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Liu X, Liu X, Fan W, Zhang Z, Zhang P, Liu X, Lei M, Li Q, Yu X, Li D. Analysis of the genotype–phenotype correlation in isovaleric acidaemia: A case report of long-term follow-up of a chinese patient and literature review. Front Neurol 2022; 13:928334. [PMID: 35968299 PMCID: PMC9366085 DOI: 10.3389/fneur.2022.928334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/06/2022] [Indexed: 12/01/2022] Open
Abstract
Background Isovaleric acidaemia (IVA), characterized by an acute metabolic crisis and psychomotor delay, is a rare inherited metabolic disease caused by a deficiency in isovaleryl-CoA dehydrogenase (IVD). Methods We report the case of a Chinese patient with IVA who was admitted to Tianjin Children's Hospital and followed up for 8 years. Genetic analysis of the patient and his parents was conducted using the whole-exome sequencing and Sanger sequencing. We searched for similar reported cases in the PubMed and Wanfang databases using the term “isovaleric acidaemia,” reviewed the related literature to obtain a summary of the clinical and genetic characteristics, and analyzed the genotype–phenotype correlations. Results The patient presented with encephalopathic symptoms, such as vomiting, lethargy, and somnolence. We identified compound heterozygous variants of the IVD gene, including the unreported variant c.224A>G (p.Asn75Ser) and the reported variant c.1195G>C (p.Asp399His). The child was prescribed a low-protein diet supplemented with L-carnitine. During the 8-year follow-up, no metabolic disorder or encephalopathic symptoms recurred. At present, the child is 11 years of age and has normal mental and motor performance. Another 154 cases identified in 25 relevant references were combined with this case, resulting in a sample of 155 patients, including 52 asymptomatic patients, 64 with neonatal onset, and 39 with the chronic intermittent disease with onset from ages of 1 month to 10 years (median age, 2 years). Among articles that reported sex, the male-to-female ratio was 1:1.06. The cardinal symptoms included vomiting, lethargy, “sweaty foot” odor, poor feeding, developmental delay, and epilepsy. The proportion of variants in regions 123–159 and 356–403 of the IVD protein was greater in symptomatic patients than in asymptomatic patients. Conversely, in asymptomatic patients, the proportion of variants in the 282–318 region was greater than in symptomatic patients. Conclusion This case report describes an unreported variant c.224A>G (p.Asn75Ser) of the IVD gene, and summarizes previously reported cases. Furthermore, the correlation between the genotype and clinical phenotype of IVA is analyzed to improve the understanding of this disease.
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Affiliation(s)
- Xingmiao Liu
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Xinquan Liu
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Wenxuan Fan
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Zhongbin Zhang
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Peiyuan Zhang
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Xiaojun Liu
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Meifang Lei
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Qing Li
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
| | - Xiaoli Yu
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
- Xiaoli Yu
| | - Dong Li
- Department of Pediatric Neurology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin, China
- *Correspondence: Dong Li
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Long Term Follow-Up of Polish Patients with Isovaleric Aciduria. Clinical and Molecular Delineation of Isovaleric Aciduria. Diagnostics (Basel) 2020; 10:diagnostics10100738. [PMID: 32977617 PMCID: PMC7598207 DOI: 10.3390/diagnostics10100738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
Isovaleric acidemia (IVA) is an autosomal recessive leucine inborn error of metabolism caused by isovaleryl-CoA dehydrogenase deficiency. The disease has various courses, from severe ones manifesting in newborns to the intermittent form with first manifestation in children and adults. The aim of this study was to analyze clinical and neurological outcomes in Polish patients with IVA. Ten patients diagnosed and treated in The Children's Memorial Health Institute were included in the study. The diagnosis was based on tandem MS (increased level of C5 acylcarnitine) and urine GCMS (increased isovalerylglycine, and 3-hydroxyisovaleric acid). Molecular analysis was performed in seven patients (70%) leading to the detection of pathogenic variants in the IVD gene in all of them. A retrospective analysis of patients' medical records included: demographics, symptoms at diagnosis, medical management, and biochemical and clinical outcomes following therapy. The median follow-up time (median; Q1-Q2) was 2.5 years (1.5-9.0) for newborn screening (NBS) and family screening (FS) children, and 17 years (5.0-20) for symptomatic patients. Five patients were in a good clinical state, four children presented mild neurological symptoms, and one-severely delayed child. In the IVD gene, five known and two novel variants (p.466C>G, c.1132G>A) were identified. Molecular analysis was performed in seven patients leading to identification of biallelic pathogenic variants in the IVD gene in all of them. We can conclude that long-term clinical and neurological outcomes of patients with IVA were satisfactory as a result of an early diagnosis and proper management. Although early treatment did not prevent decompensations, they were milder in these patients.
