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El-Kamah GY, Mosaad RM, Taher MB, Amr KS. Defining the molecular pathology and consequent phenotypes in Egyptian HB patients. J Genet Eng Biotechnol 2021; 19:75. [PMID: 33999344 PMCID: PMC8128942 DOI: 10.1186/s43141-021-00165-8] [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: 01/29/2021] [Accepted: 04/14/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Hemophilia B (HB) (also known as Christmas disease) is a rare X-linked recessive disorder characterized by spontaneous or prolonged hemorrhages caused by mutations in Factor 9 (F9) gene leading to deficient or defective coagulation F9. Our study aimed at identifying the causative mutations within a sample of HB Egyptian patients. The present study comprised clinical data of eleven HB patients descending from six unrelated families and a seventh family including a carrier mother with a history of deceased HB sibling. Sequencing of F9 gene was performed. RESULTS The study revealed four mutations; two missense NM_000133.3:c.676C>G, (P.Arg226Gly) and NM_000133.3:c.1305T>G, (p.Cys435Trp), and two nonsense mutations NM_000133.3:c.880C>T, (p.Arg294*) and NM_000133.3:c.1150C>T, (p.Arg384*), identified mutations spanned exons 6 and 8 of which a total of three mutations are located in hotspot exon 8 of F9 gene. CONCLUSIONS Reviewing the literature, this is the first molecular analysis of F9 gene in HB Egyptian patients. Consistent genotype/phenotypic severity correlation could be concluded, helping proper genetic counseling and prenatal decision taking.
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Affiliation(s)
- Ghada Y El-Kamah
- Clinical Genetics Department, Human Genetics and Genome Research division (HGGR), National Research Centre (NRC), Cairo, Egypt
| | - Rehab M Mosaad
- Molecular Genetics and Enzymology Department, HGGR, NRC, El Buhouth St., Dokki, Cairo, Egypt.
| | - Mohamed B Taher
- Clinical Genetics Department, Human Genetics and Genome Research division (HGGR), National Research Centre (NRC), Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetics, HGGR, NRC, Cairo, Egypt
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Pignani S, Todaro A, Ferrarese M, Marchi S, Lombardi S, Balestra D, Pinton P, Bernardi F, Pinotti M, Branchini A. The chaperone-like sodium phenylbutyrate improves factor IX intracellular trafficking and activity impaired by the frequent p.R294Q mutation. J Thromb Haemost 2018; 16:2035-2043. [PMID: 29993188 DOI: 10.1111/jth.14236] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Indexed: 12/25/2022]
Abstract
Essentials Missense mutations often impair protein folding, and thus intracellular trafficking and secretion. Cellular models of severe type I hemophilia B were challenged with chaperone-like compounds. Sodium phenylbutyrate improved intracellular trafficking and secretion of the frequent p.R294Q. The increased coagulant activity levels (∼3%) of p.R294Q would ameliorate the bleeding phenotype. SUMMARY Background Missense mutations often impair protein folding and intracellular processing, which can be improved by small compounds with chaperone-like activity. However, little has been done in coagulopathies, where even modest increases of functional levels could have therapeutic implications. Objectives To rescue the expression of factor IX (FIX) variants affected by missense mutations associated with type I hemophilia B (HB) through chaperone-like compounds. Methods Expression studies of recombinant (r)FIX variants and evaluation of secreted levels (ELISA), intracellular trafficking (immunofluorescence) and activity (coagulant assays) before and after treatment of cells with chaperone-like compounds. Results As a model we chose the most frequent HB mutation (p.R294Q, ~100 patients), compared with other recurrent mutations associated with severe/moderate type I HB. Immunofluorescence studies revealed retention of rFIX variants in the endoplasmic reticulum and negligible localization in the Golgi, thus indicating impaired intracellular trafficking. Consistently, and in agreement with coagulation phenotypes in patients, all missense mutations resulted in impaired secretion (< 1% wild-type rFIX). Sodium phenylbutyrate (NaPBA) quantitatively improved trafficking to the Golgi and dose dependently promoted secretion (from 0.3 ± 0.1% to 1.5 ± 0.3%) only of the rFIX-294Q variant. Noticeably, this variant displayed a specific coagulant activity that was higher (~2.0 fold) than that of wild-type rFIX in all treatment conditions. Importantly, coagulant activity was concurrently increased to levels (3.0 ± 0.9%) that, if achieved in patients, would ameliorate the bleeding phenotype. Conclusions Altogether, our data detail molecular mechanisms underlying type I HB and candidate NaPBA as affordable 'personalized' therapeutics for patients affected by the highly frequent p.R294Q mutation, and with reduced access to substitutive therapy.
