Abstract
We analyzed correlations between mutant genotypes at the human phenylalanine hydroxylase locus (gene symbol PAH) and the corresponding hyperphenylalaninemia (HPA) phenotypes (notably, phenylketonuria [OMIM 261600]). We used reports, both published and in the PAH Mutation Analysis Consortium Database, on 365 patients harboring 73 different PAH mutations in 161 different genotypes. HPA phenotypes were classified as phenylketonuria (PKU), variant PKU, and non-PKU HPA. By analysis both of homoallelic mutant genotypes and of "functionally hemizygous" heteroallelic genotypes, we characterized the phenotypic effect of 48 of the 73 different, largely missense mutations. Among those with consistent in vivo expression, 24 caused PKU, 3 caused variant PKU, and 10 caused non-PKU HPA. However, 11 mutations were inconsistent in their effect: 9 appeared in two different phenotype classes, and 2 (I65T and Y414C) appeared in all three classes. Seven mutations were inconsistent in phenotypic effect when in vitro (unit-protein) expression was compared with the corresponding in vivo phenotype (an emergent property). We conclude that the majority of PAH mutations confer a consistent phenotype and that this is concordant with their effects, when known, predicted from in vitro expression analysis. However, significant inconsistencies, both between in vitro and in vivo phenotypes and between different individuals with similar PAH genotypes, reveal that the HPA-phenotype is more complex than that predicted by Mendelian inheritance of alleles at the PAH locus.
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Selected References
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- ARMSTRONG M. D., TYLER F. H. Studies on phenylketonuria. I. Restricted phenylalanine intake in phenylketonuria. J Clin Invest. 1955 Apr;34(4):565–580. doi: 10.1172/JCI103105. [DOI] [PMC free article] [PubMed] [Google Scholar]
- BICKEL H., GERRARD J., HICKMANS E. M. The influence of phenylalanine intake on the chemistry and behaviour of a phenyl-ketonuric child. Acta Paediatr. 1954 Jan;43(1):64–77. doi: 10.1111/j.1651-2227.1954.tb04000.x. [DOI] [PubMed] [Google Scholar]
- Beutler E., McKusick V. A., Motulsky A. G., Scriver C. R., Hutchinson F. Mutation nomenclature: nicknames, systematic names, and unique identifiers. Hum Mutat. 1996;8(3):203–206. doi: 10.1002/(SICI)1098-1004(1996)8:3<203::AID-HUMU1>3.0.CO;2-A. [DOI] [PubMed] [Google Scholar]
- Burgard P., Rupp A., Konecki D. S., Trefz F. K., Schmidt H., Lichter-Konecki U. Phenylalanine hydroxylase genotypes, predicted residual enzyme activity and phenotypic parameters of diagnosis and treatment of phenylketonuria. Eur J Pediatr. 1996 Jul;155 (Suppl 1):S11–S15. doi: 10.1007/pl00014222. [DOI] [PubMed] [Google Scholar]
- Bénit P., Rey F., Melle D., Munnich A., Rey J. Five novel missense mutations of the phenylalanine hydroxylase gene in phenylketonuria. Hum Mutat. 1994;4(3):229–231. doi: 10.1002/humu.1380040311. [DOI] [PubMed] [Google Scholar]
- Desviat L. R., Pérez B., De Lucca M., Cornejo V., Schmidt B., Ugarte M. Evidence in Latin America of recurrence of V388M, a phenylketonuria mutation with high in vitro residual activity. Am J Hum Genet. 1995 Aug;57(2):337–342. [PMC free article] [PubMed] [Google Scholar]
- DiLella A. G., Kwok S. C., Ledley F. D., Marvit J., Woo S. L. Molecular structure and polymorphic map of the human phenylalanine hydroxylase gene. Biochemistry. 1986 Feb 25;25(4):743–749. doi: 10.1021/bi00352a001. [DOI] [PubMed] [Google Scholar]
