Molecular genetics of PKU in Eastern Europe: A nonsense mutation associated with haplotype 4 of the phenylalanine hydroxylase gene

Phenylketonuria (PKU) is a genetic disorder secondary to a deficiency of hepatic phenyalanine hydroxylase (PAH). Several mutations in thePAH gene have recently been reported, and linkage disequilibrium was observed between RFLP haplotypes and specific mutations. A new molecular lesion has been identified in exon 7 of thePAH gene in a Hungarian PKU patient by direct sequencing of PCR-amplified DNA. The C-to-T transition causes the substitution of Arg²⁴³ to a termination codon, and the mutant allele is associated with haplotype 4 of thePAH gene. The mutation is present in two of nine mutant haplotype 4 alleles among Eastern Europeans and is not present among Western Europeans and Asians. The rarity of this mutant allele and its restricted geographic distribution suggest that the mutational event occurred recently on a normal haplotype 4 background in Eastern Europe.     

Genetic diversity within the R408W phenylketonuria mutation lineages in Europe

The R408W phenylketonuria mutation in Europe has arisen by recurrent mutation in the human phenylalanine hydroxylase (PAH) locus and is associated with two major PAH haplotypes. R408W-2.3 exhibits a west-to-east cline of relative frequency reaching its maximum in the Balto-Slavic region, while R408W-1.8 exhibits an east-to-west cline peaking in Connacht, the most westerly province of Ireland. Spatial autocorrelation analysis has demonstrated that the R408W-2.3 cline, like that of R408W-1.8, is consistent with a pattern likely to have been established by human dispersal. Genetic diversity within wild-type and R408W chromosomes in Europe was assessed through variable number tandem repeat (VNTR) nucleotide sequence variation and tetranucleotide short tandem repeat (STR) allelic associations. Wild-type VNTR-8 chromosomes exhibited two major cassette sequence organizations: (a1)5-b3-b2-c1 and (a1)5-b5-b2-c1. R408W-1.8 was predominantly associated with (a1)5-B5-B2-C1. Both wild-type vntr-3 and r408w-2.3 chromosomes exhibited a single invariant cassette sequence organization, a2-b2-c1. STR allele distributions associated with the cassette variants were consistent with greater diversity in the wild-type VNTR-8 lineage and were suggestive of different levels of diversity between R408W-1.8 and R408W-2.3. The finding of greater genetic diversity within the wild-type VNTR-8 lineage compared to VNTR-3 suggests that VNTR-8 may be older within the European population. However, in the absence of a more extensive STR data-set, no such conclusions are possible for the respective R408W mutant lineages.     

DNA-based subtyping of glycogen storage disease type III: mutation and haplotype analysis of the AGL gene in Chinese

Glycogen storage disease type III (GSD III) is an inborn error of glycogen metabolism caused by a deficiency of glycogen debranching enzyme (AGL). Here, we investigate two unrelated Hong Kong Chinese GSD III patients and identify a novel 5-base pair deletional mutation, 2715_2719delTCAGAin exon 22, in one patient and a nonsense mutation, 1222C>T (R408X) in exon 11, in another patient. Since GSD IIIb is only caused by mutation in exon 3 of the AGL gene, we diagnose our patients to have GSD IIIa, which is consistent with the clinical diagnosis. Until now, R408X has only been reported in Faroe Islands GSDIII patients and was thought to demonstrate a founder effect. In this study, haplotyping of the disease-bearing chromosomes in the AGL locus by 19 intragenic single nucleotide polymorphisms shows that R408X is linked with IVS16+8T and IVS23-21T in our patient while R408X is linked with IVS16+8C and IVS23-21A in the Faroe Islands. The different haplotypes of R408X in Chinese and Faroese indicated that R408X is a recurrent mutation.     

CpG methylation accounts for a recurrent mutation (c.1222C>T) in the human PAH gene

The human PAH gene (GenBank: U49897.1 (cDNA), AF404777 (gDNA)) harbors alleles that either cause or are associated with hyperphenylalaninemia and phenylketonuria (http://www.pahdb.mcgill.ca). Mutation analysis has identified approximately 500 alleles of which approximately 30 produce polymorphic core haplotypes. The c.1222C>T allele (p.R408W) is the most prevalent and widely encountered PKU-causing allele. Because it occurs on multiple locus-specific polymorphic haplotypes, it is probably not identical by descent in different populations. This mutation involves a CpG dinucleotide in a so-called "hypermutable" codon suggesting that c.1222C>T could be a recurrent allele following spontaneous methylation-mediated deamination of 5 mC. This concept is widely assumed and accepted but the 5mC status of hypermutable codons has seldom been confirmed. We show that the PAH c.1222C nucleotide is indeed methylated (c.1222 mC) in somatic genomes (leukocyte and brain) of H. sapiens. Examination of a representative region in exon 12 (and also in exon 7) in the PAH gene shows that 5 mC is restricted to cytosines in CpG dinucleotides in the hypermutable codons. The methylation pattern seen in human PAH exon 12 was also observed in the corresponding codon in three nonhuman primates. The finding offers at least one explanation for the high relative frequency of the c.1222C>T (p.R408W) allele in the human population.     

