Population genetics of phenylketonuria

Phenylketonuria (PKU) is an autosomal recessive disorder caused by a large number of mutations at the phenylalanine hydroxylase (PAH) locus, most of which are strongly associated with specific RFLP or VNTR haplotypes. One of the major questions remaining in PKU research is why this apparently maladaptive disorder has been maintained at a frequency of approximately 1 in 10000 among Caucasians. A growing number of studies have provided evidence that both the relatively high frequency of PKU and the strong mutation/haplotype associations might reflect the existence of multiple founding populations for PKU. Examples of putative founding populations for PKU in both Europe and Asia will be presented. Some PAH mutations are associated with multiple haplotypes, suggesting recurrence. Evidence for and against recurrence as the mechanism responsible for the association of the R408W mutation with RFLP haplotypes 1 and 2 will be discussed.     

北京地区苯丙酮尿症基因突变构成及基因型与表型相关分析

目的 明确北京地区苯丙酮尿症(phenylketonuria,PKU)患儿苯丙氨酸羟化酶基因(phylalanine hydroxylase gene,PAH)突变图谱及其突变基因的微单体型(STR/VNTR)构成,探讨突变基因型与生化代谢表型的相关关系.方法 应用PCR/SSCP、序列分析和变性凝胶电泳等技术,对50例北京地区PKU患儿及其父母,进行PAH基因的全部外显子及两侧的内含子序列和STR与VNTR多态性分布的分析.依据由基因型预测生化代谢表型的方法进行基因型与生化代谢表型的相关关系分析.结果 (1)共检测到34种PAH突变基因,总的检出率为95%;较为常见的突变有R243Q(20%)、EX6-96A＞G(11%)、Y356X(9%)和V399V(7%),其次是R111x(5%)、R413P(5%)、R252Q(3%)和A434D(3%).(2)北京地区PKU患儿的STR杂合度较高,共检测出8种等位基因,以240 bp(34%)和244 bp(44%)最为常见;而VNTR的杂合度较低,只检测到3种等位基因,以VNTR3(83%)最为常见.(3)由基因型预测的生化代谢表型与患儿实际的生化代谢表型之间一致率为81.5%,在经典型PKU中一致率达到87.5%.结论 (1)北京地区共有34种PAH基因突变,检出率为95%,以R243Q、EX6-69A＞G、Y356X和V399V突变为常见突变.(2)PAH突变基因的微单位(STR/VNTR)构成以240/3和244/3最为常见.(3)PKU患儿基因型与生化代谢表型之间存在较好的相关关系,一致率达到80%以上.     

糖原累积病Ⅲ型十例AGL基因突变研究

目的 研究糖原累积病Ⅲ型(glycogen storage diseases type Ⅲ,GSD Ⅲ)患者糖原脱支酶AGL基因突变情况.方法 采用PeR、DNA直接测序法,对临床表现为肝大、低血糖、生长落后、运动耐力下降的10例GSDⅢ患者的糖原脱支酶基因进行突变检测.检出突变的片段再经DNA双向测序证实.采用限制性内切酶片段长度多态性和荧光PCR结合基因扫描方法证实5个新突变.结果 10例患者中共检出13种突变类型,包括4种剪切突变:IVS6+1G>A、IVS6-1G>A、IVS14+1G>T、IVS26-2A>C;5种无义突变:R469X、R864X、S929X、R977X、Y1428X;3种缺失突变:c.408-411delTTTG、c.2717-2721delAGATC、c.2823delT;1种插入突变:c.4234insT.除IVS14+1G>T、R864X和R977X,其余10种均未见报道过.限制性内切酶片段长度多态性分析证实了3个新剪切突变,荧光PCR结合基因扫描方法证实2个缺失突变的缺失碱基数.2例患者仪检出1个致病突变,其余患者均明确有2个致病突变,突变检出率为90%.IVS14+1G>T突变频率最高,占25%.结论 10例GSDⅢ型患者的糖原脱支酶基因突变呈高度异质性,发现13种突变,其中10种是新突变,IVS14+1G>T是较常见的突变类型.     