- DiSilvestre D., Koch R., Groffen J. Different clinical manifestations of hyperphenylalaninemia in three siblings with identical phenylalanine hydroxylase genes. Am J Hum Genet. 1991 May;48(5):1014–1016. [PMC free article] [PubMed] [Google Scholar]
- Dianzani I., Giannattasio S., de Sanctis L., Alliaudi C., Lattanzio P., Dionisi Vici C., Burlina A., Burroni M., Sebastio G., Carnevale F. Characterization of phenylketonuria alleles in the Italian population. Eur J Hum Genet. 1995;3(5):294–302. doi: 10.1159/000472313. [DOI] [PubMed] [Google Scholar]
- Dianzani I., Knappskog P. M., de Sanctis L., Giannattasio S., Riva E., Ponzone A., Apold J., Camaschella C. Novel missense mutation in the phenylalanine hydroxylase gene leading to complete loss of enzymatic activity. Hum Mutat. 1995;6(3):247–249. doi: 10.1002/humu.1380060308. [DOI] [PubMed] [Google Scholar]
- Dickson P. W., Jennings I. G., Cotton R. G. Delineation of the catalytic core of phenylalanine hydroxylase and identification of glutamate 286 as a critical residue for pterin function. J Biol Chem. 1994 Aug 12;269(32):20369–20375. [PubMed] [Google Scholar]
- Dworniczak B., Kalaydjieva L., Aulehla-Scholz C., Ullrich K., Kremensky I., Radeva B., Horst J. Recurrent nonsense mutation in exon 7 of the phenylalanine hydroxylase gene. Hum Genet. 1991 Oct;87(6):731–733. doi: 10.1007/BF00201735. [DOI] [PubMed] [Google Scholar]
- Eiken H. G., Knappskog P. M., Apold J., Flatmark T. PKU mutation G46S is associated with increased aggregation and degradation of the phenylalanine hydroxylase enzyme. Hum Mutat. 1996;7(3):228–238. doi: 10.1002/(SICI)1098-1004(1996)7:3<228::AID-HUMU7>3.0.CO;2-6. [DOI] [PubMed] [Google Scholar]
- Eiken H. G., Knappskog P. M., Motzfeldt K., Boman H., Apold J. Phenylketonuria genotypes correlated to metabolic phenotype groups in Norway. Eur J Pediatr. 1996 Jul;155(7):554–560. doi: 10.1007/BF01957904. [DOI] [PubMed] [Google Scholar]
- Gibbs B. S., Wojchowski D., Benkovic S. J. Expression of rat liver phenylalanine hydroxylase in insect cells and site-directed mutagenesis of putative non-heme iron-binding sites. J Biol Chem. 1993 Apr 15;268(11):8046–8052. [PubMed] [Google Scholar]
- Guldberg P., Henriksen K. F., Thöny B., Blau N., Güttler F. Molecular heterogeneity of nonphenylketonuria hyperphenylalaninemia in 25 Danish patients. Genomics. 1994 May 15;21(2):453–455. doi: 10.1006/geno.1994.1296. [DOI] [PubMed] [Google Scholar]
- Guldberg P., Levy H. L., Henriksen K. F., Guttler F. Three prevalent mutations in a patient with phenylalanine hydroxylase deficiency: implications for diagnosis and genetic counselling. J Med Genet. 1996 Feb;33(2):161–164. doi: 10.1136/jmg.33.2.161. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guldberg P., Levy H. L., Koch R., Berlin C. M., Jr, Francois B., Henriksen K. F., Güttler F. Mutation analysis in families with discordant phenotypes of phenylalanine hydroxylase deficiency. Inheritance and expression of the hyperphenylalaninaemias. J Inherit Metab Dis. 1994;17(6):645–651. doi: 10.1007/BF00712004. [DOI] [PubMed] [Google Scholar]
- Guldberg P., Mikkelsen I., Henriksen K. F., Lou H. C., Güttler F. In vivo assessment of mutations in the phenylalanine hydroxylase gene by phenylalanine loading: characterization of seven common mutations. Eur J Pediatr. 1995 Jul;154(7):551–556. doi: 10.1007/BF02074833. [DOI] [PubMed] [Google Scholar]