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Affiliation(s)
- S Pignani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - A Todaro
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - M Ferrarese
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Marchi
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - S Lombardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - D Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - P Pinton
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - F Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - M Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - A Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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3
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Synthesis of Cationic Polymer Libraries for Gene Delivery Using Diglycidyl Ethers. Methods Mol Biol 2018. [PMID: 30051420 DOI: 10.1007/978-1-4939-8661-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Gene therapy has the potential to cure many different genetic diseases, if safe and effective gene delivery vectors can be developed. This chapter describes protocols for the synthesis of novel polymers using diglycidyl ether and diamine or polyamine monomers for transgene delivery and expression. The resulting poly (amino ethers) are able to transfect a higher number of cells, with lower cytotoxicity than other commercially available polymers (e.g., Polyethyleneimine, PEI).
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Doss C GP. In silico profiling of deleterious amino acid substitutions of potential pathological importance in haemophlia A and haemophlia B. J Biomed Sci 2012; 19:30. [PMID: 22423892 PMCID: PMC3361463 DOI: 10.1186/1423-0127-19-30] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 03/16/2012] [Indexed: 01/08/2023] Open
Abstract
Background In this study, instead of current biochemical methods, the effects of deleterious amino acid substitutions in F8 and F9 gene upon protein structure and function were assayed by means of computational methods and information from the databases. Deleterious substitutions of F8 and F9 are responsible for Haemophilia A and Haemophilia B which is the most common genetic disease of coagulation disorders in blood. Yet, distinguishing deleterious variants of F8 and F9 from the massive amount of nonfunctional variants that occur within a single genome is a significant challenge. Methods We performed an in silico analysis of deleterious mutations and their protein structure changes in order to analyze the correlation between mutation and disease. Deleterious nsSNPs were categorized based on empirical based and support vector machine based methods to predict the impact on protein functions. Furthermore, we modeled mutant proteins and compared them with the native protein for analysis of protein structure stability. Results Out of 510 nsSNPs in F8, 378 nsSNPs (74%) were predicted to be 'intolerant' by SIFT, 371 nsSNPs (73%) were predicted to be 'damaging' by PolyPhen and 445 nsSNPs (87%) as 'less stable' by I-Mutant2.0. In F9, 129 nsSNPs (78%) were predicted to be intolerant by SIFT, 131 nsSNPs (79%) were predicted to be damaging by PolyPhen and 150 nsSNPs (90%) as less stable by I-Mutant2.0. Overall, we found that I-Mutant which emphasizes support vector machine based method outperformed SIFT and PolyPhen in prediction of deleterious nsSNPs in both F8 and F9. Conclusions The models built in this work would be appropriate for predicting the deleterious amino acid substitutions and their functions in gene regulation which would be useful for further genotype-phenotype researches as well as the pharmacogenetics studies. These in silico tools, despite being helpful in providing information about the nature of mutations, may also function as a first-pass filter to determine the substitutions worth pursuing for further experimental research in other coagulation disorder causing genes.
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Affiliation(s)
- George Priya Doss C
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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5
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Portman MA, Chen SH, Xiao Y, Ning XH. Maturational changes in gene expression for adenine nucleotide translocator isoforms and betaF1-ATPase in rabbit heart. Mol Genet Metab 1999; 66:75-9. [PMID: 10068509 DOI: 10.1006/mgme.1998.2793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Maturational changes in myocardial respiratory control have been related to postnatal accumulation of adenine nucleotide translocator (ANT) in the inner mitochondrial membrane. Alternatively alterations in relative isoform distribution for this nuclear-encoded gene during myocardial maturation might be responsible for changing the kinetics of respiratory control. Rabbit hearts were analyzed for adenine nucleotide translocator isoform (ANT1, ANT2, ANT3) gene expression and distribution at four ages (fetal, 29/31 days of gestation; 1 h postnatal; 9 days postnatal; and 3-4 months postnatal). Transcript levels for the coordinately expressed betaF1-ATPase were also examined in these hearts. These studies demonstrated that mRNA expression for ANT1 in coordination with betaF1-ATPase increased substantially after 9 days of age in rabbit hearts. Expression of the minor isoform ANT3 parallels ANT1, though no change in expression of the kidney-specific isoform ANT2 occurs in heart during this developmental period. Previous work has demonstrated that ANT protein accumulation is closely coordinated with mRNA expression for ANT1. These results support previous studies, which indicate that the operational mode of myocardial respiratory control depends on adenine nucleotide mRNA expression. Changes in relative adenine nucleotide translocator isoform distribution do occur during fetal to mature transition and may contribute to observed changes in the mode of respiratory control.
