HGD mutation database

homogentisate 1,2-dioxygenase (HGD) Switch gene



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Curator: Dr. Andrea Zatkova (andrea.zatkova@savba.sk)
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General information
Gene name homogentisate 1,2-dioxygenase
Gene symbol HGD
Chromosome Location 3q21-q23
Database location hgddatabase.cvtisr.sk
Curator Dr. Andrea Zatkova
PubMed references View all (unique) PubMed references in the HGD database
Date of creation October 24, 2010
Last update September 11, 2025
Version HGD250911
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Reference sequence file coding DNA reference sequence for describing sequence variants
Genomic refseq ID NG_011957.1
Transcript refseq ID NM_000187.3
Exon/intron information Exon/intron information table
Total number of unique DNA variants reported 259
Total number of individuals with variant(s) 748
Total number of variants reported 1461
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NOTE Alkaptonuria (AKU) is a rare autosomal recessive disorder of both historical and medical interest. It represents a classical example of a discrete biochemical lesion resulting from a single gene deficiency that gives rise to a degenerative disease.
The HGD gene comprises 14 exons and spans 54.363 bp. The functional HGD protein is a hexamer, organized as a dimer of trimers.
The HGD-mutation database includes all HGD variants and AKU patients reported so far. Database also incorporates the data in the original AKU mutation database located in Madrid (updated last in 2001), in agreement with Prof. Santiago Rodriguez de Cordoba.

WHEN REFERRING TO THE DATABASE, PLEASE CITE:
Zatkova et al. (2012): Identification of eleven novel homogentisate 1,2 dioxygenase (HGD) variants in alkaptonuria (AKU) patients and establishment of a novel LOVD based HGD mutation database. JIMD Reports, 2012, Volume 4, 55-65.
DOI: 10.1007/8904_2011_68

More data can be downloaded here:

Predicted Structural Effect of the HGD gene Missense Variants

HGD haplotypes associated with AKU mutations
HGD haplotypes in the normal Spanish population
HGD haplotypes in the normal Slovak population
Expression and functional characterization of AKU alleles in E. Coli
HGD variants schematic
Mutations Aspergillus nidulans
Mutations Mus musculus

Graphical displays and utilities
Summary tables Summary of all sequence variants in the HGD database, sorted by type of variant (with graphical displays and statistics)
Reading-frame checker The Reading-frame checker generates a prediction of the effect of whole-exon changes
UCSC Genome Browser Show variants in the UCSC Genome Browser (compact view)
Ensembl Genome Browser Show variants in the Ensembl Genome Browser (compact view)
NCBI Sequence Viewer Show distribution histogram of variants in the NCBI Sequence Viewer
Sequence variant tables
Unique sequence variants Listing of all unique sequence variants in the HGD database, without patient data
Complete sequence variant listing Listing of all sequence variants in the HGD database
Variants with no known pathogenicity Listing of all HGD variants reported to have no noticeable phenotypic effect (note: excluding variants of unknown effect)
Download table Download the full sequence variant table of the HGD database in tab-delimited text format.
Search the database
By type of variant View all sequence variants of a certain type
Simple search Query the database by selecting the most important variables (exon number, type of variant, disease phenotype)
Advanced search Query the database by selecting a combination of variables
Based on patient origin View all variants based on your patient origin search terms
Links to other resources
Homepage http://www.alkaptonuria.cib.csic.es/
Entrez Gene 3081
OMIM - Gene 607474
OMIM - Disease Alkaptonuria (AKU)
UniProtKB (SwissProt/TrEMBL) Q93099
HGMD HGD
GeneCards HGD
GeneTests HGD
External link #1 England: AKU Society
External link #2 France: ALCAP
External link #3 Italy: AIMAKU
External link #4 Germany: DSAKU
External link #5 Slovakia: SlovakAKU
Copyright & disclaimer
The contents of this LOVD database are the intellectual property of the respective curator(s). Any unauthorised use, copying, storage or distribution of this material without written permission from the curator(s) will lead to copyright infringement with possible ensuing litigation. Copyright © 2025. All Rights Reserved. For further details, refer to Directive 96/9/EC of the European Parliament and the Council of March 11 (1996) on the legal protection of databases.

We have used all reasonable efforts to ensure that the information displayed on these pages and contained in the databases is of high quality. We make no warranty, express or implied, as to its accuracy or that the information is fit for a particular purpose, and will not be held responsible for any consequences arising out of any inaccuracies or omissions. Individuals, organisations and companies which use this database do so on the understanding that no liability whatsoever either direct or indirect shall rest upon the curator(s) or any of their employees or agents for the effects of any product, process or method that may be produced or adopted by any part, notwithstanding that the formulation of such product, process or method may be based upon information here provided.


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