Molecular basis of phenylketonuria in Venezuela: Presence of two novel null mutations

This report describes the mutational spectrum and linked haplotypes of the phenylalanine hydroxylase gene in Venezuela. In this study, we have detected European mutations such as IVS10nt-11, R243Q, and R408W on the same haplotype background (6.7, 1.8, and 2.3, respectively) as in Europe. In this sample, we have found two novel mutations: S349L detected in two homozygous siblings on the background of haplotype 6.7, and a small deletion, P314fsdelC, that results in a frameshift and a premature stop codon detected on the background of haplotype 4.3. The definite demonstration that mutation S349L results in a nonfunctional protein was shown by expression analysis in prokaryotic and eukaryotic systems. This mutation results in an unstable phenylalanine hydroxylase (PAH) protein completely devoid of enzymatic activity well correlated with the severe form of the disease exhibited by the homozygous patients. Hum Mutat 11:354–359, 1998. © 1998 Wiley-Liss, Inc.     

Mucopolysaccharidosis type I: characterization of a common mutation that causes Hurler syndrome in Moroccan subjects

A group of 13 Moroccan patients with MPS I and their families, including three siblings and twin siblings, was screened for mutations of the α- l -iduronidase gene using fluorescence-assisted mismatch analysis (FAMA) and cycle sequencing of PCR products. The P533R mutation, which is rare in Europeans, was identified in 92% of mutant alleles (24/26). This is the highest frequency of this mutation detected in patients with Hurler syndrome. None of the patients carried the W402X or Q70X alleles, the most common MPS I mutations in Europeans. These results suggest that the P533R mutation constitutes the genetic lesion which results in MPS I in people of Moroccan descent and provides yet more evidence for the uneven geographical distribution of mutations in MPS I.     

Genetic background of clinical homogeneity of phenylketonuria in Poland.

In order to elucidate the clinical homogeneity and severity of the hyperphenylalaninaemias in Poland, a total of 71 children with typical phenylketonuria (PKU) originating from western and northern Poland were screened for 13 mutations in the phenylalanine hydroxylase (PAH) gene. Eighty percent of all PKU alleles tested were found to carry an identified mutation. One mutation, namely the R408W mutation, accounted for more than 63% of mutant PAH alleles in Poland, the other 27% being accounted for by six mutations: IVS12nt1 (5%), IVSnt546 (5%), Y414C (4%), R252W (1.5%), R261Q (< 1%), and G272ter (< 1%). The predominance of the R408W mutation resulted in a high rate of homozygotes (35.2%) and compound heterozygotes for this mutation in children from western and northern Poland. The frequency and deleterious nature of this mutation probably accounts for the clinical homogeneity and severity of the hyperphenylalaninaemias in Poland. In addition, the high rate of the R408W mutation and its association with mutant haplotype 2 at the PAH locus in Poland give additional support to the Balto-Slavic origin of this mutant gene.     

Molecular heterogeneity at the phenylalanine hydroxylase locus in the population of the south-west of England.

The phenylalanine hydroxylase gene locus has been studied in 35 independent phenylketonuric families in the south-west of England using RFLP haplotype patterns and allele specific oligonucleotide probes. Haplotype 3 was the most common pattern on mutant chromosomes and there was strict linkage disequilibrium between this haplotype and the splice mutation in exon 12. The R408W mutation in exon 12 occurred on both haplotypes 1 and 2. The R126Q mutation in exon 7 was found only on a rare haplotype 28 pattern. No gene carried the R158Q mutation. More than 60% of mutant genes did not carry these four mutations which were originally described in other European populations. We suggest that the splice mutation arose as a single event and spread throughout northern Europe by population migration and admixture. In addition, we believe the haplotype/mutation associations seen in our population are a reflection of the mixed ancestry of the inhabitants of the British Isles.     