In vivo assessment of mutations in the phenylalanine hydroxylase gene by phenylalanine loading: Characterization of seven common mutations

Abstract Mutations in the gene encoding phenylalanine hydroxylase (PAH) cause persistent hyperphenyl-alaninaemia. To date, more than 200 point mutations and microdeletions have been characterized. Each mutation has a particular quantitative effect on enzyme activity and recessive expression of different mutant alleles results in a marked interindividual heterogeneity of metabolic and clinical phenotypes. In this paper we demonstrate how a simple clinical test can be used to evaluate the correlation between mutation genotype and phenylalanine metabolism. In hyperphenylalaninaemic patients with known PAH mutation genotype, we have investigated phenylalanine turnover in vivo by measuring the ability to eliminate a test dose ofl-phenyl-alanine. All patients could be considered functionally hemizygous for one of their mutant alleles by carrying on the other allele a mutation that is known to completely abolish PAH activity and encode a peptide with no immunoreactivity. Seven mutations (R408W, IVS-12nt1, R261Q, G46S, Y414C, A104D, and D415N) were characterized by oral phenylalanine loading, each mutation being represented by at least three patients. The elimination profile determined for a 3-day period provides a measure to compare residual activity of the mutant proteins and to assign each mutation to a particular metabolic phenotype. The established relation between genotype and phenotype may enable prediction of the severity of the disease by genotype determination in the newborn period. This will aid in the management of hyperphenylalaninaemia and may improve prognosis.Conclusion The possibility of predicting the residual enzyme activity by DNA analysis performed already in the newborn period allows the prompt implementation of a diet that is adjusted to the degree of PAH deficiency. This may improve management and prognosis of hyperphenylalaninaemia.     

Automated sequencing detects all mutations in Northern Irish patients with phenylketonuria and mild hyperphenylalaninaemia

In the first phase of the Northern Ireland PKU Study, we used automated sequencing to identify the spectrum of mutations in a random group of 32 unrelated phenylketonuria (PKU) families. We also investigated 7 Northern Irish patients with mild hyperphenylalaninaemia not requiring dietary intervention (MHP, previously referred to as non-PKU HPA). Disease-causing mutations were identified on all 78 investigated chromosomes. We found 23 different mutations, including 20 missense, 1 nonsense and 2 splice site mutations. All mutations were located within exons or at intronexon boundaries of the phenylalanine hydroxylase gene. Seven mutations occurred at CpG sites, confirming these sites as mutation hot-spots in PKU. Mutations R408W and I65T are the two commonest PKU mutations in the Northern Irish population. Two mutations (T380M and V245A) can be characterized as MHP mutations; they are quasi dominant markers for MHP since they cause mild hyperphenylalaninaemia even when occurring in conjunction with the most severe PKU mutations. The results have proven valuable for the development of a routine PKU mutation analysis system in Northern Ireland.     

PKU and NON-PKU Hyperphenylalaninemia: Differentiation, Indication for Therapy and Therapeutic Results

