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Righetti S, Allcock RJN, Yaplito-Lee J, Adams L, Ellaway C, Jones KJ, Selvanathan A, Fletcher J, Pitt J, van Kuilenburg ABP, Delatycki MB, Laing NG, Kirk EP. The relationship between beta-ureidopropionase deficiency due to UPB1 variants and human phenotypes is uncertain. Mol Genet Metab 2022; 137:62-67. [PMID: 35926322 DOI: 10.1016/j.ymgme.2022.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND Beta-ureidopropionase deficiency, caused by variants in UPB1, has been reported in association with various neurodevelopmental phenotypes including intellectual disability, seizures and autism. AIM We aimed to reassess the relationship between variants in UPB1 and a clinical phenotype. METHODS Literature review, calculation of carrier frequencies from population databases, long-term follow-up of a previously published case and reporting of additional cases. RESULTS Fifty-three published cases were identified, and two additional cases are reported here. Of these, 14 were asymptomatic and four had transient neurological features; clinical features in the remainder were variable and included non-neurological presentations. Several of the variants previously reported as pathogenic are present in population databases at frequencies higher than expected for a rare condition. In particular, the variant most frequently reported as pathogenic, p.Arg326Gln, is very common among East Asians, with a carrier frequency of 1 in 19 and 1 in 907 being homozygous for the variant in gnomAD v2.1.1. CONCLUSION Pending the availability of further evidence, UPB1 should be considered a 'gene of uncertain clinical significance'. Caution should be used in ascribing clinical significance to biochemical features of beta-ureidopropionase deficiency and/or UPB1 variants in patients with neurodevelopmental phenotypes. UPB1 is not currently suitable for inclusion in gene panels for reproductive genetic carrier screening. SYNOPSIS The relationship between beta-ureidopropionase deficiency due to UPB1 variants and clinical phenotypes is uncertain.
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Affiliation(s)
| | | | - Joy Yaplito-Lee
- Department of Metabolic Medicine, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Louisa Adams
- Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | | | - Kristi J Jones
- Sydney Children's Hospitals Network, Sydney, NSW, Australia; University of Sydney, NSW, Australia
| | | | | | - James Pitt
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - André B P van Kuilenburg
- Amsterdam UMC location, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Martin B Delatycki
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Nigel G Laing
- Centre for Medical Research University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Edwin P Kirk
- University of New South Wales, Sydney, NSW, Australia; Sydney Children's Hospitals Network, Sydney, NSW, Australia; New South Wales Health Pathology, Sydney, NSW, Australia.
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2
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Dobritzsch D, Meijer J, Meinsma R, Maurer D, Monavari AA, Gummesson A, Reims A, Cayuela JA, Kuklina N, Benoist JF, Perrin L, Assmann B, Hoffmann GF, Bierau J, Kaindl AM, van Kuilenburg ABP. β-Ureidopropionase deficiency due to novel and rare UPB1 mutations affecting pre-mRNA splicing and protein structural integrity and catalytic activity. Mol Genet Metab 2022; 136:177-185. [PMID: 35151535 DOI: 10.1016/j.ymgme.2022.01.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 01/04/2023]
Abstract
β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyses the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, ammonia and CO2. To date, only a limited number of genetically confirmed patients with a complete β-ureidopropionase deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 10 newly identified β-ureidopropionase deficient individuals. Patients presented mainly with neurological abnormalities and markedly elevated levels of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid in urine. Analysis of UPB1, encoding β-ureidopropionase, showed 5 novel missense variants and two novel splice-site variants. Functional expression of the UPB1 variants in mammalian cells showed that recombinant ß-ureidopropionase carrying the p.Ala120Ser, p.Thr129Met, p.Ser300Leu and p.Asn345Ile variant yielded no or significantly decreased β-ureidopropionase activity. Analysis of the crystal structure of human ß-ureidopropionase indicated that the point mutations affect substrate binding or prevent the proper subunit association to larger oligomers and thus a fully functional β-ureidopropionase. A minigene approach showed that the intronic variants c.[364 + 6 T > G] and c.[916 + 1_916 + 2dup] led to skipping of exon 3 and 8, respectively, in the process of UPB1 pre-mRNA splicing. The c.[899C > T] (p.Ser300Leu) variant was identified in two unrelated Swedish β-ureidopropionase patients, indicating that β-ureidopropionase deficiency may be more common than anticipated.