The FBN1 (R2726W) mutation is not fully penetrant

The R2726W mutation in the fibrillin 1 (FBN1, Marfan syndrome) gene segregates with isolated skeletal features of Marfan syndrome and/or high stature. Here we report a family in which two out of four individuals, an 18‐year‐old son and his mother, a 41‐year‐old woman, had the R2726W mutation of FBN1. Both family members carrying the mutation were of average height. The son had a Marfan‐like phenotype, but his mother did not. The FBN1 R2776W mutation, which is associated with skeletal features of Marfan syndrome, appears incompletely penetrant. Consequently, genetic counselling in the presence of this mutation is difficult.     

Evolution of the human RH (rhesus) blood group genes: a 50 year old prediction (partially) fulfilled [published erratum appears in Hum Mol Genet 1997 Aug;6(8):1390]

Almost exactly 50 years ago, R. A. Fisher and R. Race proposed a model for the evolution of the RH (rhesus) genes in which the less common haplotypes were derived from the commoner ones by recombination, and in which the gene order was D-C-E. No direct-evidence bearing on this model was available then, and has not been until now. Here we present evidence for non-reciprocal intergenic exchange (gene conversion) occurring once in human history to generate the common RHCE allele, Ce. We have also used new polymorphisms to construct haplotypes which suggest that intragenic recombination played a major role in the generation of the less common haplotypes, but only if RHD lies 3' of RHCE, i.e. the order is C-E-D. We provide both genetic and physical evidence supporting this arrangement.      

The molecular basis of phenylketonuria in Latvia

Characterization of the molecular basis of phenylketonuria (PKU) in Latvia has been accomplished through the analysis of 96 unrelated chromosomes from 50 Latvian PKU patients. Phenylalanine hydroxylase (PAH) gene mutations have been analyzed through a combined approach in which R158Q, R252W, R261Q, G272X, IVS10-11G>A and R408W mutations were first screened for by PCR or restriction generating PCR amplification of PAH gene exons 5, 7, 11 and 12 followed by digestion with the appropriate diagnostic enzyme. Subsequently 'broad range' denaturing gradient gel electrophoresis analysis of the 13 PAH gene exons has been used to study uncharacterized PKU chromosomes. A mutation detection rate of 98% was achieved. 12 different mutations were found, with the most frequent mutation, R408W, accounting for 76% of Latvian PKU alleles. Six mutations (R408W, E280K, R158Q, A104D, R261Q and P281L) represent 92% of PKU chromosomes. PAH VNTR and STR alleles have been also identified and minihaplotype associations with PKU mutations were also determined.     

A comprehensive study of phenylalanine hydroxylase gene mutations in the Iranian phenylketonuria patients

Phenylketonuria (PKU) is a metabolic disorder caused by mutations in the phenylalanine hydroxylase (PAH) gene. After thalassemia, PKU is considered as the most common autosomal recessive diseases in the Iranian population. Therefore, an efficient diagnostic strategy is required to identify disease-causing mutations in this population. Following our first report in 2003, here we presented a comprehensive study on the mutation spectrum of the PAH gene in the Iranian population. This study was performed on 280 unrelated chromosomes from 140 Iranian patients with classic PKU. All 13 exons as well as exon-intron boundaries of the PAH gene were analyzed by direct DNA sequencing. Thirty four different mutations were identified by a mutation detection rate of 100%. IVS10-11G > A, p.P281L, R261Q, p.F39del and IVS11+1G > C were the most prevalent mutations with frequencies of 26.07%, 19.3%, 12.86%, 6.07 and 3.93%, respectively. All other mutations represented a relative frequency less than 3.5%. The data from this study provided a comprehensive spectrum of the PAH gene mutations which can facilitate carrier detection and prenatal diagnosis of PKU disease in the Iranian population.     

Gene mutation and V(D)J recombination in the radiosensitive irs lines

lines irs1, irs2 and irs3, derived from V79-4 hamster cells,are sensitive to DNA-damaging agents including ionizing radiations.However, unlike some other radiosensitive lines, the irs linesshow no apparent defect in the repair of DNA strand breaks.We have now assessed the mis-repair of DNA damage in the irslines by measuring spontaneous and X-ray induced frequenciesof mutation in the HPRT gene, irsl was found to be hypermutable,showing instability in spontaneous mutant frequency and an elevationof the radiation-induced frequency relative to the parentalline. In contrast, irs2 and irs3 showed similar mutational responsesto the parental line. The results support other lines of evidencesuggesting that irs1 has a mis-repair phenotype. The irs2 linehas previously been shown to have a phenotype similar to cellsfrom the human disorder ataxia-telangiectasia and this similarityis maintained in their mutational response to X-rays. The irslines were also tested for ability to undergo V(D)J recombination,since this process has recently been found to be defective insome radiosensitive lines with impaired double-strand breakrepair. Using an extrachromosomal vector containing a V(D)Jrearrangement cassette, correct recombination was shown to occurat similar frequencies to parental V79-4 cells in each of thethree irs lines. Thus the irs lines indicate that processesother than DNA double-strand break repair also control radiosensitivity,in particular those processes which may affect the regulationof DNA repair.     

