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Selamioğlu A, Karaca M, Balcı MC, Körbeyli HK, Durmuş A, Yıldız EP, Karaman S, Gökçay GF. Triosephosphate Isomerase Deficiency: E105D Mutation in Unrelated Patients and Review of the Literature. Mol Syndromol 2023; 14:231-238. [PMID: 37323194 PMCID: PMC10267495 DOI: 10.1159/000528192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2023] Open
Abstract
Introduction Chronic haemolytic anaemia, increased susceptibility to infections, cardiomyopathy, neurodegeneration, and death in early childhood are the clinical findings of triosephosphate isomerase (TPI) deficiency, which is an ultra-rare disorder. The clinical and laboratory findings and the outcomes of 2 patients with TPI deficiency are reported, with a review of cases reported in the literature. Case Presentation Two unrelated patients with haemolytic anaemia and neurologic findings who were diagnosed as having TPI deficiency are presented. Neonatal onset of initial symptoms was observed in both patients, and the age at diagnosis was around 2 years. The patients had increased susceptibility to infections and respiratory failure, but cardiac symptoms were not remarkable. Screening for inborn errors of metabolism revealed a previously unreported metabolic alteration determined using tandem mass spectrometry in acylcarnitine analysis, causing elevated propionyl carnitine levels in both patients. The patients had p.E105D (c.315G>C) homozygous mutations in the TPI1 gene. Although severely disabled, both patients are alive at the ages of 7 and 9 years. Discussion For better management, it is important to investigate the genetic aetiology in patients with haemolytic anaemia with or without neurologic symptoms who do not have a definitive diagnosis. The differential diagnosis of elevated propionyl carnitine levels using tandem mass spectrometry screening should also include TPI deficiency.
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Affiliation(s)
- Arzu Selamioğlu
- Division of Paediatric Metabolism, Department of Paediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Meryem Karaca
- Division of Paediatric Metabolism, Department of Paediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Mehmet Cihan Balcı
- Division of Paediatric Metabolism, Department of Paediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Hüseyin Kutay Körbeyli
- Division of Paediatric Metabolism, Department of Paediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Aslı Durmuş
- Division of Paediatric Metabolism, Department of Paediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Edibe Pembegül Yıldız
- Division of Paediatric Neurology, Department of Pediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Serap Karaman
- Division of Paediatric Haematology-Oncology, Department of Pediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Gülden Fatma Gökçay
- Division of Paediatric Metabolism, Department of Paediatrics, Istanbul University Faculty of Medicine, Istanbul, Turkey
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In silico prediction of the effects of mutations in the human triose phosphate isomerase gene: Towards a predictive framework for TPI deficiency. Eur J Med Genet 2017; 60:289-298. [PMID: 28341520 DOI: 10.1016/j.ejmg.2017.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 02/27/2017] [Accepted: 03/20/2017] [Indexed: 01/24/2023]
Abstract
Triose phosphate isomerase (TPI) deficiency is a rare, but highly debilitating, inherited metabolic disease. Almost all patients suffer severe neurological effects and the most severely affected are unlikely to live beyond early childhood. Here, we describe an in silico study into well-characterised variants which are associated with the disease alongside an investigation into 79 currently uncharacterised TPI variants which are known to occur in the human population. The majority of the disease-associated mutations affected amino acid residues close to the dimer interface or the active site. However, the location of the altered amino acid residue did not predict the severity of the resulting disease. Prediction of the effect on protein stability using a range of different programs suggested a relationship between the degree of instability caused by the sequence variation and the severity of the resulting disease. Disease-associated variations tended to affect well-conserved residues in the protein's sequence. However, the degree of conservation of the residue was not predictive of disease severity. The majority of the 79 uncharacterised variants are potentially associated with disease since they were predicted to destabilise the protein and often occur in well-conserved residues. We predict that individuals homozygous for the corresponding mutations would be likely to suffer from TPI deficiency.