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Affiliation(s)
- Doreen Dobritzsch
- Uppsala University, Department of Chemistry-BMC, Biomedical Center, Uppsala, Sweden
| | - Judith Meijer
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands
| | - Rutger Meinsma
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands
| | | | - Ardeshir A Monavari
- National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street, Temple Street, Dublin, Ireland
| | - Anders Gummesson
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Annika Reims
- Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Jorge A Cayuela
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Natalia Kuklina
- Drammen Hospital, Pediatric Department/Habilitation Center, Vestre Viken HF, Drammen, Norway
| | - Jean-François Benoist
- Hôpital Universitaire Robert Debré, Service de Biochimie Hormonologie, Paris, France
| | - Laurence Perrin
- Hôpital Universitaire Robert Debré, Service de Biochimie Hormonologie, Paris, France
| | - Birgit Assmann
- University Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- University Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Jörgen Bierau
- Maastricht University Medical Centre, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Center for Chronically Sick Children, Institute for Cell and Neurobiology, Berlin, Germany
| | - André B P van Kuilenburg
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands.
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3
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Xu X, Zheng J, Zou Q, Wang C, Zhang X, Wang X, Liu Y, Shu J. Rapid screening of UPB1 gene variations by high resolution melting curve analysis. Exp Ther Med 2021; 21:403. [PMID: 33692834 PMCID: PMC7938451 DOI: 10.3892/etm.2021.9834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
The present study aimed to analyze gene mutations in patients with β-ureidopropinoase deficiency and establish a rapid detection method for β-ureidopropinoase (UPB1) pathogenic variations by high resolution melting (HRM) analysis. DNA samples with known UPB1 mutations in three patients with β-ureidopropinoase deficiency were utilized to establish a rapid detection method for UPB1 pathogenic variations by HRM analysis. Further rapid screening was performed on two patients diagnosed with β-ureidopropinoase deficiency and 50 healthy control individuals. The results showed that all known UPB1 gene mutations can be analyzed by a specially designed HRM assay. Each mutation has specific HRM profiles which could be used in rapid screening. The HRM method could correctly identify all genetic mutations in two children with β-ureidopropinoase deficiency. In addition, the HRM assay also recognized four unknown mutations. To conclude, the results support future studies of applying HRM analysis as a diagnostic approach for β-ureidopropinoase deficiency and a rapid screening method for UPB1 mutation carriers.
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Affiliation(s)
- Xiaowei Xu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Jie Zheng
- Graduate College, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Qianqian Zou
- Graduate College, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Chao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Xinjie Zhang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Xuetao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Yang Liu
- Department of Neonatology, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
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4
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Meijer J, Nakajima Y, Zhang C, Meinsma R, Ito T, Van Kuilenburg ABP. Identification of a novel synonymous mutation in the human β -Ureidopropionase Gene UPB1 affecting pre-mRNA splicing. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:639-45. [PMID: 24328561 DOI: 10.1080/15257770.2013.847189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and it catalyzes the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, respectively, and ammonia and CO2. To date, only 16 genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report the clinical, biochemical, and molecular analysis of a newly identified patient with β-ureidopropionase deficiency. Mutation analysis of the UPB1 gene showed that the patient was compound heterozygous for a novel synonymous mutation c.93C >T (p.Gly31Gly) in exon 1 and a previously described missense mutation c.977G >A (p.Arg326Gln) in exon 9. The in silico predicted effect of the synonymous mutation p.Gly31Gly on pre-mRNA splicing was investigated using a minigene approach. Wild-type and the mutated minigene constructs, containing the entire exon 1, intron 1, and exon 2 of UPB1, yielded different splicing products after expression in HEK293 cells. The c.93C >T (p.Gly31Gly) mutation resulted in altered pre-mRNA splicing of the UPB1 minigene construct and a deletion of the last 13 nucleotides of exon 1. This deletion (r.92_104delGCAAGGAACTCAG) results in a frame shift and the generation of a premature stop codon (p.Lys32SerfsX31). Using a minigene approach, we have thus identified the first synonymous mutation in the UPB1 gene, creating a cryptic splice-donor site affecting pre-mRNA splicing.