Haplotype analysis of Norwegian and Swedish patients with acute intermittent porphyria (AIP): Extreme haplotype heterogeneity for the mutation R116W

Acute intermittent porphyria (AIP), the most common of the acute porphyrias, is caused by mutations in the gene encoding hydroxymethylbilane synthase (HMBS) also called porphobilinogen deaminase (PBGD). The mutation spectrum in the HMBS gene is characterized by a majority of family specific mutations. Among the exceptions are R116W and W198X, with high prevalence in both the Dutch and Swedish populations. These two mutations were also detected in unrelated Norwegian patients. Thus, Norwegian and Swedish patients were haplotyped using closely linked flanking microsatellites and intragenic single nucleotide polymorphisms (SNPs) to see if the high frequency of these two mutations is due to a founder effect. Twelve intragenic SNPs were determined by a method based on fluorescent restriction enzyme fingerprinting single-strand conformation polymorphism (F-REF-SSCP). W198X occurred exclusively on one haplotype in both Norwegian and Swedish patients, showing that it has originated from a common gene source. In contrast, R116W was found on three different haplotypes in three Norwegian families, and in five Swedish families on four or five haplotypes. This extreme haplotype heterogeneity indicates that R116W is a recurrent mutation, maybe explained by the high mutability of CpG dinucleotides. This can also explain why it is the only AIP mutation reported to occur in seven different populations (Norway, Sweden, Finland, Netherlands, France, Spain and South Africa).     

Novel FGFR2 mutations in Crouzon and Jackson-Weiss syndromes show allelic heterogeneity and phenotypic variability

Mutations have been reported for several craniosynostotic disordersin exon Illa (exon U or 7) or Illc (exon B or 9) of the fibroblastgrowth factor receptor 2 gene (FGFR2). Among the conditionswith FGFR2 mutations are two autosomal dominant syndromes, Crouzonand Jackson–Weiss. In this study, 24 Crouzon and one Jackson–Weisssyndrome patients were screened for mutations in the two exonsby direct sequencing, and mutations were detected in 28% (7/25)of all cases. Five different mutations were found includingtwo novel (W290G, C342W) and two previously reported, recurrentmutations for Crouzon syndrome (A344A, S354C), and one new mutationfor Jackson-Weiss syndrome (C342R). The W290G mutation was foundin exon Illa which is common to both alternatively spliced formsof FGFR2, BEK (expressed predominantly in primordial bones)and KGFR (expressed preferentially in epithelia). Atypical Crouzonsyndrome features of epithelial-derived anal and/or externalear anomalies were present in the two affected family memberswith the mutation. This phenotype possibly reflects the expressionof both mutant BEK and KGFR. In addition, the Jackson-Weisssyndrome mutation, C342R, in exon Illc was observed previouslyin other craniosynostotic syndromes, Crouzon and Pfeiffer. Theseresults underscore the allelic heterogeneity of these conditionsand the complexity of the phenotypic consequences of FGFR2 mutations.     

Crouzon syndrome: mutations in two spliceoforms of FGFR2 and a common point mutation shared with Jackson--Weiss syndrome

Dominant mutations in the fibroblast growth factor receptor2 (FGFR2) gene have been recently identified as causes of fourphenotypically distinct craniosynostosis syndromes, includingCrouzon, Jackson—Weiss, Pfeiffer, and Apert syndromes.These data suggest that the genetics of the craniosynostosissyndromes is more complex than would be expected from theirsimple autosomal-dominant inheritance pattern. Identical mutationsin the FGFR2 gene have been reported to cause both Pfeifferand Crouzon syndrome phenotypes. We now report the finding ofa mutation in exon Illc of the FGFR2 gene in a kindred affectedwith Crouzon syndrome (C1043 to G; Ala344Gly) that is identicalto the mutation previously associated with Jackson—Weisssyndrome. We also report finding in a Crouzon kindred a mutationin the 3' end of exon Illu (formerly referred to as exon 5,exon 7, or exon U) (A878 to C; Gln289Pro) which encodes theamino terminal portion of the lg-like III domain of the FGFR2protein. This exon is common to both the FGFR2 and the KGFRspliceoforms of the FGFR2 gene, unlike all previously reportedCrouzon mutations, which have been found only in the FGFR2 spliceoform.These findings reveal further unexpected complexity in the moleculargenetics of these craniosynostosis syndromes. The data impliesthat second-site mutations in FGFR2 itself (outside of exonIllc) or in other genes may determine specific aspects of thephenotypes of craniosynostosis syndromes.     