- Güttler F., Ledley F. D., Lidsky A. S., DiLella A. G., Sullivan S. E., Woo S. L. Correlation between polymorphic DNA haplotypes at phenylalanine hydroxylase locus and clinical phenotypes of phenylketonuria. J Pediatr. 1987 Jan;110(1):68–71. doi: 10.1016/s0022-3476(87)80290-1. [DOI] [PubMed] [Google Scholar]
- John S. W., Scriver C. R., Laframboise R., Rozen R. In vitro and in vivo correlations for I65T and M1V mutations at the phenylalanine hydroxylase locus. Hum Mutat. 1992;1(2):147–153. doi: 10.1002/humu.1380010210. [DOI] [PubMed] [Google Scholar]
- Kacser H., Burns J. A. The molecular basis of dominance. Genetics. 1981 Mar-Apr;97(3-4):639–666. doi: 10.1093/genetics/97.3-4.639. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kalaydjieva L., Dworniczak B., Kremensky I., Koprivarova K., Radeva B., Milusheva R., Aulehla-Scholz C., Horst J. Heterogeneity of mutations in Bulgarian phenylketonuria haplotype 1 and 4 alleles. Clin Genet. 1992 Mar;41(3):123–128. doi: 10.1111/j.1399-0004.1992.tb03647.x. [DOI] [PubMed] [Google Scholar]
- Kleiman S., Vanagaite L., Bernstein J., Schwartz G., Brand N., Elitzur A., Woo S. L., Shiloh Y. Phenylketonuria: variable phenotypic outcomes of the R261Q mutation and maternal PKU in the offspring of a healthy homozygote. J Med Genet. 1993 Apr;30(4):284–288. doi: 10.1136/jmg.30.4.284. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Konecki D. S., Wang Y., Trefz F. K., Lichter-Konecki U., Woo S. L. Structural characterization of the 5' regions of the human phenylalanine hydroxylase gene. Biochemistry. 1992 Sep 8;31(35):8363–8368. doi: 10.1021/bi00150a033. [DOI] [PubMed] [Google Scholar]
- Kowlessur D., Yang X. J., Kaufman S. Further studies of the role of Ser-16 in the regulation of the activity of phenylalanine hydroxylase. Proc Natl Acad Sci U S A. 1995 May 23;92(11):4743–4747. doi: 10.1073/pnas.92.11.4743. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kwok S. C., Ledley F. D., DiLella A. G., Robson K. J., Woo S. L. Nucleotide sequence of a full-length complementary DNA clone and amino acid sequence of human phenylalanine hydroxylase. Biochemistry. 1985 Jan 29;24(3):556–561. doi: 10.1021/bi00324a002. [DOI] [PubMed] [Google Scholar]
- Ledley F. D., Levy H. L., Woo S. L. Molecular analysis of the inheritance of phenylketonuria and mild hyperphenylalaninemia in families with both disorders. N Engl J Med. 1986 May 15;314(20):1276–1280. doi: 10.1056/NEJM198605153142002. [DOI] [PubMed] [Google Scholar]
- Lidsky A. S., Ledley F. D., DiLella A. G., Kwok S. C., Daiger S. P., Robson K. J., Woo S. L. Extensive restriction site polymorphism at the human phenylalanine hydroxylase locus and application in prenatal diagnosis of phenylketonuria. Am J Hum Genet. 1985 Jul;37(4):619–634. [PMC free article] [PubMed] [Google Scholar]
- Lyonnet S., Caillaud C., Rey F., Berthelon M., Frézal J., Rey J., Munnich A. Molecular genetics of phenylketonuria in Mediterranean countries: a mutation associated with partial phenylalanine hydroxylase deficiency. Am J Hum Genet. 1989 Apr;44(4):511–517. [PMC free article] [PubMed] [Google Scholar]
- Martínez-Pardo M., Colmenares A. R., García M. J., Pérez B., Desviat L. R., Ugarte M. Phenotype distribution in the Spanish phenylketonuria population and related genotypes. J Inherit Metab Dis. 1994;17(3):366–368. doi: 10.1007/BF00711832. [DOI] [PubMed] [Google Scholar]