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Affiliation(s)
- M A Portman
- Department of Pediatrics, University of Washington, Seattle, Washington, 98105-0371, USA
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Li L, Darden T, Hiskey R, Pedersen L. Homology Modeling and Molecular Dynamics Simulations of the Gla Domains of Human Coagulation Factor IX and Its G[12]A Mutant. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952190j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Leping Li
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Tom Darden
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Richard Hiskey
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Lee Pedersen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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7
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Giannelli F, Green PM, Sommer SS, Poon MC, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A, Brownlee GG. Haemophilia B (sixth edition): a database of point mutations and short additions and deletions. Nucleic Acids Res 1996; 24:103-18. [PMID: 8594556 PMCID: PMC145614 DOI: 10.1093/nar/24.1.103] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The sixth edition of the haemophilia B database lists in easily accessible form all known factor IX mutations due to small changes (base substitutions and short additions and/or deletions of <30 bp) identified in haemophilia B patients. The 1380 patient entries are ordered by the nucleotide number of their mutation. Where known, details are given on factor IX activity, factor IX antigen in circulation and origin of mutation. References to published mutations are given and the laboratories generating the data are indicated.
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Giannelli F, Green PM, Sommer SS, Lillicrap DP, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A, Brownlee GG. Haemophilia B: database of point mutations and short additions and deletions, fifth edition, 1994. Nucleic Acids Res 1994; 22:3534-46. [PMID: 7937052 PMCID: PMC308314 DOI: 10.1093/nar/22.17.3534] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The fifth edition of the haemophilia B database lists in easily accessible form all known factor IX mutations due to small changes (base substitutions and short additions and/or deletions of < 30bp) identified in haemophilia B patients. The 1,142 patient entries are ordered by the nucleotide number of their mutation. Where known, details are given on: factor IX activity, factor IX antigen in circulation, and origin of mutation. References to published mutations are given and the laboratories generating the data are indicated.
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Giannelli F, Green PM, High KA, Sommer S, Poon MC, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions--fourth edition, 1993. Nucleic Acids Res 1993; 21:3075-87. [PMID: 8392713 PMCID: PMC309734 DOI: 10.1093/nar/21.13.3075] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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10
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Affiliation(s)
- A R Thompson
- Department of Medicine, University of Washington, Seattle 98104
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Giannelli F, Green PM, High KA, Sommer S, Lillicrap DP, Ludwig M, Olek K, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions--third edition, 1992. Nucleic Acids Res 1992; 20 Suppl:2027-63. [PMID: 1598234 PMCID: PMC333981 DOI: 10.1093/nar/20.suppl.2027] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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12
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Reiner AP, Thompson AR. Screening for nonsense mutations in patients with severe hemophilia A can provide rapid, direct carrier detection. Hum Genet 1992; 89:88-94. [PMID: 1349567 DOI: 10.1007/bf00207049] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite marked genetic heterogeneity in families with hemophilic patients, transition mutations in CG dinucleotides occur frequently. Of 71 CG dinucleotides in the factor VIII cDNA, a C-to-T transition in 12 would lead to a new Stop codon (CGA to TGA). Using restriction enzyme digestion of 11 amplified DNA fragments, seven point mutations were localized among 60 patients with severe hemophilia A. Five were detected as loss of a natural or introduced TaqI site at codons -5, 583, 1941, 2116, and 2209 and were confirmed as CGA (Arg) to TGA (Stop) nonsense mutations by DNA sequencing. A novel C-to-T nonsense mutation was detected as loss of the RsaI site at codon 1966 and confirmed by sequence in two unrelated individuals. Two partial gene deletions were detected as selective failure to amplify exon 1 and exons 15-22, respectively. In an additional (61st) patient who was subsequently found to have mild (instead of severe) hemophilia, digests suggested a mutation in codon 1696. Upon sequencing, this codon contained a novel missense mutation, a C-to-G transversion changing CGA (Arg 1696) to GGA (Gly). In four families with women available for testing, carrier status was rapidly determined by direct screening for the point mutation. In two of three with sporadic occurrences, the mother was a carrier as were two of four sisters. In the other family, the mother and a sister were homozygous for the TaqI cleavage site in their amplified exon 24 fragment, indicating a de novo C-to-T transition in codon 2209 in the patient's factor VIII gene. This final patient's sister was a noncarrier even though by linkage analysis she inherited the same factor VIII gene as her brother.