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Del Orbe Barreto R, Arrizabalaga B, De la Hoz AB, García-Orad Á, Tejada MI, Garcia-Ruiz JC, Fidalgo T, Bento C, Manco L, Ribeiro ML. Detection of new pathogenic mutations in patients with congenital haemolytic anaemia using next-generation sequencing. Int J Lab Hematol 2016; 38:629-638. [PMID: 27427187 DOI: 10.1111/ijlh.12551] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 06/07/2016] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Congenital haemolytic anaemia (CHA) refers to a group of genetically heterogeneous disorders, mainly caused by changes in genes encoding globin chains, cytoskeletal proteins and red cell enzymes, in which accurate diagnosis can be challenging with conventional techniques. METHODS To set-up a comprehensive assay for detecting mutations that could improve aetiological diagnosis, we designed a custom panel for sequencing coding regions from 40 genes known to be involved in the pathogenesis of CHA, using the Ion Torrent™ (Thermo Fisher Scientific, S.L. Waltham, MA, USA) Personal Genome Machine (PGM) Sequencer. A control group of 16 samples with previously known mutations and a test group of 10 patients with unknown mutations were included for assay validation and application, respectively. RESULTS In the test group, we identified pathogenic mutations in all cases: four patients had novel mutations in genes related to membrane defects (SPTB, ANK1, SLC4A1 and EPB41), four were homozygous or compound heterozygous for mutations in genes related to enzyme deficiencies (GPI, TPI1 and GSS), one had a mutation in the HBB gene and another presented a homozygous mutation in the ADAMTS13 gene. CONCLUSIONS Ion PGM sequencing with our custom panel is a highly efficient way to detect mutations causing haemolytic anaemia, including new variations. It is a high-throughput detection method that is ready for application in clinical laboratories.
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Affiliation(s)
| | - B Arrizabalaga
- BioCruces Health Research Institute, Barakaldo, Spain.,Department of Haematology, Cruces University Hospital, Barakaldo, Spain
| | - A B De la Hoz
- BioCruces Health Research Institute, Barakaldo, Spain
| | - Á García-Orad
- BioCruces Health Research Institute, Barakaldo, Spain.,Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Odontology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - M I Tejada
- BioCruces Health Research Institute, Barakaldo, Spain.,Molecular Genetics Laboratory, Genetics Service, Cruces University Hospital, Barakaldo, Spain
| | - J C Garcia-Ruiz
- BioCruces Health Research Institute, Barakaldo, Spain.,Department of Haematology, Cruces University Hospital, Barakaldo, Spain
| | - T Fidalgo
- Serviço de Hematologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - C Bento
- Serviço de Hematologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - L Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - M L Ribeiro
- Serviço de Hematologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
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Li Z, He Y, Liu Q, Zhao L, Wong L, Kwoh CK, Nguyen H, Li J. Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. BMC Bioinformatics 2013; 14 Suppl 16:S11. [PMID: 24564410 PMCID: PMC3853089 DOI: 10.1186/1471-2105-14-s16-s11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are directly related to the excessive thermolability of the mutant have not been investigated in structural biology. Results This work compares the structure of the E104D mutant with its wild type counterparts. It is found that the water topology in the dimer interface of HsTIM is atypical, having a "wet-core-dry-rim" distribution with 16 water molecules tightly packed in a small deep region surrounded by 22 residues including GLU104. These water molecules are co-conserved with their surrounding residues in non-archaeal TIMs (dimers) but not conserved across archaeal TIMs (tetramers), indicating their importance in preserving the overall quaternary structure. As the structural permutation induced by the mutation is not significant, we hypothesize that the excessive thermolability of the E104D mutant is attributed to the easy propagation of atoms' flexibility from the surface into the core via the large cluster of water. It is indeed found that the B factor increment in the wet region is higher than other regions, and, more importantly, the B factor increment in the wet region is maintained in the deeply buried core. Molecular dynamics simulations revealed that for the mutant structure at normal temperature, a clear increase of the root-mean-square deviation is observed for the wet region contacting with the large cluster of interfacial water. Such increase is not observed for other interfacial regions or the whole protein. This clearly suggests that, in the E104D mutant, the large water cluster is responsible for the subunit interface flexibility and overall thermolability, and it ultimately leads to the deficiency of this enzyme. Conclusions Our study reveals that a large cluster of water buried in protein interfaces is fragile and high-maintenance, closely related to the structure, function and evolution of the whole protein.
