Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria

Hum Mutat. 2009 Dec;30(12):1611-9. doi: 10.1002/humu.21120.


Alkaptonuria (AKU) is a rare autosomal recessive metabolic disorder, characterized by accumulation of homogentisic acid, leading to darkened urine, pigmentation of connective tissue (ochronosis), joint and spine arthritis, and destruction of cardiac valves. AKU is due to mutations in the homogentisate dioxygenase gene (HGD) that converts homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway. Here we report a comprehensive mutation analysis of 93 patients enrolled in our study, as well as an extensive update of all previously published HGD mutations associated with AKU. Within our patient cohort, we identified 52 HGD variants, of which 22 were novel. This yields a total of 91 identified HGD variations associated with AKU to date, including 62 missense, 13 splice site, 10 frameshift, 5 nonsense, and 1 no-stop mutation. Most HGD variants reside in exons 3, 6, 8, and 13. We assessed the potential effect of all missense variations on protein function, using five bioinformatic tools specifically designed for interpretation of missense variants (SIFT, POLYPHEN, PANTHER, PMUT, and SNAP). We also analyzed the potential effect of splice-site variants using two different tools (BDGP and NetGene2). This study provides valuable resources for molecular analysis of alkaptonuria and expands our knowledge of the molecular basis of this disease.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Alkaptonuria / diagnostic imaging
  • Alkaptonuria / enzymology*
  • Alkaptonuria / genetics*
  • Alkaptonuria / pathology
  • Cohort Studies
  • Exons / genetics
  • Genotype
  • Homogentisate 1,2-Dioxygenase / genetics*
  • Homogentisate 1,2-Dioxygenase / urine
  • Homogentisic Acid / urine
  • Humans
  • Mutation / genetics*
  • National Institutes of Health (U.S.)
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics
  • Radiography
  • Siblings
  • United States


  • Homogentisate 1,2-Dioxygenase
  • Homogentisic Acid