The differential diagnosis of phenylalanine hydroxylase deficiency (PAHD) by biochemical methods is difficult. Using standardized oral protein loading or the intravenous deuterated phenylalanine (phe) load in 46 patients with PAHD, three groups could be distinguished: 1) Phenylketonuria (PKU) with plasma phe levels over 20 mg% under the protein load and with residual activities of less than 1% of normal; 2) mild PKU with plasma phe of 10–20 mg% and residual enzyme activities of 1–3%; 3) Non-PKU hyperphenylalaninemia with plasma phe levels of less than 10 mg% and residual enzyme activities of more than 3%. Psychomotor development in 32 untreated patients with PAHD showed that there is a high risk of brain damage for all patients with in vivo residual activities of less than 3% of normal. Restriction fragment length polymorphism (RFLP) haplotypes at the phenylalanine hydroxylase (PAH) locus in 60 German patients with PAHD showed that 90% of the mutant alleles are confined to four distinct haplotypes. Using an oligonucleotide probe for the splicing mutation associated with mutant haplotype 3 a close association between the mutation and the haplotype 3 has been observed. There is also an association between haplotypes 2 and 3 and PKU patients with residual enzyme activities of less than 1%. However, in only 37% of our patients with PAHD could a direct diagnosis of the mutations in the PAH gene be made. More knowledge of other mutations in the PAH gene is necessary to differentiate patients with PAHD on the DNA level.     

苯丙酮尿症患儿苯丙氨酸羟化酶基因突变的研究

目的了解宁夏地区苯丙酮尿症(PKU)儿童苯丙氨酸羟化酶(PAH)基因突变的特征。方法以经新生儿疾病筛查及气相色谱-质谱联用技术确诊的30例宁夏PKU儿童为病例组,30例正常儿童为对照组,应用PCR技术扩增PAH基因的3、5、6、7、11和12,六个外显子,再经单链构象多态性分析和DNA测序分析PCR扩增产物。结果在60个等位基因中检出51个突变基因,检出率85%;六个外显子共检出16种致病突变,包括8种错义突变(R241C、R243Q、R252Q、G 257 V、R359K*、R408Q、R 413 P、Q419R),3种剪接突变(IVS 4-1 GA、Y 204 C、IVS 7+2 TA),3种无义突变(R 111 X、Q160X、Y356X),1种同义突变(V399V)和1种缺失突变(N183del);R243Q突变频率最高,检出率为18.3%,其次是Y 204 C(11.7%)、IVS 4-1 GA(10.0%)、R 111 X(6.7%)和IVS 7+2 TA(6.7%)。病例组中发现Exon 6的N183del(C.547-549del GAA)缺失突变和Exon 11的R359K(C.1078GA)错义突变,为国内首次发现;病例组和对照组中均检出V245V(C.735GA)和Q232Q(C.696AG)两种静止突变,且差异无统计学意义(P0.05)。结论宁夏PKU儿童PAH基因六个外显子最常见的突变类型是错义突变,特别是R243Q;发现中国人群PAH基因的2种新的突变。     

Direct detection of a major mutation responsible for phenylketonuria in the population of the Federal Republic of Germany

Forty-six individuals having phenylketonuria (PKU) alleles at the phenylalanine hydroxylase (PAH) locus were tested for the haplotype 2 PKU mutation by allele-specific hybridization following in vitro DNA amplification. Patients and carriers previously shown to have a mutant haplotype 2 PAH allele demonstrated conservation of this mutation. In vitro DNA amplification greatly facilitated this analysis and provides the possibility of population screening for 37% of the mutant German PAH alleles.     

Relation between genotype and phenotype in Swedish phenylketonuria and hyperphenylalaninemia patients

Phenylketonuria (PKU) and hyperphenylalaninemia (HPA) are caused mostly by an inherited (autosomal recessive) deficiency in hepatic phenylalanine hydroxylase (PAH) activity. More than 50 PAH mutations have ben reported. The goal of the present study was to examine the molecular basis for the clinical heterogeneity of Swedish PKU and HPA patients. Mutations were identified through allele-specific oligonucleotide hybridization or DNA sequencing on 128 of the 176 mutant alleles (73%). Three mutations (R408W, Y414C and IVS12) together accounted for 56% of all mutant alleles and ten relatively infrequent mutations were found on another 17% of all mutant alleles. Patients from 50 of the 88 families (57%) had identified mutations in both PAH genes and allowed use to compare the clinical effects of different combinations of PAH mutations. The in vitro activity of all of these mutations, including the newly identified G272X and L364, have been tested in a eukaryotic expression system. There was a strong relationship between the average in vitro PAH activity of the two mutant enzymes and both the phenylalanine tolerance and the neonatal pretreatment serum phenylalanine concentration. This confirms previous observations in Danish and German PKU patients that disease phenotype is a consequence of the nature of the mutations at the PAH locus and not significantly influenced by other loci. The sample population in the previous study did not, however, include mild HPA patients, and the observed correlation is thus restricted to severe and moderate mutant alleles. Since a comparatively high proportion of the Swedish patients were mildly affected, we have provided additional evidence that this correlation is valid throughout a continuous spectrum of clinical varieties. PAH genotyping could therefore help predict prognosis of a recently diagnosed PKU or HPA child.     