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Lin Y, Chen D, Peng W, Wang K, Lin W, Zhuang J, Zheng Z, Li M, Fu Q. Newborn screening for isovaleric acidemia in Quanzhou, China. Clin Chim Acta 2020; 509:25-29. [PMID: 32505769 DOI: 10.1016/j.cca.2020.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Isovaleric acidemia (IVA) is a rare autosomal recessive disorder of leucine metabolism caused by a defective isovaleryl-CoA dehydrogenase (IVD) gene. Reports of IVA diagnoses following newborn screening (NBS) in the Chinese population are few. METHODS We investigated the biochemical, clinical, and molecular profiles of 5 patients with IVA in China. The estimated incidence of IVA in Quanzhou, China is 1 in 1:84,469. RESULTS Initial NBS revealed mild to markedly increased isovalerylcarnitine (C5) concentrations in all 5 patients, and differential diagnosis revealed increased urinary isovaleryglycine concentrations in 2 patients. One patient presented with acute neonatal symptoms, whereas the other 4 remained asymptomatic. Eight distinct IVD gene variants were identified. The most common variant was c.1208A > G (p.Y403C), with an allele frequency of 30%. Five variants were previously unreported, namely, c.499A > G (p.M167V), c.640A > G (p.T214A), c.740G > A (p.G247E), c.832G > C (p.V278L), and c.1195G > C (p.D399H). Different in silico prediction analyses suggested that these previously unreported missense variants are pathogenic. Protein modelling analyses also showed that these missense variants may cause structural damage and dysfunction in IVD. CONCLUSIONS Patients with IVA may have C5 concentrations approaching the cut-off values, highlighting the need for stringent recall criteria and second-tier tests to improve screening performance.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Dongmei Chen
- Department of Neonatal Intensive Care Unit, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Weilin Peng
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Kunyi Wang
- Integrated Technical Service Center, Quanzhou Customs, Quanzhou, Fujian Province 362000, China
| | - Weihua Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Zhenzhu Zheng
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Min Li
- Hangzhou Genuine Clinical Laboratory Co. Ltd, Hangzhou, Zhejiang Province 310007, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China.
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Ibarra-González I, Fernández-Lainez C, Guillén-López S, López-Mejía L, Belmont-Matínez L, Sokolsky TD, Amin VR, Kitchener RL, Vela-Amieva M, Naylor EW, Bhattacharjee A. Molecular analysis using targeted next generation DNA sequencing and clinical spectrum of Mexican patients with isovaleric acidemia. Clin Chim Acta 2020; 501:216-221. [DOI: 10.1016/j.cca.2019.10.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 10/07/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
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Sarker SK, Islam MT, Hasib SH, Sultana N, Hossain SR, Biswas A, Sultana R, Bhuyan GS, Begum MN, Konica FA, Qadri SK, Qadri SS, Saha N, Qadri F, Mannoor K. A novel missense mutation of Isovaleryl-CoA dehydrogenase gene associated with chronic intermittent Isovaleric acidemia in a Bangladeshi patient. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Schlune A, Riederer A, Mayatepek E, Ensenauer R. Aspects of Newborn Screening in Isovaleric Acidemia. Int J Neonatal Screen 2018; 4:7. [PMID: 33072933 PMCID: PMC7548899 DOI: 10.3390/ijns4010007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 01/22/2018] [Indexed: 12/19/2022] Open
Abstract
Isovaleric acidemia (IVA), an inborn error of leucine catabolism, is caused by mutations in the isovaleryl-CoA dehydrogenase (IVD) gene, resulting in the accumulation of derivatives of isovaleryl-CoA including isovaleryl (C5)-carnitine, the marker metabolite used for newborn screening (NBS). The inclusion of IVA in NBS programs in many countries has broadened knowledge of the variability of the condition, whereas prior to NBS, two distinct clinical phenotypes were known, an "acute neonatal" and a "chronic intermittent" form. An additional biochemically mild and potentially asymptomatic form of IVA and its association with a common missense mutation, c.932C>T (p.A282V), was discovered in subjects identified through NBS. Deficiency of short/branched chain specific acyl-CoA dehydrogenase (2-methylbutyryl-CoA dehydrogenase), a defect of isoleucine degradation whose clinical significance remains unclear, also results in elevated C5-carnitine, and may therefore be detected by NBS for IVA. Treatment strategies for the long-term management of symptomatic IVA comprise the prevention of catabolism, dietary restriction of natural protein or leucine intake, and supplementation with l-carnitine and/or l-glycine. Recommendations on how to counsel and manage individuals with the mild phenotype detected by NBS are required.
