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Diversity of cystathionine beta-synthase haplotypes bearing the most common homocystinuria mutation c.833T>C: a possible role for gene conversion.

Vyletal P, Sokolová J, Cooper DN, Kraus JP, Krawczak M, Pepe G, Rickards O, Koch HG, Linnebank M, Kluijtmans LA, Blom HJ, Boers GH, Gaustadnes M, Skovby F, Wilcken B, Wilcken DE, Andria G, Sebastio G, Naughten ER, Yap S, Ohura T, Pronicka E, Laszlo A, Kozich V - Hum. Mutat. (2007)

Bottom Line: We have sought to study the relationship between the pathogenic and nonpathogenic c.833C-bearing chromosomes and to determine whether the pathogenic c.[833C; -] chromosomes are identical-by-descent or instead arose by recurrent mutation.Initial haplotype analysis of 780 randomly selected Czech and sub-Saharan African wild-type chromosomes, employing 12 intragenic markers, revealed 29 distinct CBS haplotypes, of which 10 carried the c.[833C; 844_845ins68] combination; none carried an isolated c.833C or c.844_845ins68 mutation.Since c.833T does not reside within an obvious mutational hotspot, we surmise that the three pathogenic and comparatively prevalent c.[833C; -] chromosomes may have originated by recurrent gene conversion employing the common nonpathogenic c.[833C; 844_845ins68] chromosomes as templates.

View Article: PubMed Central - PubMed

Affiliation: Center for Applied Genomics, Institute of Inherited Metabolic Disorders, Charles University 1st Faculty of Medicine, Prague, Czech Republic.

ABSTRACT
Homozygosity or compound heterozygosity for the c.833T>C transition (p.I278 T) in the cystathionine beta-synthase (CBS) gene represents the most common cause of pyridoxine-responsive homocystinuria in Western Eurasians. However, the frequency of the pathogenic c.833C allele, as observed in healthy newborns from several European countries (q(c.833C) approximately equals 3.3 x 10(-3)), is approximately 20-fold higher than expected on the basis of the observed number of symptomatic homocystinuria patients carrying this mutation (q(c.833C) approximately equals 0.18 x 10(-3)), implying clinical underascertainment. Intriguingly, the c.833C mutation is also present in combination with a 68-bp insertion, c.[833C; 844_845ins68], in a substantial proportion of chromosomes from nonhomocystinuric individuals worldwide. We have sought to study the relationship between the pathogenic and nonpathogenic c.833C-bearing chromosomes and to determine whether the pathogenic c.[833C; -] chromosomes are identical-by-descent or instead arose by recurrent mutation. Initial haplotype analysis of 780 randomly selected Czech and sub-Saharan African wild-type chromosomes, employing 12 intragenic markers, revealed 29 distinct CBS haplotypes, of which 10 carried the c.[833C; 844_845ins68] combination; none carried an isolated c.833C or c.844_845ins68 mutation. Subsequent examination of 69 pathogenic c.[833C; -] chromosomes, derived from homocystinuria patients of predominantly European origin, disclosed three unrelated haplotypes that differed from their wild-type counterparts by virtue of the presence of c.833C, thereby indicating that c.833T>C transition has occurred repeatedly and independently in the past. Since c.833T does not reside within an obvious mutational hotspot, we surmise that the three pathogenic and comparatively prevalent c.[833C; -] chromosomes may have originated by recurrent gene conversion employing the common nonpathogenic c.[833C; 844_845ins68] chromosomes as templates.

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Structure of the wild-type c. [833T; –] and c. [833C; 844_845ins68] CBS chromosomes. A:The genomic organization of the CBS gene, with exons depicted as numbered black boxes and the initiator ATG in exon 1 indicated by an upward-pointing arrow. Markers genotyped in this study are denoted by downward-pointing arrows. B: Boxed uppercase letters represent the sequence of wild-type exon 8. The lowercase sequence corresponds to flanking intronic regions. The thymidine residue at nucleotide position 833 is marked by an arrow. C:The sequence of the variant c. [833C; 844_845ins68] chromosome. The 68-bp insertion between nucleotides 844 and 845 is bracketed. Both the mutation c.833C in exon 8 and the wild-type thymidine 833 within the 68-bp insertion sequence are indicated by arrows. Motifs corresponding to DNA polymerase α/β frameshift hotspots and inverted repeats are shaded and underlined, respectively.
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fig01: Structure of the wild-type c. [833T; –] and c. [833C; 844_845ins68] CBS chromosomes. A:The genomic organization of the CBS gene, with exons depicted as numbered black boxes and the initiator ATG in exon 1 indicated by an upward-pointing arrow. Markers genotyped in this study are denoted by downward-pointing arrows. B: Boxed uppercase letters represent the sequence of wild-type exon 8. The lowercase sequence corresponds to flanking intronic regions. The thymidine residue at nucleotide position 833 is marked by an arrow. C:The sequence of the variant c. [833C; 844_845ins68] chromosome. The 68-bp insertion between nucleotides 844 and 845 is bracketed. Both the mutation c.833C in exon 8 and the wild-type thymidine 833 within the 68-bp insertion sequence are indicated by arrows. Motifs corresponding to DNA polymerase α/β frameshift hotspots and inverted repeats are shaded and underlined, respectively.