A prevalent missense mutation in Northern Europe associated with hyperphenylalaninaemia

A missense mutation has been identified in the phenylalanine hydroxylase (PAH) gene of a Danish patient with hyperphenylalaninaemia (HPA). An A-to-G transition at the second base of codon 414 results in the substitution of Cys for Tyr in the mutant PAH protein. In in vitro expression studies, the Tyr⁴¹⁴-to-Cys⁴¹⁴ mutant construct produced a protein which exhibited a significant amount of normal PAH enzyme activity, which is consistent with both in vitro and in vivo measurements of PAH activity in HPA patients. Population genetic studies reveal that this mutation is present on 50% of mutant haplotype 4 chromosomes in the Danish population. Together with the previously reported codon 158 mutation, these two mutant alleles comprise over 90% of all mutant haplotype 4 chromosomes in the Northern Europcan population. Thus, two allele-specific oligonucleotide probes can detect most mutant haplotype 4 chromosomes in Northern Europe.     

Identification of frequency and distribution of the nine most frequent mutations among patients with 21-hydroxylase deficiency in Turkey

Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders mainly due to defects in the steroid 21-hydroxylase (CYP21A2) gene. METHODS: To determine the mutational spectrum in the Turkish population, the CYP21A2 active gene was analyzed in 100 unrelated patients with the classical form of 21-hydroxylase deficiency using PCR and RFLP. RESULTS: Mutations were detected in 78 patients: 64 patients were homozygous for one mutation, seven patients were compound heterozygous with different mutations on each chromosome, two patients were homozygous for two different mutations, five patients were heterozygous, and 22 patients harbored none of the tested mutations. The most frequent mutation was IVS2-13A/C (28.5%), followed by large gene deletion (17%), Q318X (11.5%), I172N (4%), V281L (3.5%), R356W (3.5%), 8-bp (3%), complex alleles (2%), P30L (1%) and E6 cluster (1%). CONCLUSION: The distribution of mutation frequencies in our study was slightly different from those previously reported in Turkey and in other parts of the world.     

Phenylketonuria genotypes correlated to metabolic phenotype groups in Norway

In order to establish a genotype-phenotype relationship, we have identified both mutant phenylalanine hydroxylase (PAH) genes in 108 phenylketonuria (PKU) patients (27 different alleles, 54 different genotypes). One major group of patients with very high pretreatment phenylalanine values (classical PKU) exclusively comprised homozygotes of the PKU mutations I65T, G272X, F299C, Y356X, R408W, IVS12nt1, and compound heterozygotes of various combinations of these alleles with G46S, R261Q, R252W, A259T, R158Q, D143G, R243X, E280 K, or Y204C. A second major group of patients with lower phenylalanine values (mild PKU) comprised mutations A300S, R408Q, Y414C in various compound heterozygous states, and R261Q, R408Q, Y414C in homozygotes. The phenylalanine values in these groups were non-overlapping. In addition, a smaller group of patients formed the transition between the two main groups. In sib pairs 4 of 15 had discordant pretreatment phenylalanine values.     