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Affiliation(s)
- Andrea Schlune
- Experimental Pediatrics and Metabolism, Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Anselma Riederer
- Department of Obstetrics and Gynecology, Hospital Altötting-Burghausen, Teaching Hospital of the Ludwig-Maximilians-Universität München, Vinzenz-von-Paul-Strasse 10, 84503 Altötting, Germany
| | - Ertan Mayatepek
- Experimental Pediatrics and Metabolism, Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Regina Ensenauer
- Experimental Pediatrics and Metabolism, Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
- Correspondence: ; Tel.: +49-211-81-17687
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Zaki OK, Priya Doss C G, Ali SA, Murad GG, Elashi SA, Ebnou MSA, Kumar D T, Khalifa O, Gamal R, El Abd HSA, Nasr BN, Zayed H. Genotype-phenotype correlation in patients with isovaleric acidaemia: comparative structural modelling and computational analysis of novel variants. Hum Mol Genet 2018; 26:3105-3115. [PMID: 28535199 DOI: 10.1093/hmg/ddx195] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/06/2023] Open
Abstract
Isovaleric acidaemia (IVA) is an autosomal recessive inborn error of leucine metabolism. It is caused by a deficiency in the mitochondrial isovaleryl-CoA dehydrogenase (IVD) enzyme. In this study, we investigated eight patients with IVA. The patients' diagnoses were confirmed by urinary organic acid analysis and the blood C5-Carnitine value. A molecular genetic analysis of the IVD gene revealed nine different variants: five were missense variants (c.1193G > A; p. R398Q, c.1207T > A; p. Y403N, c.872C > T; p. A291V, c.749G > C; p. G250A, c.1136T > C; p.I379T), one was a frameshift variant (c.ins386 T; p. Y129fs), one was a splicing variant (c.465 + 2T > C), one was a polymorphism (c.732C > T; p. D244D), and one was an intronic benign variant (c.287 + 14T > C). Interestingly, all variants were in homozygous form, and four variants were novel (p. Y403N, p. Y129fs, p. A291V, p. G250A) and absent from 200 normal chromosomes. We performed protein modelling and dynamics analyses, pathogenicity and stability analyses, and a physiochemical properties analysis of the five missense variants (p.Y403N, R398Q, p.A291V, p.G250A, and p.I379T). Variants p.I379T and p.R398Q were found to be the most deleterious and destabilizing compared to variants p.A291V and p.Y403N. However, the four variants were predicted to be severe by the protein dynamic and in silico analysis, which was consistent with the patients' clinical phenotypes. The p.G250A variant was computationally predicted as mild, which was consistent with the severity of the clinical phenotype. This study reveals a potentially meaningful genotype-phenotype correlation for our patient cohort and highlights the development and use of this computational analysis for future assessments of genetic variants in the clinic.