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Affiliation(s)
- A P Reiner
- Department of Medicine, University of Washington, Seattle
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13
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Reiner AP, Stray SM, Thompson AR. Three missense mutations in Arg codons of the factor VIII genes of mild to moderately severe hemophilia A patients. Thromb Res 1992; 66:93-9. [PMID: 1412186 DOI: 10.1016/0049-3848(92)90159-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- A P Reiner
- Department of Medicine, University of Washington, Seattle 98195
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14
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Chen SH, Zhang M, Lovrien EW, Scott CR, Thompson AR. CG dinucleotide transitions in the factor IX gene account for about half of the point mutations in hemophilia B patients: a Seattle series. Hum Genet 1991; 87:177-82. [PMID: 2066105 DOI: 10.1007/bf00204177] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hemophilia B is due to multiple molecular defects in the factor IX gene. Over 80% of mutations are single base substitutions. By amplification and direct sequencing, 51 single base substitutions were found in the transcribed sequence of the factor IX genes of patients from 50 distinct families with hemophilia B. These include 30 mutations in 29 families not previously reported by us; of these, 12 are novel, i.e., not previously published in other series. Of the 51 substitutions in our overall series 23 (45%) occurred as C-to-T or G-to-A transitions at 11 sites within CG dinucleotides. It is estimated that CG transitions occur from one to two orders of magnitude more frequently than mutations in nucleotides that are not within a CG pair. More than one family had identical defects for 6 of the CG mutations. At 4 of these sites, most patients had different haplotypes compatible with distinct mutations. Non-CG-type mutations occurred throughout the coding regions with only one mutation in more than one family. The latter included 7 families with a 397 Ile-to-Thr defect that all share a rare haplotype, suggesting a common ancestor.
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Affiliation(s)
- S H Chen
- Department of Pediatrics, University of Washington, Seattle 98195
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Giannelli F, Green PM, High KA, Sommer S, Lillicrap DP, Ludwig M, Olek K, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions--second edition. Nucleic Acids Res 1991; 19 Suppl:2193-219. [PMID: 2041805 PMCID: PMC331353 DOI: 10.1093/nar/19.suppl.2193] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- F Giannelli
- Paediatric Research Unit, Guy's Tower, London, UK
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Giannelli F, Green PM, High KA, Lozier JN, Lillicrap DP, Ludwig M, Olek K, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions. Nucleic Acids Res 1990; 18:4053-9. [PMID: 2377450 PMCID: PMC331159 DOI: 10.1093/nar/18.14.4053] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- F Giannelli
- Paediatric Research Unit, Guy's Tower, London Bridge, London, UK
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Green PM, Montandon AJ, Bentley DR, Ljung R, Nilsson IM, Giannelli F. The incidence and distribution of CpG----TpG transitions in the coagulation factor IX gene. A fresh look at CpG mutational hotspots. Nucleic Acids Res 1990; 18:3227-31. [PMID: 1972560 PMCID: PMC330927 DOI: 10.1093/nar/18.11.3227] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The mutations of 76 haemophilia B patients representing the whole population registered with the Malmö haemophilia centre (42) and referrals from the UK, were characterised. RFLP haplotype analysis of the defective genes indicated that 51 single base pair substitutions were definitely of independent origin and 27 of these were CpG----TpG or CpA transitions. This represents a 38-fold excess over other single-base changes. Most of such transitions (82%) occur at 9 CpG sites occupying critical positions (transitions at 3 sites substitute essential arginines, while at 6 sites transition to TpG creates stop codons). Sixteen of the 18 possible transitions at these 9 sites cause clear haemophilia B and should be fully ascertained in our haemophilia B population. This allowed the direct estimate of the rate of CpG transitions. This is 1.05 x 10(-7) substitutions per base per gamete per generation. The marked excess of CpG transitions in haemophilia B appears partly due to the high proportion of CpG sites at critical positions (at least 9 out of 20). We propose that this follows from the fact that male hemizygosity makes X-linked genes particularly susceptible to selective forces that tend to fix CpG sites arising at critical positions.
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Affiliation(s)
- P M Green
- Paediatric Research Unit, Guy's Hospital Tower, London Bridge, UK
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