Mutation analysis of the phenylalanine hydroxylase gene using heteroduplex analysis with synthetic DNA constructs

Using heteroduplex analysis generated with synthetic PCR-amplifiable DNA we have screened the PKU populations of southwest England and Wales, western Scotland, and southeast and central England for mutations in exons 3, 7 and 12 of the phenylalanine hydroxylase (PAH) gene. The technique characterized three mutations in exon 12, two in exon 3 and five in exon 7. Altogether over 370 PKU chromosomes were screened. In all geographical regions exon 12 mutations (R408W, IVS12ntlg- > a and Y414C) accounted for about 40% of mutant chromosomes. Exon 3 mutations (principally I65T) were found on between 9 and 12% of mutant alleles and exon 7 mutations accounted for a further 5-7%. Heteroduplex analysis is rapid, simple and safe and three constructs covering three exons can identify between 55 and 60% of mutations in various PKU populations of the UK.     

宁夏苯丙酮尿症患儿苯丙氨酸羟化酶基因外显子7突变分析

目的 探讨宁夏地区苯丙酮尿症（PKU）患儿苯丙氨酸羟化酶（PAH）基因外显子7 突变类型及频率,为该地区PKU 的基因诊断和产前诊断提供依据。方法 应用PCR 产物直接测序方法,对宁夏73 例经典型PKU 患儿（回族39 例,汉族34 例）的146 个PAH 等位基因外显子7 及其旁侧内含子区域进行序列分析。结果 共检测出6 种突变基因型,分别是R243Q（14.4%）、R241C（6.8%）、IVS7+2T → A（2.7%）、L255S（0.7%）、G247V（0.7%）和G247R（0.7%）。外显子7 突变基因总频率为26.0%（38/146）,包括错义突变和剪接位点突变两种。回族患儿R241C 等位基因突变检出率高于汉族（10% vs 3%,P<0.05）。结论 宁夏地区PKU 患儿PAH 基因外显子7 突变频率最高的是R243Q,其次为R241C;回族和汉族PKU 患儿R241C 等位基因突变率不同。     

Association between haplotypes, Hind III-VNTR alleles and mutations at the PAH locus in Sicily

In this study we report previously undescribed associations between mutations, haplotypes and a minisatellite polymorphism (Hind III VNTR) of the PAH gene in the Sicilian population. Analysis of the association between mutations and linked polymorphisms between Sicilians and other Mediterranean populations may be a useful tool to study the time-space origin of mutant PAH genes in Southern Europe.     

Correlation between polymorphic DNA haplotypes at phenylalanine hydroxylase locus and clinical phenotypes of phenylketonuria

Eight polymorphic sites for seven restriction endonucleases have been reported at the human phenylalanine hydroxylase locus. The composite profile of the presence or absence for each of the eight polymorphic sites within an allele defines the haplotype of the corresponding allele. Twelve such haplotypes associated with normal and mutant phenylalanine hydroxylase alleles have been identified in 33 Danish families with children with phenylketonuria. Of the 66 mutant alleles analyzed, 59 (89%) were associated with only four haplotypes. The identification of individual phenylalanine hydroxylase alleles by haplotype analysis enables correlation of the hyperphenylalaninemic phenotypes of the patients with their genotypes. Patients who were either homozygous or heterozygous for the mutant alleles of haplotypes 2 and 3 had a severe clinical course. Patients who had a mutant allele of either haplotype 1 or 4 usually had a less severe clinical phenotype. The recent demonstration that the mutation responsible for classic phenylketonuria associated with haplotype 3 is not present in mutant alleles of other haplotypes provides unambiguous evidence that there are multiple mutations in the phenylalanine hydroxylase gene and supports the hypothesis that different combinations of mutant alleles may be responsible for the clinical diversity of phenylketonuria.     