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Affiliation(s)
- Osama K Zaki
- Department of Medical Genetics, Ain Shams Paediatrics Hospital, Cairo, Egypt
| | - George Priya Doss C
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Salsabil A Ali
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Ghadeer G Murad
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Shaima A Elashi
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Maryam S A Ebnou
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Thirumal Kumar D
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Ola Khalifa
- Department of Medical Genetics, Ain Shams Paediatrics Hospital, Cairo, Egypt
| | - Radwa Gamal
- Department of Medical Genetics, Ain Shams Paediatrics Hospital, Cairo, Egypt
| | - Heba S A El Abd
- Department of Medical Genetics, Ain Shams Paediatrics Hospital, Cairo, Egypt
| | - Bilal N Nasr
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
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8
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Genotype and phenotype characterization in a Spanish cohort with isovaleric acidemia. J Hum Genet 2016; 62:355-360. [DOI: 10.1038/jhg.2016.144] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 11/09/2022]
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9
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Tan JQ, Chen DY, Mo ZQ, Li ZT, Huang JW, Cai R, Yan TZ. [Pancytopenia and metabolic decompensation in a neonate]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:1150-1153. [PMID: 27817783 PMCID: PMC7389842 DOI: 10.7499/j.issn.1008-8830.2016.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
A 9-day-old male patient was admitted to the hospital because of cough, anhelation, feeding difficulty and lethargy. The diagnostic examinations indicated pulmonary infection, severe metabolic acidosis, hyperglycemia, hyperammonemia and pancytopenia in the patient. Blood and urine screening and isovaleryl-CoA dehydrogenase (IVD) gene detection for inherited metabolic diseases were performed to clarify the etiology. Tandem mass spectrometric screening for blood showed an elevated isovalerylcarnitine (C5) level. The organic acid analysis of urine by gas chromatography-mass spectrometry showed significantly increased levels in isovaleryl glycine and 3-hydroxyisovaleric acid. Homozygous mutations (c.1208A>G, p.Tyr403Cys) in the IVD gene were identified in the patient. His parents were heterozygous carriers. After the treatment with low-leucine diets and L-carnitine for 3 days, the patient showed a significant improvement in symptoms, but he died one week later. It is concluded that the neonates with pneumonia and metabolic decompensation of unknown etiology should be screened for genetic metabolic disease.
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Affiliation(s)
- Jian-Qiang Tan
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, Guangxi 545001, China.
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Zayed H, Ouhtit A. Accredited genetic testing in the Arab Gulf region: reinventing the wheel. J Hum Genet 2016; 61:673-4. [DOI: 10.1038/jhg.2016.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Caminsky NG, Mucaki EJ, Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis. F1000Res 2015. [DOI: 10.12688/f1000research.5654.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.
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12
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Sakamoto O, Arai-Ichinoi N, Mitsubuchi H, Chinen Y, Haruna H, Maruyama H, Sugawara H, Kure S. Phenotypic Variability and Newly Identified Mutations of the IVD Gene in Japanese Patients with Isovaleric Acidemia. TOHOKU J EXP MED 2015; 236:103-6. [DOI: 10.1620/tjem.236.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Osamu Sakamoto
- Department of Pediatrics, Tohoku University School of Medicine
| | | | | | - Yasutsugu Chinen
- Department of Pediatrics, Faculty of Medicine, University of the Ryukyus
| | - Hidenori Haruna
- Department of Pediatrics, Juntendo University Faculty of Medicine
| | - Hidehiko Maruyama
- Department of Pediatrics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | | | - Shigeo Kure
- Department of Pediatrics, Tohoku University School of Medicine
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13
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Caminsky N, Mucaki EJ, Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis. F1000Res 2014; 3:282. [PMID: 25717368 PMCID: PMC4329672 DOI: 10.12688/f1000research.5654.1] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2014] [Indexed: 12/14/2022] Open
Abstract
The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.