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Affiliation(s)
- J Meijer
- a Laboratory of Genetic Metabolic Diseases , Academic Medical Center , Amsterdam , The Netherlands
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5
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Contribution of the β-ureidopropionase (UPB1) gene alterations to the development of fluoropyrimidine-related toxicity. Pharmacol Rep 2012; 64:1234-42. [DOI: 10.1016/s1734-1140(12)70919-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 05/11/2012] [Indexed: 11/18/2022]
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van Kuilenburg ABP, Dobritzsch D, Meijer J, Krumpel M, Selim LA, Rashed MS, Assmann B, Meinsma R, Lohkamp B, Ito T, Abeling NGGM, Saito K, Eto K, Smitka M, Engvall M, Zhang C, Xu W, Zoetekouw L, Hennekam RCM. ß-ureidopropionase deficiency: phenotype, genotype and protein structural consequences in 16 patients. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1096-108. [PMID: 22525402 DOI: 10.1016/j.bbadis.2012.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 03/29/2012] [Accepted: 04/09/2012] [Indexed: 12/26/2022]
Abstract
ß-ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyzes the conversion of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid to ß-alanine and ß-aminoisobutyric acid, ammonia and CO(2). To date, only five genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 11 newly identified ß-ureidopropionase deficient patients as well as the analysis of the mutations in a three-dimensional framework. Patients presented mainly with neurological abnormalities (intellectual disabilities, seizures, abnormal tonus regulation, microcephaly, and malformations on neuro-imaging) and markedly elevated levels of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid in urine and plasma. Analysis of UPB1, encoding ß-ureidopropionase, showed 6 novel missense mutations and one novel splice-site mutation. Heterologous expression of the 6 mutant enzymes in Escherichia coli showed that all mutations yielded mutant ß-ureidopropionase proteins with significantly decreased activity. Analysis of a homology model of human ß-ureidopropionase generated using the crystal structure of the enzyme from Drosophila melanogaster indicated that the point mutations p.G235R, p.R236W and p.S264R lead to amino acid exchanges in the active site and therefore affect substrate binding and catalysis. The mutations L13S, R326Q and T359M resulted most likely in folding defects and oligomer assembly impairment. Two mutations were identified in several unrelated ß-ureidopropionase patients, indicating that ß-ureidopropionase deficiency may be more common than anticipated.
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Affiliation(s)
- André B P van Kuilenburg
- Academic Medical Center, Emma Children's Hospital, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105 AZ Amsterdam, The Netherlands.
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7
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Schnackerz KD, Dobritzsch D. Amidohydrolases of the reductive pyrimidine catabolic pathway purification, characterization, structure, reaction mechanisms and enzyme deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:431-44. [PMID: 18261476 DOI: 10.1016/j.bbapap.2008.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 01/07/2008] [Accepted: 01/09/2008] [Indexed: 12/26/2022]
Abstract
In the reductive pyrimidine catabolic pathway uracil and thymine are converted to beta-alanine and beta-aminoisobutyrate. The amidohydrolases of this pathway are responsible for both the ring opening of dihydrouracil and dihydrothymine (dihydropyrimidine amidohydrolase) and the hydrolysis of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyrate (beta-alanine synthase). The review summarizes what is known about the properties, kinetic parameters, three-dimensional structures and reaction mechanisms of these proteins. The two amidohydrolases of the reductive pyrimidine catabolic pathway have unrelated folds, with dihydropyrimidine amidohydrolase belonging to the amidohydrolase superfamily while the beta-alanine synthase from higher eukaryotes belongs to the nitrilase superfamily. beta-Alanine synthase from Saccharomyces kluyveri is an exception to the rule and belongs to the Acyl/M20 family.
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