The mutation spectrum of hyperphenylalaninaemia in the Republic of Ireland: the population history of the Irish revisited

Phenylketonuric and hyperphenylalaninaemic patients in the population of the Republic of Ireland were screened for mutations at the human phenylalanine hydroxylase (PAH) locus. A composite data set for the island of Ireland was generated by merging the findings of this study with extant data for Northern Ireland. Analysis of this data on the basis of the four historic provinces (Munster, Leinster, Connacht and Ulster) revealed genetic diversity that is informative in terms of demographic forces that shaped the Irish population. R408W, the predominant Irish PAH mutation associated with haplotype 1.8, reached its highest relative frequency in the most westerly province, Connacht. This suggests that the gradient of R408W-1.8 observed across north-western Europe continues into Ireland and peaks in Connacht. Spatial autocorrelation analysis demonstrated that the gradient is consistent with a localised cline of R408W-1.8 likely to have been established by human migration. This and parallel allele frequency clines may represent the genetic traces of the Palaeolithic colonisation of Europe, a pattern not substantially altered in north-western Europe by subsequent Neolithic migrations. An analysis of mutant allele distributions in Ulster, Scotland and the rest of Ireland confirmed that Ulster has been a zone of considerable admixture between the Irish and Scottish populations, indicating a proportion of Scottish admixture in Ulster approaching 46%. Mutations primarily associated with Scandinavia accounted for 6.1% of mutations overall, illustrating the influence of Viking incursions on Irish population history.     

127例PKU患者PAH基因第12外显子点突变及其频率研究

目的　了解中国人苯丙酮尿症 ( phenylketonuria,PKU)患者的苯丙氨酸羟化酶( phenylalanine hydroxylase,PAH)基因第 12外显子点突变种类和频率。方法　应用单链构象多态性( single strand conformation polymorphism,SSCP)、变性梯度凝胶电泳 ( denaturing gradient gelelectrophoresis,DGGE)、DNA测序分析了 12 7例 PKU患者的 PAH基因第 12外显子点突变种类及频率。结果　 DNA测序分析显示 10例患者存在 R4 13P、S4 11X、R4 0 8W、R4 0 8Q 4种杂合突变 ,其突变频率分别为 2 .76 %、0 .39%、0 .39%、0 .39% ,S4 11X突变为中国人中首次报道。 SSCP分析仅发现 2例 R4 13P杂合突变 ,DGGE分析显示 10例出现 3种类型的异常电泳带型。R4 13P突变在南北方人之间、在经典型 PKU和高苯丙氨酸血症之间的分布差异无显著性。结论　 DGGE对 PAH基因第 12外显子点突变检出率明显高于 SSCP。 DGGE结合 DNA测序是明确 PAH基因第 12外显子点突变种类和频率较好的方法。 R4 13P突变在南北方人中分布无明显差异     

Mutation spectrum and phenylalanine hydroxylase RFLP/VNTR background in 44 Romanian phenylketonuric alleles

The mutation spectrum and polymorphic haplotype background in 22 Romanian families have been analysed in this study using the restriction digestion of phenylalanine hydroxylase (PAH) regions specifically amplified or the DGGE/direct sequencing methods. Eleven PAH mutations specifically associated with six mutant haplotypes were detected. In spite of the relative heterogeneity of the molecular defects in the PAH gene, three mutations covered almost 70% of all alleles: R408W, 47.72%, 21/44; K363fsdelG 13.63%, 6/44; and P225T 6.81%, 3/44. Among these, R408W, the most frequent mutation in our population, represented 50% of all the phenylketonuric (PKU) chromosomes. Splice mutation IVS12nt1g→a affected two PAH alleles (4.54%); the remaining seven mutations were rare, each having an effect on just one chromosome (1/44), resulting in a relative frequency of 2.27%. A high frequency was observed in our PKU samples for the relatively uncommon mutations, K363fsdelG and P225T mutation, suggesting a possible founder effect at origin. Within the investigated panel, these mutations, both very rare among other Caucasians were exclusively linked to haplotype 5.8 and 1.7, respectively. These results provide a basis for the development of a routine molecular analysis of Romanian PKU families. Hum Mutat 12:314–319, 1998.© 1998 Wiley-Liss, Inc.