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Gene

HGD

homogentisate 1,2-dioxygenase

Summary

Cytogenetic location
3q13.33
Coordinates
Chromosome 3: 120,628,172–120,682,239 (GRCh38)
Exons
14 exons across 54.1 kb
Protein
445 amino acids
Inheritance
Autosomal recessive
Also known as
HGO
Previous symbols
AKU
MANE Select transcript
ENST00000283871.10NM_000187.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Alkaptonuria

    • Autosomal recessive

      A metabolic disease characterized by the accumulation of homogentisic acid (HGA) and its oxidized product, benzoquinone acetic acid (BQA), in various tissues (e.g. cartilage, connective tissue) and body fluids (urine, sweat), causing urine to darken when exposed to air as well as grey-blue coloration of the sclera and ear helix (ochronosis), and a disabling joint disease involving both the axial and peripheral joints (ochronotic arthropathy).

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How HGD is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where HGD sits. HGD and 7 genes near it on chromosome 3, from 120,155,206 to 121,155,205.Chromosome 33q13.33p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29120.2 Mb120.4 Mb120.6 Mb120.8 Mb121 MbGPR156: 120,164,645–120,285,426, reverse strandGPR156LRRC58: 120,324,509–120,349,412, reverse strandLRRC58FSTL1: 120,392,293–120,596,764, reverse strandFSTL1NDUFB4: 120,596,273–120,602,507, forward strandNDUFB4HGD: 120,628,172–120,682,239, reverse strandHGDRABL3: 120,684,938–120,742,993, reverse strandRABL3GTF2E1: 120,742,370–120,783,368, forward strandGTF2E1STXBP5L: 120,908,072–121,424,761, forward strandSTXBP5LDiagram of HGD: 14 exons on the reverse strand of chromosome 3Exon 14: 6 known disease-causing sitesExon 13: 17 known disease-causing sitesExon 12: 8 known disease-causing sitesExon 11: 10 known disease-causing sitesExon 10: 12 known disease-causing sitesExon 9: 8 known disease-causing sitesExon 8: 9 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 6: 10 known disease-causing sitesExon 5: 8 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 16 known disease-causing sitesExon 2: 1 known disease-causing siteExon 1: 4 known disease-causing sitesExon 14: 120,628,172–120,628,529, 358 basesExon 13: 120,633,147–120,633,328, 182 basesExon 12: 120,638,455–120,638,581, 127 basesExon 11: 120,641,589–120,641,693, 105 basesExon 10: 120,644,319–120,644,443, 125 basesExon 9: 120,646,267–120,646,366, 100 basesExon 8: 120,646,973–120,647,052, 80 basesExon 7: 120,647,877–120,647,911, 35 basesExon 6: 120,650,774–120,650,865, 92 basesExon 5: 120,652,592–120,652,651, 60 basesExon 4: 120,670,427–120,670,532, 106 basesExon 3: 120,674,901–120,674,989, 89 basesExon 2: 120,675,792–120,675,863, 72 basesExon 1: 120,682,097–120,682,239, 143 bases141210864215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.7 kb of the gene's 54.1 kb; 1,338 of those bases code for the protein.

How a genome test reads HGD

140

positions in HGD where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 54.1 kb of HGD, introns included, not only the 1.7 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). HGD gene: homogentisate 1,2-dioxygenase. Retrieved 16 October 2026, from https://dantelabs.com/genes/hgd

Vancouver

Dante Labs. HGD gene: homogentisate 1,2-dioxygenase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hgd

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