 11 pathogenic variants in seven affected individuals; they would benefit from uridine treatment. We also tested nine variants previously reported as pathogenic and confirmed the damaging effect of seven. However, we reclassified two variants as likely benign based on our assay, which is consistent with their long-term follow-up with uridine. We found that several computational methods are unreliable predictors of pathogenic CAD variants, so we extended the functional assay results by studying the impact of pathogenic variants at the protein level. We focused on CAD's dihydroorotase (DHO) domain because it accumulates the largest density of damaging missense changes. The atomic-resolution structures of eight DHO pathogenic variants, combined with functional and molecular dynamics analyses, provided a comprehensive structural and functional understanding of the activity, stability, and oligomerization of CAD's DHO domain. Combining our functional and protein structural analysis can help refine clinical diagnostic workflow for CAD variants in the genomics era.
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Affiliation(s)
- Francisco del Caño-Ochoa
- Structure of Macromolecular Targets Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Antonio Rubio-del-Campo
- Structure of Macromolecular Targets Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
| | - Sonal Mahajan
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Matthew P. Wilson
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
| | - Daisy Rymen
- Department of Pediatrics - Center for Metabolic Diseases, University Hospitals of Leuven, Belgium
| | - Paula Sánchez-Pintos
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. C.S.U.R. de Enfermedades Metabólicas. MetabERN. Hospital Clínico Universitario de Santiago de Compostela, La Coruña, Spain
- Instituto de Investigación Sanitaria Santiago de Compostela (IDIS), La Coruña, Spain
| | - Janna Kenny
- Children's Health Ireland at Crumlin, Ireland
| | - Myriam Ley Martos
- Pediatric Neurology Unit. Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - Teresa Campos
- Reference Center of Inherited Metabolic Diseases of Hospital de São João, Porto, Portugal
| | - Saskia B. Wortmann
- University Children’s Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Santiago Ramón-Maiques
- Structure of Macromolecular Targets Unit. Instituto de Biomedicina de Valencia (IBV), CSIC. Valencia, Spain
- Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)–Instituto de Salud Carlos III, Valencia, Spain
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Ley Martos M, Salado Reyes MJ, Marín Iglesias R, Gutiérrez Moro C, Lubián Gutiérrez M, Estepa Pedregosa L. A New Allelic Variant in the PANK2 Gene in a Patient with Incomplete HARP Syndrome. J Mov Disord 2020; 13:229-231. [PMID: 32654475 PMCID: PMC7502299 DOI: 10.14802/jmd.19071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/08/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Myriam Ley Martos
- Department of Neuropediatrics, Puerta del Mar Hospital, Cádiz, Spain
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Ley Martos M, Salado Reyes MJ, Espinosa Rosso R, Solera García J, Jiménez Jiménez L. Variabilidad en la presentación clínica en la enfermedad de Pompe: evolución tras terapia de reemplazo enzimático. Rev Neurol 2015. [DOI: 10.33588/rn.6109.2015336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tomás Vila M, Menor Serrano F, Ley Martos M, Chumillas Luján MJ, Marco Hernández AV, Barbero Aguirre P. Hipomielinización con atrofia de ganglios basales y de cerebelo. Aportación de dos nuevos casos a una entidad de descripción reciente. Rev Neurol 2014. [DOI: 10.33588/rn.5804.2013438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Barba Romero MÁ, Barrot Cortes E, Bautista Lorite J, Gutiérrez Rivas E, Illa Sendra I, Jiménez LM, Ley Martos M, López de Munain Arregui A, Pardo Fernández J, Pascual Pascual SI, Pérez López J, Solera J, Vílchez Padilla JJ. Guía clínica de la enfermedad de Pompe de inicio tardío. Rev Neurol 2012. [DOI: 10.33588/rn.5408.2012088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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