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De La Mora-De La Mora I, Torres-Larios A, Mendoza-Hernández G, Enriquez-Flores S, Castillo-Villanueva A, Mendez ST, Garcia-Torres I, Torres-Arroyo A, Gómez-Manzo S, Marcial-Quino J, Oria-Hernández J, López-Velázquez G, Reyes-Vivas H. The E104D mutation increases the susceptibility of human triosephosphate isomerase to proteolysis. Asymmetric cleavage of the two monomers of the homodimeric enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2702-11. [PMID: 24056040 DOI: 10.1016/j.bbapap.2013.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/27/2022]
Abstract
The deficiency of human triosephosphate isomerase (HsTIM) generates neurological alterations, cardiomyopathy and premature death. The mutation E104D is the most frequent cause of the disease. Although the wild type and mutant exhibit similar kinetic parameters, it has been shown that the E104D substitution induces perturbation of an interfacial water network that, in turn, reduces the association constant between subunits promoting enzyme inactivation. To gain further insight into the effects of the mutation on the structure, stability and function of the enzyme, we measured the sensitivity of recombinant E104D mutant and wild type HsTIM to limited proteolysis. The mutation increases the susceptibility to proteolysis as consequence of the loss of rigidity of its overall 3-D structure. Unexpectedly, it was observed that proteolysis of wild type HsTIM generated two different stable nicked dimers. One was formed in relatively short times of incubation with proteinase K; as shown by spectrometric and crystallographic data, it corresponded to a dimer containing a nicked monomer and an intact monomer. The formation of the other nicked species requires relatively long incubation times with proteinase K and corresponds to a dimer with two clipped subunits. The first species retains 50% of the original activity, whereas the second species is inactive. Collectively, we found that the E104D mutant is highly susceptible to proteolysis, which in all likelihood contributes to the pathogenesis of enzymopathy. In addition, the proteolysis data on wild type HsTIM illustrate an asymmetric conduct of the two monomers.
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Shishkin SS, Kovalyov LI, Kovalyova MA. Proteomic studies of human and other vertebrate muscle proteins. BIOCHEMISTRY (MOSCOW) 2004; 69:1283-98. [PMID: 15627382 DOI: 10.1007/s10541-005-0074-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review summarizes results of some systemic studies of muscle proteins of humans and some other vertebrates. The studies, started after introduction of two-dimensional gel electrophoresis of O'Farrell, were significantly extended during development of proteomics, a special branch of functional genomics. Special attention is paid to analysis of characteristic features of strategy for practical realization of the systemic approach during three main stages of these studies: pre-genomic, genomic (with organizational registration of proteomics), and post-genomic characterized by active use of structural genomics data. Proteomic technologies play an important role in detection of changes in isoforms of various muscle proteins (myosins, troponins, etc.). These changes possibly reflecting tissue specificity of gene expression may underline functional state of muscle tissues under normal and pathological conditions, and such proteomic analysis is now used in various fields of medicine.
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Affiliation(s)
- S S Shishkin
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia.