Mentions: Only a small proportion of human chromosomes carry the pathogenic mutation c.833C on its own (henceforth referred to as c.[833C; –] chromosomes), whereas a much larger proportion contain a nonpathogenic combination of two mutations (termed c.[833C; 844_845ins68] chromosomes). In the latter chromosomes, the pathogenic effect of c.833C is completely ified by the downstream insertion of a 68-bp duplicated portion of the intron 7/exon 8 junction (Fig. 1C). Although this insertion creates two intron 7 splice donor sites in close proximity, the splicing machinery strongly favors the use of the more distal splice donor site, thereby removing the upstream segment of exon 8 together with the c.833C mutation while preserving the rest [Romano et al., 2002; Sperandeo et al., 1996b; Tsai et al., 1996]. Consequently, both heterozygotes and homozygotes carrying the nonpathogenic c. [833C; 844_845ins68] chromosomes synthesize normal CBS mRNA molecules lacking the pathogenic r.833U > C mutation; these individuals therefore exhibit neither biochemical nor clinical signs of homocystinuria [Pepe et al., 1999; Tsai et al., 1996]. The nonpathogenic c. [833C; 844_845ins68] chromosomes are very common in sub-Saharan Africa (up to 40% of control chromosomes), less frequent throughout Europe and America (5–10% of control chromosomes) [Franco et al., 1998b; Pepe et al., 1999], and comparatively rare in Asia (0.16–2.5% of control chromosomes) [Song et al., 2001; Zhang and Dai, 2001].


Diversity of cystathionine beta-synthase haplotypes bearing the most common homocystinuria mutation c.833T>C: a possible role for gene conversion.

Vyletal P, Sokolová J, Cooper DN, Kraus JP, Krawczak M, Pepe G, Rickards O, Koch HG, Linnebank M, Kluijtmans LA, Blom HJ, Boers GH, Gaustadnes M, Skovby F, Wilcken B, Wilcken DE, Andria G, Sebastio G, Naughten ER, Yap S, Ohura T, Pronicka E, Laszlo A, Kozich V - Hum. Mutat. (2007)

Structure of the wild-type c. [833T; –] and c. [833C; 844_845ins68] CBS chromosomes. A:The genomic organization of the CBS gene, with exons depicted as numbered black boxes and the initiator ATG in exon 1 indicated by an upward-pointing arrow. Markers genotyped in this study are denoted by downward-pointing arrows. B: Boxed uppercase letters represent the sequence of wild-type exon 8. The lowercase sequence corresponds to flanking intronic regions. The thymidine residue at nucleotide position 833 is marked by an arrow. C:The sequence of the variant c. [833C; 844_845ins68] chromosome. The 68-bp insertion between nucleotides 844 and 845 is bracketed. Both the mutation c.833C in exon 8 and the wild-type thymidine 833 within the 68-bp insertion sequence are indicated by arrows. Motifs corresponding to DNA polymerase α/β frameshift hotspots and inverted repeats are shaded and underlined, respectively.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2630376&req=5

