Mutation spectrum of PAH gene in phenylketonuria patients in Northwest China: identification of twenty novel variants
This study was performed to analyze the mutational spectrum of the phenylalanine hydroxylase (PAH) gene in phenylketonuria (PKU) patients in Northwest China, to identify mutational hot spots, and to determine the correlation between variants and clinical phenotypes of PKU. A large cohort of 475 PKU families in Northwest China was enrolled to analyze PAH gene variants using Sanger sequencing, Multiplex ligation-dependent probe amplification (MLPA), and gap-PCR. Bioinformatics software was used to predict the pathogenicity of novel variants and analyze the correlations between PAH gene variants and phenotypes of PKU patients. A total of 895 variants were detected in the 950 alleles of 475 patients with PKU (detection rate: 94.21%), 20 of which were novel variants. Other 108, previously known variants, were also identified, with the three most frequent variants being p.Arg243Gln (14.00%), c.611A > G (5.58%), and p.Tyr356* (4.95%). Seven different large deletion/duplication variants were identified by the MLPA method, including the large deletion c.-4163_-406del3758 with high frequency. A correlation analysis between patient phenotype and gene variant frequency showed that p.Arg53His and p.Gln419Arg were correlated with mild hyperphenylalaninemia (MHP). In conclusion, the mutational spectrum underlying PKU in Northwest China was established for the first time. Functional analysis of 20 novel PAH gene variants enriched the PAH gene mutational spectrum. Correlation analysis between variants frequencies in compound heterozygous patients and phenotype severity is helpful for phenotypic prediction.
KeywordsPhenylketonuria Phenylalanine hydroxylase Sanger sequencing MLPA Gap-PCR Gene variant
We would like to thank Professor Shangzhi Huang (from Chinese Academy of Medical Sciences & Peking Union Medical College) for his guidance and precious suggestions of this research, and thank the patients and their families for their participation and valuable blood samples.
This study was supported by National Key Research and Development Program of China (Grant No.: 2016YFC1000307, and 2018YFC1002201) and Natural Science Foundation of Gansu Province (Grant No.: 1606RJZA151).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
All procedures performed in this study involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
Informed consent was obtained from all individual participants included in this study.
- Bercovich D, Elimelech A, Zlotogora J, Korem S, Yardeni T, Gal N, Goldstein N, Vilensky B, Segev R, Avraham S, Loewenthal R, Schwartz G, Anikster Y (2008) Genotype-phenotype correlations analysis of mutations in the phenylalanine hydroxylase (PAH) gene. J Hum Genet 53(5):407–418CrossRefGoogle Scholar
- den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PEM, on behalf of the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organisation (HUGO) (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum Mutat 37(6):564–569CrossRefGoogle Scholar
- Dobrowolski SF, Heintz C, Miller T, Ellingson C, Ellingson C, Özer I, Gökçay G, Baykal T, Thöny B, Demirkol M, Blau N (2011) Molecular genetics and impact of residual in vitro phenylalanine hydroxylase activity on tetrahydrobiopterin responsiveness in Turkish PKU population. Mol Genet Metab 102(2):116–121CrossRefGoogle Scholar
- Gao WH et al (2011) Study on the mutations of phenylalanine hydroxylase gene in patients with phenylketonuria in Shanxi Province. Chin J Med Genet 28(4):393–396Google Scholar
- Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, Chui D, Scriver C, Phommarinh M, Patnaik SK, Blumenfeld O, Gottlieb B, Vihinen M, Väliaho J, Kent J, Miller W, Hardison RC (2007) PhenCode: connecting ENCODE data with mutations and phenotype. Human Mutat 28(6):554–562CrossRefGoogle Scholar
- Gu XF, Wang ZG (2004) Screening for phenylketonuria and congenital hypothyroidism in 5.8 million neonates in China. Chin J Prev Med 38(2):99–102Google Scholar
- Guo HJ, Zhao ZH, Jiang M, Shi HR, Kong XD (2011) Mutation analysis of phenylalanine hydroxylase gene in patients with phenylketonuria in Henan Province. Chin J Med Genet 28(2):142–146sGoogle Scholar
- He J, Xu FL, Wang HZ, Yang X, Wang R, Zou HY, Yu WZ (2015) Mutation analysis of the phenylalanine hydroxylase gene in patients with phenylketonuria in Han ethnic group of Qinghai Province, China. Chin J Reprod Heal 26(6):512–517Google Scholar
- Lu CX et al (2011) Mutation analysis of phenylalanine hydroxylase gene in 55 patients with phenylketonuria from Hebei Province. Natl Med J China 91(42):2971–2976Google Scholar
- Qiang R et al (2014) Mutations of the phenylalanine hydroxylase gene in phenylketonuria patients from Shaanxi. Chin J Med Genet 31(1):74–77Google Scholar
- Song W, Gardner SA, Hovhannisyan H, Natalizio A, Weymouth KS, Chen W, Thibodeau I, Bogdanova E, Letovsky S, Willis A, Nagan N (2016) Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification. Genet Med 18(8):850–854CrossRefGoogle Scholar
- Wang X, Hao SJ, Cheng PL, Feng X, Yan YS (2015) Analysis on screening results of phenylketonuria among 567691 neonates in Gansu Province. Int J Lab Med 36(24):3588–3590Google Scholar
- Yang YL, Ye Y (2014) Consensus about the diagnosis and treatment of hyperphenylalaninemia. Chin J Pediatr 52(6):420–425Google Scholar
- Yan YS, Wang Z, Hao SJ, Meng Y, Zheng L, Huang SZ (2009) Mutation analysis of the PAH gene in patients with phenylketonuria in Gansu province. Chin J Med Genet 26(4):419–422Google Scholar
- Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R, ClinGen Inborn Errors of Metabolism Working Group (2018) Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): the ClinGen IEM working group and the phenylalanine hydroxylase gene. Hum Mutat 39(11):1569–1580CrossRefGoogle Scholar
- Zhang NJ, Yan YS, Dai NL, Wang DF, Wang G, Jiao HY (2015) Mutational spectrum of phenylalanine hydroxylase gene in Ningxia patients with phenylketonuria. J Appl Clin Pediatr 30(20):1557–1560Google Scholar
- Zhao DH, Li XL, Jia CL, Ni M, Kong XD (2016) Genotype and phenotype correlation of phenylalanine hydroxylase deficiency among patients from Henan. Chin J Med Genet 33(3):300–305Google Scholar