OMIA:001243-9601 : Alkaptonuria in Pongo abelii (Sumatran orangutan)

In other species: crab-eating macaque , chimpanzee , Bornean orangutan , domestic cat , rabbit

Categories: Renal / urinary system phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 203500 (trait) , 607474 (gene)

Links to relevant human diseases in MONDO:

Mendelian trait/disorder: yes

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2023

Molecular basis: Fayette et al. (2023): "Sequence analysis [of a functional candidate gene] identified a homozygous missense variant, c.1081G>A (p.Gly361Arg), of the homogentisate 1,2-dioxygenase (HGD) gene."

Clinical features: Fayette et al. (2023): "A 6-yr-old female orangutan presented with a history of dark urine that turned brown upon standing since birth. Repeated routine urinalysis and urine culture were unremarkable. Urine organic acid analysis showed elevation in homogentisic acid consistent with alkaptonuria."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
HGD homogentisate 1,2-dioxygenase Pongo abelii 2 NC_085928.1 (17418915..17479537) HGD Homologene, Ensembl , NCBI gene


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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
1584 Alkaptonuria HGD missense Naturally occurring variant Susiae_PABv2/ponAbe3 3 g.17314095G>A c.1081G>A p.(G361R) 2023 37354891

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:001243-9601: Online Mendelian Inheritance in Animals (OMIA) [dataset].


2023 Fayette, M.A., Booth, K.T.A., Lynnes, T.C., Luna, C., Minich, D.J., Wilson, T.E., Miller, M.J. :
Biochemical and molecular confirmation of alkaptonuria in a Sumatran orangutan (Pongo abelii). Mol Genet Metab 139:107628, 2023. Pubmed reference: 37354891. DOI: 10.1016/j.ymgme.2023.107628.

Edit History

  • Created by Imke Tammen2 on 26 Jun 2023
  • Changed by Imke Tammen2 on 26 Jun 2023
  • Changed by Imke Tammen2 on 15 Oct 2023