fig01: Structure of the wild-type c. [833T; –] and c. [833C; 844_845ins68] CBS chromosomes. A:The genomic organization of the CBS gene, with exons depicted as numbered black boxes and the initiator ATG in exon 1 indicated by an upward-pointing arrow. Markers genotyped in this study are denoted by downward-pointing arrows. B: Boxed uppercase letters represent the sequence of wild-type exon 8. The lowercase sequence corresponds to flanking intronic regions. The thymidine residue at nucleotide position 833 is marked by an arrow. C:The sequence of the variant c. [833C; 844_845ins68] chromosome. The 68-bp insertion between nucleotides 844 and 845 is bracketed. Both the mutation c.833C in exon 8 and the wild-type thymidine 833 within the 68-bp insertion sequence are indicated by arrows. Motifs corresponding to DNA polymerase α/β frameshift hotspots and inverted repeats are shaded and underlined, respectively.
Mentions: Only a small proportion of human chromosomes carry the pathogenic mutation c.833C on its own (henceforth referred to as c.[833C; –] chromosomes), whereas a much larger proportion contain a nonpathogenic combination of two mutations (termed c.[833C; 844_845ins68] chromosomes). In the latter chromosomes, the pathogenic effect of c.833C is completely ified by the downstream insertion of a 68-bp duplicated portion of the intron 7/exon 8 junction (Fig. 1C). Although this insertion creates two intron 7 splice donor sites in close proximity, the splicing machinery strongly favors the use of the more distal splice donor site, thereby removing the upstream segment of exon 8 together with the c.833C mutation while preserving the rest [Romano et al., 2002; Sperandeo et al., 1996b; Tsai et al., 1996]. Consequently, both heterozygotes and homozygotes carrying the nonpathogenic c. [833C; 844_845ins68] chromosomes synthesize normal CBS mRNA molecules lacking the pathogenic r.833U > C mutation; these individuals therefore exhibit neither biochemical nor clinical signs of homocystinuria [Pepe et al., 1999; Tsai et al., 1996]. The nonpathogenic c. [833C; 844_845ins68] chromosomes are very common in sub-Saharan Africa (up to 40% of control chromosomes), less frequent throughout Europe and America (5–10% of control chromosomes) [Franco et al., 1998b; Pepe et al., 1999], and comparatively rare in Asia (0.16–2.5% of control chromosomes) [Song et al., 2001; Zhang and Dai, 2001].

Bottom Line: We have sought to study the relationship between the pathogenic and nonpathogenic c.833C-bearing chromosomes and to determine whether the pathogenic c.[833C; -] chromosomes are identical-by-descent or instead arose by recurrent mutation.Initial haplotype analysis of 780 randomly selected Czech and sub-Saharan African wild-type chromosomes, employing 12 intragenic markers, revealed 29 distinct CBS haplotypes, of which 10 carried the c.[833C; 844_845ins68] combination; none carried an isolated c.833C or c.844_845ins68 mutation.Since c.833T does not reside within an obvious mutational hotspot, we surmise that the three pathogenic and comparatively prevalent c.[833C; -] chromosomes may have originated by recurrent gene conversion employing the common nonpathogenic c.[833C; 844_845ins68] chromosomes as templates.

View Article: PubMed Central - PubMed

Affiliation: Center for Applied Genomics, Institute of Inherited Metabolic Disorders, Charles University 1st Faculty of Medicine, Prague, Czech Republic.

ABSTRACT
Homozygosity or compound heterozygosity for the c.833T>C transition (p.I278 T) in the cystathionine beta-synthase (CBS) gene represents the most common cause of pyridoxine-responsive homocystinuria in Western Eurasians. However, the frequency of the pathogenic c.833C allele, as observed in healthy newborns from several European countries (q(c.833C) approximately equals 3.3 x 10(-3)), is approximately 20-fold higher than expected on the basis of the observed number of symptomatic homocystinuria patients carrying this mutation (q(c.833C) approximately equals 0.18 x 10(-3)), implying clinical underascertainment. Intriguingly, the c.833C mutation is also present in combination with a 68-bp insertion, c.[833C; 844_845ins68], in a substantial proportion of chromosomes from nonhomocystinuric individuals worldwide. We have sought to study the relationship between the pathogenic and nonpathogenic c.833C-bearing chromosomes and to determine whether the pathogenic c.[833C; -] chromosomes are identical-by-descent or instead arose by recurrent mutation. Initial haplotype analysis of 780 randomly selected Czech and sub-Saharan African wild-type chromosomes, employing 12 intragenic markers, revealed 29 distinct CBS haplotypes, of which 10 carried the c.[833C; 844_845ins68] combination; none carried an isolated c.833C or c.844_845ins68 mutation. Subsequent examination of 69 pathogenic c.[833C; -] chromosomes, derived from homocystinuria patients of predominantly European origin, disclosed three unrelated haplotypes that differed from their wild-type counterparts by virtue of the presence of c.833C, thereby indicating that c.833T>C transition has occurred repeatedly and independently in the past. Since c.833T does not reside within an obvious mutational hotspot, we surmise that the three pathogenic and comparatively prevalent c.[833C; -] chromosomes may have originated by recurrent gene conversion employing the common nonpathogenic c.[833C; 844_845ins68] chromosomes as templates.

Show MeSH
Related in: MedlinePlus