- Nowacki P., Byck S., Prevost L., Scriver C. R. The PAH mutation analysis consortium database: update 1996. Nucleic Acids Res. 1997 Jan 1;25(1):139–142. doi: 10.1093/nar/25.1.139. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Okano Y., Eisensmith R. C., Güttler F., Lichter-Konecki U., Konecki D. S., Trefz F. K., Dasovich M., Wang T., Henriksen K., Lou H. Molecular basis of phenotypic heterogeneity in phenylketonuria. N Engl J Med. 1991 May 2;324(18):1232–1238. doi: 10.1056/NEJM199105023241802. [DOI] [PubMed] [Google Scholar]
- Okano Y., Wang T., Eisensmith R. C., Longhi R., Riva E., Giovannini M., Cerone R., Romano C., Woo S. L. Phenylketonuria missense mutations in the Mediterranean. Genomics. 1991 Jan;9(1):96–103. doi: 10.1016/0888-7543(91)90225-4. [DOI] [PubMed] [Google Scholar]
- Okano Y., Wang T., Eisensmith R. C., Steinmann B., Gitzelmann R., Woo S. L. Missense mutations associated with RFLP haplotypes 1 and 4 of the human phenylalanine hydroxylase gene. Am J Hum Genet. 1990 Jan;46(1):18–25. [PMC free article] [PubMed] [Google Scholar]
- Pérez B., Desviat L. R., García M. J., Ugarte M. Different phenotypic manifestations associated with identical phenylketonuria genotypes in two Spanish families. J Inherit Metab Dis. 1994;17(3):377–378. doi: 10.1007/BF00711839. [DOI] [PubMed] [Google Scholar]
- Pérez B., Desviat L. R., Ugarte M. Expression analysis of mutation P244L, which causes mild hyperphenylalaninemia. Hum Mutat. 1995;5(2):188–190. doi: 10.1002/humu.1380050217. [DOI] [PubMed] [Google Scholar]
- Quinsey N. S., Lenaghan C. M., Dickson P. W. Identification of Gln313 and Pro327 as residues critical for substrate inhibition in tyrosine hydroxylase. J Neurochem. 1996 Mar;66(3):908–914. doi: 10.1046/j.1471-4159.1996.66030908.x. [DOI] [PubMed] [Google Scholar]
- Ramus S. J., Forrest S. M., Pitt D. B., Saleeba J. A., Cotton R. G. Comparison of genotype and intellectual phenotype in untreated PKU patients. J Med Genet. 1993 May;30(5):401–405. doi: 10.1136/jmg.30.5.401. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Romano V., Guldberg P., Güttler F., Meli C., Mollica F., Pavone L., Giovannini M., Riva E., Biasucci G., Luotti D. PAH deficiency in Italy: correlation of genotype with phenotype in the Sicilian population. J Inherit Metab Dis. 1996;19(1):15–24. doi: 10.1007/BF01799343. [DOI] [PubMed] [Google Scholar]
- Salter M., Knowles R. G., Pogson C. I. Quantification of the importance of individual steps in the control of aromatic amino acid metabolism. Biochem J. 1986 Mar 15;234(3):635–647. doi: 10.1042/bj2340635. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Scriver C. R., Gregory D. M., Sovetts D., Tissenbaum G. Normal plasma free amino acid values in adults: the influence of some common physiological variables. Metabolism. 1985 Sep;34(9):868–873. doi: 10.1016/0026-0495(85)90112-x. [DOI] [PubMed] [Google Scholar]
- Scriver C. R. Phenylketonuria--genotypes and phenotypes. N Engl J Med. 1991 May 2;324(18):1280–1281. doi: 10.1056/NEJM199105023241810. [DOI] [PubMed] [Google Scholar]
- Svensson E., Eisensmith R. C., Dworniczak B., von Döbeln U., Hagenfeldt L., Horst J., Woo S. L. Two missense mutations causing mild hyperphenylalaninemia associated with DNA haplotype 12. Hum Mutat. 1992;1(2):129–137. doi: 10.1002/humu.1380010208. [DOI] [PubMed] [Google Scholar]
- Svensson E., von Döbeln U., Eisensmith R. C., Hagenfeldt L., Woo S. L. Relation between genotype and phenotype in Swedish phenylketonuria and hyperphenylalaninemia patients. Eur J Pediatr. 1993 Feb;152(2):132–139. doi: 10.1007/BF02072490. [DOI] [PubMed] [Google Scholar]