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Affiliation(s)
- Natasha Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Peter K Rogan
- Departments of Biochemistry and Computer Science, Western University, London, ON, N6A 2C1, Canada
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Ozgul RK, Karaca M, Kilic M, Kucuk O, Yucel-Yilmaz D, Unal O, Hismi B, Aliefendioglu D, Sivri S, Tokatli A, Coskun T, Dursun A. Phenotypic and genotypic spectrum of Turkish patients with isovaleric acidemia. Eur J Med Genet 2014; 57:596-601. [DOI: 10.1016/j.ejmg.2014.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
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Al-Shamsi A, Hertecant JL, Al-Hamad S, Souid AK, Al-Jasmi F. Mutation Spectrum and Birth Prevalence of Inborn Errors of Metabolism among Emiratis: A study from Tawam Hospital Metabolic Center, United Arab Emirates. Sultan Qaboos Univ Med J 2014; 14:e42-9. [PMID: 24516753 DOI: 10.12816/0003335] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 08/07/2013] [Accepted: 10/10/2013] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES This study aimed to determine the mutation spectrum and prevalence of inborn errors of metabolism (IEM) among Emiratis. METHODS The reported mutation spectrum included all patients who were diagnosed with IEM (excluding those with lysosomal storage diseases [LSD]) at Tawam Hospital Metabolic Center in Abu Dhabi, United Arab Emirates, between January 1995 and May 2013. Disease prevalence (per 100,000 live births) was estimated from data available for 1995-2011. RESULTS In 189 patients, 57 distinct IEM were diagnosed, of which 20 (35%) entities were previously reported LSD (65 patients with 39 mutations), with a birth prevalence of 26.87/100,000. This study investigated the remaining 37 (65%) patients with other IEM (124 patients with 62 mutations). Mutation analysis was performed on 108 (87%) of the 124 patients. Five patients with biotinidase deficiency had compound heterozygous mutations, and two siblings with lysinuric protein intolerance had two homozygous mutations. The remaining 103 (95%) patients had homozygous mutations. As of this study, 29 (47%) of the mutations have been reported only in Emiratis. Two mutations were found in three tribes (biotinidase deficiency [BTD, c.1330G>C] and phenylketonuria [PAH, c.168+5G>C]). Two mutations were found in two tribes (isovaleric aciduria [IVD, c.1184G>A] and propionic aciduria [PCCB, c.990dupT]). The remaining 58 (94%) mutations were each found in individual tribes. The prevalence was 48.37/100,000. The most prevalent diseases (2.2-4.9/100,000) were biotinidase deficiency; tyrosinemia type 1; phenylketonuria; propionic aciduria; glutaric aciduria type 1; glycogen storage disease type Ia, and mitochondrial deoxyribonucleic acid depletion. CONCLUSION The IEM birth prevalence (LSD and non-LSD) was 75.24/100,000. These results justify implementing prevention programmes that incorporate genetic counselling and screening.
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Affiliation(s)
| | | | - Sania Al-Hamad
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Abdul-Kader Souid
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Fatma Al-Jasmi
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Qadi AMH, Hamadah HK, Jijeh AMZ, Hijazi OM, Kabbani MS. Ebstein cardiac anomaly, functional pulmonary atresia and isovaleric acidemia: A case report. J Saudi Heart Assoc 2014; 26:170-3. [PMID: 24954991 DOI: 10.1016/j.jsha.2014.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/12/2014] [Indexed: 10/25/2022] Open
Abstract
In this report, we present a rare association between Ebstein anomaly (EA) and isovaleric acidemia (IVA) in a newborn who was admitted to our cardiac center. He underwent for PDA stenting to maintain adequate pulmonary blood flow, later he developed recurrent metabolic acidosis, prominent sweaty feet odor, neutropenia and thrombocytopenia. His organic acids profile in the urine confirmed the diagnosis of IVA. To the best of our knowledge, there is no association between these two rare diseases. We are presenting this case report to highlight this rare association.
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Affiliation(s)
- Ammar M H Qadi
- King Abdul-Aziz Cardiac Center (KACC), King Abdul-Aziz Medical City (KAMC), King Saud University, Riyadh
| | - Hussam K Hamadah
- King Abdul-Aziz Cardiac Center (KACC), King Abdul-Aziz Medical City (KAMC), King Saud University, Riyadh
| | - Abdulraouf M Z Jijeh
- King Abdul-Aziz Cardiac Center (KACC), King Abdul-Aziz Medical City (KAMC), King Saud University, Riyadh
| | - Omar M Hijazi
- King Abdul-Aziz Cardiac Center (KACC), King Abdul-Aziz Medical City (KAMC), King Saud University, Riyadh
| | - Mohamad S Kabbani
- King Abdul-Aziz Cardiac Center (KACC), King Abdul-Aziz Medical City (KAMC), King Saud University, Riyadh
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