Abstract
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.
Similar content being viewed by others
References
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):407–418
Blau N, van Spronsen FJ, Levy HL (2010) Phenylketonuria. Lancet 376(9750):1417–1427
Chen KJ, Chao HK, Hsiao KJ, Su TS (2002) Identification and characterization of a novel liver-specific enhancer of the human phenylalanine hydroxylase gene. Hum Genet 110(3):235–243
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):564–569
Desviat LR, Perez B, Ugarte M (2006) Identification of exonic deletions in the PAH gene causing phenylketonuria by MLPA analysis. Clin Chim Acta 373(1–2):164–167
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):116–121
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):393–396
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):554–562
Gu XF, Wang ZG (2004) Screening for phenylketonuria and congenital hypothyroidism in 5.8 million neonates in China. Chin J Prev Med 38(2):99–102
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):142–146s
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):512–517
Hubbard TD, Murray IA, Bisson WH, Sullivan AP, Sebastian A, Perry GH, Jablonski NG, Perdew GH (2016) Divergent ah receptor ligand selectivity during hominin evolution. Mol Biol Evol 33(10):2648–2658
Li N, Jia H, Liu Z, Tao J, Chen S, Li X, Deng Y, Jin X, Song J, Zhang L, Liang Y, Wang W, Zhu J (2015) Molecular characterisation of phenylketonuria in a Chinese mainland population using next-generation sequencing. Sci Rep 5:15769
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):2971–2976
Pey AL, Stricher F, Serrano L, Martinez A (2007) Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet 81(5):1006–1024
Polak E et al (2013) Phenylalanine hydroxylase deficiency in the Slovak population: genotype-phenotype correlations and genotype-based predictions of BH4-responsiveness. Gene 526(2):347–355
Qiang R et al (2014) Mutations of the phenylalanine hydroxylase gene in phenylketonuria patients from Shaanxi. Chin J Med Genet 31(1):74–77
Richards S et al (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17(5):405–424
Song F, Qu YJ, Zhang T, Jin YW, Wang H, Zheng XY (2005) Phenylketonuria mutations in northern China. Mol Genet Metab 86(Suppl 1):S107–S118
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):850–854
Sudmant PH et al (2015) An integrated map of structural variation in 2,504 human genomes. Nature 526(7571):75–81
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):3588–3590
Woo SL, Lidsky AS, Guttler F, Chandra T, Robson KJ (1983) Cloned human phenylalanine hydroxylase gene allows prenatal diagnosis and carrier detection of classical phenylketonuria. Nature 306(5939):151–155
Yang YL, Ye Y (2014) Consensus about the diagnosis and treatment of hyperphenylalaninemia. Chin J Pediatr 52(6):420–425
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):419–422
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):1569–1580
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):1557–1560
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):300–305
Acknowledgements
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.
Funding
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).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
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
Informed consent was obtained from all individual participants included in this study.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(DOCX 16 kb)
Rights and permissions
About this article
Cite this article
Yan, Y., Zhang, C., Jin, X. et al. Mutation spectrum of PAH gene in phenylketonuria patients in Northwest China: identification of twenty novel variants. Metab Brain Dis 34, 733–745 (2019). https://doi.org/10.1007/s11011-019-0387-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11011-019-0387-7