- Treacy E. P., Delente J. J., Elkas G., Carter K., Lambert M., Waters P. J., Scriver C. R. Analysis of phenylalanine hydroxylase genotypes and hyperphenylalaninemia phenotypes using L-[1-13C]phenylalanine oxidation rates in vivo: a pilot study. Pediatr Res. 1997 Oct;42(4):430–435. doi: 10.1203/00006450-199710000-00002. [DOI] [PubMed] [Google Scholar]
- Treacy E., Pitt J. J., Seller K., Thompson G. N., Ramus S., Cotton R. G. In vivo disposal of phenylalanine in phenylketonuria: a study of two siblings. J Inherit Metab Dis. 1996;19(5):595–602. doi: 10.1007/BF01799832. [DOI] [PubMed] [Google Scholar]
- Trefz F. K., Burgard P., König T., Goebel-Schreiner B., Lichter-Konecki U., Konecki D., Schmidt E., Schmidt H., Bickel H. Genotype-phenotype correlations in phenylketonuria. Clin Chim Acta. 1993 Jul 30;217(1):15–21. doi: 10.1016/0009-8981(93)90233-t. [DOI] [PubMed] [Google Scholar]
- Tyfield L. A., Zschocke J., Stephenson A., Cockburn F., Harvie A., Bidwell J. L., Wood N. A., Hunt L. P. Discordant phenylketonuria phenotypes in one family: the relationship between genotype and clinical outcome is a function of multiple effects. J Med Genet. 1995 Nov;32(11):867–870. doi: 10.1136/jmg.32.11.867. [DOI] [PMC free article] [PubMed] [Google Scholar]
- WOOLF L. I., GRIFFITHS R., MONCRIEFF A. Treatment of phenylketonuria with a diet low in phenylalanine. Br Med J. 1955 Jan 8;1(4905):57–64. doi: 10.1136/bmj.1.4905.57. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Waters P. J., Parniak M. A., Nowacki P., Scriver C. R. In vitro expression analysis of mutations in phenylalanine hydroxylase: linking genotype to phenotype and structure to function. Hum Mutat. 1998;11(1):4–17. doi: 10.1002/(SICI)1098-1004(1998)11:1<4::AID-HUMU2>3.0.CO;2-L. [DOI] [PubMed] [Google Scholar]
- Weinstein M., Eisensmith R. C., Abadie V., Avigad S., Lyonnet S., Schwartz G., Munnich A., Woo S. L., Shiloh Y. A missense mutation, S349P, completely inactivates phenylalanine hydroxylase in north African Jews with phenylketonuria. Hum Genet. 1993 Feb;90(6):645–649. doi: 10.1007/BF00202483. [DOI] [PubMed] [Google Scholar]
- Weiss K. M. Is there a paradigm shift in genetics? Lessons from the study of human diseases. Mol Phylogenet Evol. 1996 Feb;5(1):259–265. doi: 10.1006/mpev.1996.0019. [DOI] [PubMed] [Google Scholar]
- Woo S. L., Lidsky A. S., Güttler F., Chandra T., Robson K. J. Cloned human phenylalanine hydroxylase gene allows prenatal diagnosis and carrier detection of classical phenylketonuria. Nature. 1983 Nov 10;306(5939):151–155. doi: 10.1038/306151a0. [DOI] [PubMed] [Google Scholar]
- Zschocke J., Graham C. A., Stewart F. J., Carson D. J., Nevin N. C. Non-phenylketonuria hyperphenylalaninaemia in Northern Ireland: frequent mutation allows screening and early diagnosis. Hum Mutat. 1994;4(2):114–118. doi: 10.1002/humu.1380040204. [DOI] [PubMed] [Google Scholar]
- Zygulska M., Eigel A., Dworniczak B., Sutkowska A., Pietrzyk J. J., Horst J. Phenylketonuria in Poland: 66% of PKU alleles are caused by three mutations. Hum Genet. 1991 Nov;88(1):91–94. doi: 10.1007/BF00204935. [DOI] [PubMed] [Google Scholar]
- Zygulska M., Eigel A., Pietrzyk J. J., Horst J. Phenylketonuria in southern Poland: a new splice mutation in intron 9 at the PAH locus. Hum Mutat. 1994;4(4):297–299. doi: 10.1002/humu.1380040412. [DOI] [PubMed] [Google Scholar]