Analysis of HGD gene mutations in patients with alkaptonuria from the United Kingdom: Identification of novel mutations

JIMD Reports

Volumn 24, Issue , 2015, Pages 3-11

  Usher, Jeannette L ^a   Ascher, David B ^b   Pires, Douglas E V ^b   Milan, Anna M ^a   Blundell, Tom L ^b   Ranganath, Lakshminarayan R ^a  

^a ROYAL LIVERPOOL AND BROADGREEN UNIVERSITY HOSPITALS NHS TRUST   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Alkaptonuria; Homogentisic acid; Novel mutation; Rare genetic disorder; Sequencing

Indexed keywords

EID: 84929366156     PISSN: 21928304     EISSN: 21928312     Source Type: Book Series    
DOI: 10.1007/8904_2014_380     Document Type: Chapter

References (27)

1. Bromberg Y, Rost B (2007) SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 35 (11):3823–3835
2. Brunak S, Engelbrecht J, Knudsen S (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol 220(1):49–65
3. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effects of amino acid substitutions and indels. PLoS One 7(10):e46688
4. Davison AS, Milan AM, Hughes AT, Dutton JJ, Ranganath LR (2014) Serum concentrations and urinary excretion of homogentisic acid and tyrosine in normal subjects. Clin Chem Lab Med. doi:10.1515/cclm-2014-0668
5. Divina P, Kvitkovicova A, Buratti E, Vorechovsky I (2009) Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet 17:759–765
6. Fernandez-Canon JM, Granadino B, Beltran-Valero de Bernabe D et al (1996) The molecular basis of alkaptonuria. Nat Genet 14:19–24
7. Garrod AE (1908) The Croonian lectures on inborn errors of metabolism. Lecture II. Alkaptonuria. Lancet 2:73–79
8. Helliwell TR, Gallagher JA, Ranganath L (2008) Alkaptonuria-a review of surgical and autopsy pathology. Histopathology 53 (5):503–512
9. Hughes AT, Milan AM, Christensen P et al (2014) Urine homogentisic acid and tyrosine: simultaneous analysis by liquid chromatography tandem mass spectrometry. J Chromatogr B 963:106–112
10. Keller JM, Macaulay W, Ohannes A et al (2005) New developments in ochronosis: review of the literature. Rheumatol Int 25(2):81–85
11. Kralovicova J, Vorechovsky I (2007) Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition. Nucleic Acids Res 5 (19):6399–6413
12. La Du BN, Zannoni VG, Laster L et al (1958) The nature of the defect in tyrosine metabolism in alkaptonuria. J Biol Chem 230:251–260
13. Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31(13):3812–3814
14. Phornphutkul C, Introne WJ, Perry MB et al (2002) Natural history of alkaptonuria. N Engl J Med 347:2111–2121
15. Pires DE, Ascher DB, Blundell TL (2014a) mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics 30:335–342
16. Pires DE, Ascher DB, Blundell TL (2014b) DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res 42(W1):W314–W319
17. Pollak MR, Chou YH, Cerda JJ et al (1993) Homozygosity mapping of the gene for alkaptonuria to chromosome 3q2. Nat Genet 5:201–204
18. Ramensky V, Bork P, Sunyaev S (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30(17):3894–3900
19. Ranganath LR, Jarvis JC, Gallagher JA (2013) Recent advances in management of alkaptonuria. J Clin Pathol 66:367–373
20. Reese MG, Eeckman FH, Kulp D, Haussler D (1997) Improved splice site detection in genie. J Comp Biol 4(3):311–323
21. Srsen S, Muller CR, Fregin A et al (2002) Alkaptonuria in Slovakia: thirty-two years of research on phenotype and genotype. Mol Genet Metab 75(4):353–359
22. Taylor AM, Preston AJ, Paulk NK et al (2012) Ochronosis in a murine model of alkaptonuria is synonymous to that in the human condition. Osteoarthritis Cartilage 20(8):880–886
23. Titus GP, Mueller CR, Burgner J et al (2000) Crystal structure of human homogentisate dioxygenase. Nat Struct Biol 7:542–546
24. Vilboux T, Kayser M, Introne W et al (2009) Mutation spectrum of homogentisic acid oxidase (HGD)in alkaptonuria. Hum Mutat 30 (12):1611–1619
25. Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE (2008) Improving sequence variant descriptions in mutation databases and literature using the MUTALYZER sequence variation nomenclature checker. Hum Mutat 29(1):6–13
26. Worth CL, Preissner R, Blundell TL (2011) SDM-a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res 39:W215–W222
27. Zatkova A, Sedlackova T, Radvansky J et al (2011) Identification of 11 novel homogentisate 1,2 dioxygenase variants in alkaptonuria patients and establishment of a novel LOVD-based HGD mutation database. JIMD Rep 4:455–465