青海地区苯丙酮尿症患者苯丙氨酸羟化酶基因突变分析

目的 明确青海地区苯丙酮尿症患者苯丙氨酸羟化酶(PAH)基因的突变特征,为该地区苯丙酮尿症(PKU)的产前诊断和遗传咨询提供理论依据。方法 选取2006年1月至2012年12月经新生儿疾病筛查及门诊遗传咨询发现并确诊的49例青海地区PKU患儿为研究对象,应用PCR产物直接测序法对49例PKU患儿及其父母的PAH基因启动子、第1~13外显子及其旁侧内含子区域进行基因突变分析。结果 在98个PAH等位基因中检测出30种、共计80个不同的突变基因,总检出率为82%(80/98),主要包括19种错义突变(63%)、5种无义突变(17%)、3种剪切位点突变(10%)和3种缺失突变(10%),大部分突变集中在第3、6、7、11外显子及第4内含子区域,常见的4种突变是p.R243Q(19%)、IVS4-1G>A(9%)、p.Y356X(7%)和p.EX6-96A>G(5%);p.N93fsX5(c.279-282delCATC)、p.G171E(c.512G>A)突变是国际上未见报道的新的PAH基因突变,p.H64fsX9(c.190delC)突变为国内第2次报道。青海地区PAH基因的突变构成有一部分与北方各省份相似,与中国南方部分省区及日本、欧洲等国家差异显著。结论 青海地区表现出多民族聚居地区PAH基因突变特有的多样性和复杂性。     

Association between haplotypes and specific mutations in Swiss cystic fibrosis families.

Cystic fibrosis (CF) is the most common severe autosomal recessive genetic disorder in Caucasian populations, with an incidence of about 1 in 2000 live births, implying a carrier frequency of about 1 in 22. In 1989, the CF gene was isolated and characterized and the major mutation (delta F508), a 3-bp deletion that results in the loss of a phenylalanine residue at position 508, was detected. To determine the frequency of the delta F508 mutation and the predicted number of additional mutations in our population, we have undertaken a collaborative study of 215 CF patients and 175 CF parents in Switzerland. The delta F508 mutation in exon 10 has been found in 70% of the CF chromosomes, and the exon-11 mutation R553X seems to be the second most common CF mutation in our population, with a frequency of 5.3%, whereas the G551D mutation (also in exon 11) has not been detected at all. Haplotype determination of 430 CF and 175 normal chromosomes using XV-2c, KM19, MP6d-9, and J3.11 has been proven to be very helpful in providing additional carrier risk calculations: Haplotypes 1 (1221), 2 (1222), 6 (2111), and 7 (2221) increase the risk of being a carrier from 1 in 55 (haplotype 6) to 1 in 17 (haplotype 1), whereas haplotypes 3 (1122), 4 (1112), 8 (2222) and 10 (1111) lower the risk from 1 in 144 (haplotype 3) to 1 in 1678 (haplotype 10). Moreover, the mutation R553X shows strong correlation with haplotype 3, leading to the suggestion that haplotypes 1, 2, 5, and 6 may account for four additional mutations in Switzerland.(ABSTRACT TRUNCATED AT 250 WORDS)     

First study of CF mutations in the CFTR gene of Iranian patients: detection of DeltaF508, G542X, W1282X, A120T, R117H, and R347H mutations

Thirty-seven unrelated Iranian CF families were screened for the presence of seven common mutations (DeltaF508, G542X, W1282X, G551D, N1303K, 1717-1G-->A, and 621-1G-->T) using ARMS PCR and exons 4 and 7 of the CFTR gene by SSCP method. This study resulted in the identification of 26.8 per cent of all CF alleles: DeltaF508 (16.2 per cent), W1282X (4 per cent), G542X (2.7 per cent), R117H (1.3 per cent), R347H (1.3 per cent), and A120T (1.3 per cent) mutations were detected. To the best of our knowledge, it is the first report of an Asian subject carrying the A120T mutation. Our findings suggest heterogeneity in the Iranian population, stressing the need to draw attention to sequence analysis in order to find population-specific mutations.