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Proteomic studies of human and other vertebrate muscle proteins. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Overkamp KM, Bakker BM, Kötter P, Luttik MAH, Van Dijken JP, Pronk JT. Metabolic engineering of glycerol production in Saccharomyces cerevisiae. Appl Environ Microbiol 2002; 68:2814-21. [PMID: 12039737 PMCID: PMC123913 DOI: 10.1128/aem.68.6.2814-2821.2002] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2002] [Accepted: 04/01/2002] [Indexed: 11/20/2022] Open
Abstract
Inactivation of TPI1, the Saccharomyces cerevisiae structural gene encoding triose phosphate isomerase, completely eliminates growth on glucose as the sole carbon source. In tpi1-null mutants, intracellular accumulation of dihydroxyacetone phosphate might be prevented if the cytosolic NADH generated in glycolysis by glyceraldehyde-3-phosphate dehydrogenase were quantitatively used to reduce dihydroxyacetone phosphate to glycerol. We hypothesize that the growth defect of tpi1-null mutants is caused by mitochondrial reoxidation of cytosolic NADH, thus rendering it unavailable for dihydroxyacetone-phosphate reduction. To test this hypothesis, a tpi1delta nde1delta nde2delta gut2delta quadruple mutant was constructed. NDE1 and NDE2 encode isoenzymes of mitochondrial external NADH dehydrogenase; GUT2 encodes a key enzyme of the glycerol-3-phosphate shuttle. It has recently been demonstrated that these two systems are primarily responsible for mitochondrial oxidation of cytosolic NADH in S. cerevisiae. Consistent with the hypothesis, the quadruple mutant grew on glucose as the sole carbon source. The growth on glucose, which was accompanied by glycerol production, was inhibited at high-glucose concentrations. This inhibition was attributed to glucose repression of respiratory enzymes as, in the quadruple mutant, respiratory pyruvate dissimilation is essential for ATP synthesis and growth. Serial transfer of the quadruple mutant on high-glucose media yielded a spontaneous mutant with much higher specific growth rates in high-glucose media (up to 0.10 h(-1) at 100 g of glucose. liter(-1)). In aerated batch cultures grown on 400 g of glucose. liter(-1), this engineered S. cerevisiae strain produced over 200 g of glycerol. liter(-1), corresponding to a molar yield of glycerol on glucose close to unity.
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Affiliation(s)
- Karin M Overkamp
- Kluyver Laboratory of Biotechnology, Delft University of Technology, NL-2628 BC Delft, Amsterdam
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Arya R, Lalloz MR, Bellingham AJ, Layton DM. Evidence for founder effect of the Glu104Asp substitution and identification of new mutations in triosephosphate isomerase deficiency. Hum Mutat 2000; 10:290-4. [PMID: 9338582 DOI: 10.1002/(sici)1098-1004(1997)10:4<290::aid-humu4>3.0.co;2-l] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Triosephosphate isomerase (TPI) deficiency is an autosomal recessive disorder of glycolysis characterized by multisystem disease and lethality in early childhood. Among seven unrelated Northern European kindreds with clinical TPI deficiency studied, a single missense mutation at codon 104 (GAG;Glu-->GAC;Asp) predominated, accounting for 11/14 (79%) mutant alleles. In three families molecular analysis revealed compound heterozygosity for Glu104Asp and novel missense mutations. In two cases the second mutation was a Cys to Tyr substitution at codon 41 (TGT-->TAT) and in one an Ile to Val substitution at codon 170(ATT-->GTT). The origin of the Glu104Asp mutation was defined by haplotype analysis using a novel G/A polymorphism at nucleotide 2898 of the TPI gene. Cosegregation of the low frequency 2898A allele with the G-->C base change at nucleotide 315 supports a single origin for the Glu104Asp mutation in a common ancestor.
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Affiliation(s)
- R Arya
- Department of Haematological Medicine, King's College School of Medicine & Dentistry, London, UK
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Schneider AS. Triosephosphate isomerase deficiency: historical perspectives and molecular aspects. Best Pract Res Clin Haematol 2000; 13:119-40. [PMID: 10916682 DOI: 10.1053/beha.2000.0061] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this chapter, the original descriptions and pre-molecular studies of triosephosphate isomerase (TPI) deficiency are summarized, and the molecular aspects of the disease presented. The gene is well characterized, and several mutations have been described. Structure-function studies have led to an increased understanding of impaired catalysis. All kindreds that have been studied with the predominant Glu104Asp mutation are linked by a common haplotype, indicating descent from a common ancestor. Variant upstream substitutions occur in high frequency in persons of African and East Asian lineage and in lower frequency in other groups, but the possible role, if any, of these variants in clinical TPI deficiency requires further investigation. The possible contribution of deviant lipid metabolism to the pathogenesis of the disorder has been extensively investigated, and an intriguing new area of inquiry is the apparent cell-to-cell transfer of enzyme in cell culture systems, raising the question of the feasibility of enzyme or gene replacement therapy.
