Genetic study of the PAH locus in the Iranian population: familial gene mutations and minihaplotypes

Abstract

Phenylketonuria (PKU), one of the most common inborn errors of amino acid metabolism, is caused by mutations in the phenylalanine hydroxylase (PAH) gene (PAH). PKU has wide allelic heterogeneity, and over 600 different disease-causing mutations in PAH have been detected to date. Up to now, there have been no reports on the minihaplotype (VNTR/STR) analysis of PAH locus in the Iranian population. The aims of the present study were to determine PAH mutations and minihaplotypes in Iranian families with PAH deficiency and to investigate the correlation between them. A total of 81 Iranian families with PAH deficiency were examined using PCR-sequencing of all 13 PAH exons and their flanking intron regions to identify sequence variations. Fragment analysis of the PAH minihaplotypes was performed by capillary electrophoresis for 59 families. In our study, 33 different mutations were found accounting for 95% of the total mutant alleles. The majority of these mutations (72%) were distributed across exons 7, 11, 2 and their flanking intronic regions. Mutation c.1066-11G > A was the most common with a frequency of 20.37%. The less frequent mutations, p.Arg261Gln (8%), p.Arg243Ter (7.4%), p.Leu48Ser (7.4%), p.Lys363Asnfs*37 (6.79%), c.969 + 5G > A (6.17%), p.Pro281Leu (5.56), c.168 + 5G > C (5.56), and p.Arg261Ter (4.94) together comprised about 52% of all mutant alleles. In this study, a total of seventeen PAH gene minihaplotypes were detected, six of which associated exclusively with particular mutations. Our findings indicate a broad PAH mutation spectrum in the Iranian population, which is consistent with previous studies reporting a wide range of PAH mutations, most likely due to ethnic heterogeneity. High prevalence of c.1066-11G > A mutation linked to minihaplotype 7/250 among both Iranian and Mediterranean populations is indicative of historical and geographical links between them. Also, strong association between particular mutations and minihaplotypes could be useful for prenatal diagnosis (PND) and preimplantation genetic diagnosis (PGD) in affected families.

The status of PAH gene-VNTR alleles and mini-haplotypes associations with PAH gene mutations in Iranian Kurdish PKU patients

“…Unfortunately, the data on mini-haplotypes were linked to IVS2+5G>C and IVS9+5G>A, as the most frequent mutations in individuals with PKU in Kermanshah province, are rare in the literature (Table 5). In the present study, IVS2+5G>C and IVS9+5G>A mutations were strongly associated with mini-haplotype 9/242 and 8/238, respectively that are compatible with the results of Razipour et al (12). The IVS10−11G>A is a common mutation in parts of Southern Europe and in Mediterranean countries and Iran (20).…”

“…Due to a Mendelian fashion inheritance and high polymorphic nature, these last 2 genetic markers could be used to give a risk estimation of linked defective alleles, alone or in combination. Moreover, this VNTR may prove useful in studies on the origins and distributions of PAH mutations in different human populations (3,12,13). According to our previous studies (16)(17)(18)(19)(20), there are at least 15 different PAH-causing mutations, including 2 novel mutations, possibly specific to Kurdish population, among phenylketonuria patients in Kermanshah province.…”

“…Along with a large number of informative haplotypes derived from PAH locus polymorphic markers, including several RFLPs, a VNTR, and a series of short tandem repeats or STRs of tetra-nucleotides TCTA (12)(13)(14), a VNTR/STR mini-haplotype was developed (3,12,15). Due to a Mendelian fashion inheritance and high polymorphic nature, these last 2 genetic markers could be used to give a risk estimation of linked defective alleles, alone or in combination.…”

Experiences with offering pro bono medical genetics services in the West Indies: Benefits to patients, physicians, and the community

“…References: 1 (Wardeh et al, 2018); 2 (Miyake et al, 2005); 3 (Thompson et al, 2020); 4 (Helbig et al, 2016), 5 (Ope et al, 2020), 6 (Chang et al, 2013), 7 (Kim et al, 2000), 8 (Jiao et al, 2019), 9 (Zarate et al, 2018), 10 (Zurflüh et al, 2008), 11 (Razipour et al, 2017), 12 (Hoffbuhr et al, 2001), 13 (Yuen, Guella, Roland, Sargent, & Boelman, 2019). …”

Molecular-genetic causes for the high frequency of phenylketonuria in the population from the North Caucasus

“…Authors from Japan, who first described the variant p.Arg261*, identified the association of this variant with haplotype 2 [ 25 ]. In Iran, where the allele frequency of variant p.Arg261* is 4.9%, PAH mini-haplotypes have been analyzed (8/230) [ 26 ], and they did not match those of the Karachays. Nevertheless, it is obvious that the variant R261* has a common origin in the Karachays individuals studied.…”