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Affiliation(s)
- A S Schneider
- Department of Pathology, Finch University of Health Sciences/Chicago Medical School, IL 60044, USA
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Abstract
Red blood cell enzyme activities are measured mainly to diagnose hereditary nonspherocytic hemolytic anemia associated with enzyme anomalies. At least 15 enzyme anomalies associated with hereditary hemolytic anemia have been reported. Some nonhematologic disease can also be diagnosed by the measurement of red blood cell enzyme activities in the case in which enzymes of red blood cells and the other organs are under the same genetic control. Progress in molecular biology has provided a new perspective. Techniques such as the polymerase chain reaction and single-strand conformation polymorphism analysis have greatly facilitated the molecular analysis of erythroenzymopathies. These studies have clarified the correlation between the functional and structural abnormalities of the variant enzymes. In general, the mutations that induce an alteration of substrate binding site and/or enzyme instability might result in markedly altered enzyme properties and severe clinical symptoms.
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Affiliation(s)
- H Fujii
- Department of Blood Transfusion Medicine, Tokyo Women's Medical College, Japan
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Miwa S, Fujii H. Molecular basis of erythroenzymopathies associated with hereditary hemolytic anemia: tabulation of mutant enzymes. Am J Hematol 1996; 51:122-32. [PMID: 8579052 DOI: 10.1002/(sici)1096-8652(199602)51:2<122::aid-ajh5>3.0.co;2-#] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Molecular abnormalities of erythroenzymopathies associated with hereditary hemolytic anemia have been determined by means of molecular biology. Pyruvate kinase (PK) deficiency is the most common and well-characterized enzyme deficiency in the glycolytic pathway, and it causes hereditary hemolytic anemia. To date, 47 gene mutations have been identified. We identified one base deletion, one splicing mutation, and six distinct missense mutations in 12 unrelated families with a homozygous PK deficiency. Mutations located near the substrate or fructose-1,6- diphosphate binding site may change the conformation of the active site, resulting in a drastic loss of activity and severe clinical symptoms. Glucose-6-phosphate dehydrogenase (G6PD)deficiency is the most common metabolic disorder, and it is associated with chronic hemolytic anemia and/or drug- or infection-induced acute hemolytic attack. An estimated 400 million people are affected worldwide. The mutations responsible for about 78 variants have been determined. Some have polymorphic frequencies in different populations. Most variants are produced by one or two nucleotide substitutions. Molecular studies have disclosed that most of the class 1 G6PD variants associated with chronic hemolysis have the mutations surrounding either the substrate or the NADP binding site. Among rare enzymopathies, missense mutations have been determined in deficiencies of glucosephosphate isomerase, (TPI), phosphoglycerate kinase, and adenylate kinase. Compound heterozygosity with missense mutation and base deletion has been determined in deficiencies of hexokinase and diphosphoglyceromutase. Compound heterozygosity with missense and nonsense mutations has been identified in TPI deficiency. One base junction mutations resulting in abnormally spliced PFK-M mRNA have been identified in homozygous PFK deficiency. An exception is hemolytic anemia due to increased adenosine deaminase activity. The basic abnormality appears to result from the overproduction of a structurally normal enzyme.
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Affiliation(s)
- S Miwa
- Okinawa Memorial Institute for Medical Research, Tokyo Women's Medical College, Japan
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Schneider A, Westwood B, Yim C, Prchal J, Berkow R, Labotka R, Warrier R, Beutler E. Triosephosphate isomerase deficiency: repetitive occurrence of point mutation in amino acid 104 in multiple apparently unrelated families. Am J Hematol 1995; 50:263-8. [PMID: 7485100 DOI: 10.1002/ajh.2830500407] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The molecular basis of triosephosphate isomerase (TPI) deficiency was studied in 3 patients from three separate families. In all 3 patients, genomic DNA directly sequenced after amplification by the polymerase chain reaction exhibited the point mutation TPI315C amino acid 104 Glu-->Asp. Although other mutations known to cause TPI deficiency have been restricted to single families, the amino acid 104 defect has now been described in nine apparently unrelated families throughout the world and is clearly the most frequently occurring form of the disorder. The basis of the repetitive occurrence of this mutation remains unexplained.
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Affiliation(s)
- A Schneider
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California, USA
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