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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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HGD
homogentisate 1,2-dioxygenase
Chromosome 3 Β· 3q13.33
NCBI Gene: 3081Ensembl: ENSG00000113924.13HGNC: HGNC:4892UniProt: B3KW64
52PubMed Papers
21Diseases
0Drugs
272Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingextracellular exosomeidentical protein bindinghomogentisate 1,2-dioxygenase activityalkaptonuriacomplicationhemorrhagenervous system disease
✦AI Summary

Homogentisate 1,2-dioxygenase (HGD) is a cytosolic enzyme that catalyzes the conversion of homogentisate to maleylacetoacetate, a critical step in the degradation pathway of the amino acids tyrosine and phenylalanine 1. The HGD gene is located on chromosome 3 and encodes a 445-amino acid protein 2. Pathogenic variants in HGD cause alkaptonuria (AKU), a rare autosomal recessive metabolic disorder characterized by deficient HGD enzyme activity and accumulation of homogentisic acid (HGA) in tissues 13. This accumulation leads to complications in joints, heart valves, and kidneys 3. Over 28 novel HGD variants have been identified globally, including missense mutations, splicing variants, and genomic deletions 1. Notably, genotype-phenotype correlation studies reveal that HGD variants causing 1% versus >30% residual enzyme activity produce small but statistically significant differences in urinary HGA excretion; however, dietary protein intake is more important than HGD variant type in determining HGA accumulation 1. Certain populations, including nomadic groups in India and Slovakia, exhibit elevated AKU prevalence (1:19,000) due to founder effects and consanguinity 4. The recent availability of nitisinone as a therapeutic option underscores the clinical importance of early genetic confirmation for AKU patients to prevent serious complications 3.

Sources cited
1
HGD catalyzes homogentisate to maleylacetoacetate conversion; deficiency causes AKU with HGA accumulation; >28 novel variants identified; genotype-phenotype correlations show variant residual activity affects urinary HGA excretion
PMID: 30737480
2
HGD gene located on chromosome 3q13 with 14 exons encoding 445 amino acids; novel and recurrent variants identified in Iranian AKU patients
PMID: 41236909
3
HGD pathogenic variants cause autosomal recessive AKU; HGA accumulation affects joints, heart valves, kidneys; nitisinone available for therapy; early genetic confirmation recommended
PMID: 37658095
4
HGD mutations cause AKU with founder effects in specific populations (India, Slovakia with 1:19,000 incidence); splicing mutations identified
PMID: 24575791
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
alkaptonuriaOpen Targets
0.85Strong
complicationOpen Targets
0.32Weak
hemorrhageOpen Targets
0.32Weak
nervous system diseaseOpen Targets
0.27Weak
genetic disorderOpen Targets
0.19Weak
Barrett's esophagusOpen Targets
0.07Suggestive
primary hyperoxaluria type 3Open Targets
0.07Suggestive
iminoglycinuriaOpen Targets
0.07Suggestive
uridine-cytidineuriaOpen Targets
0.06Suggestive
hyperdibasic aminoaciduria type 1Open Targets
0.06Suggestive
isolated sedoheptulokinase deficiencyOpen Targets
0.06Suggestive
pentosuriaOpen Targets
0.06Suggestive
phosphohydroxylysinuriaOpen Targets
0.06Suggestive
cystinuriaOpen Targets
0.06Suggestive
Seizures - intellectual disability due to hydroxylysinuriaOpen Targets
0.06Suggestive
seizures-intellectual disability due to hydroxylysinuria syndromeOpen Targets
0.06Suggestive
carnosinemiaOpen Targets
0.06Suggestive
beta-aminoisobutyric acid, urinary excretion ofOpen Targets
0.05Suggestive
cystathioninuriaOpen Targets
0.05Suggestive
esophageal adenocarcinomaOpen Targets
0.05Suggestive
AlkaptonuriaUniProt
Pathogenic Variants272
NM_000187.4(HGD):c.482G>A (p.Gly161Glu)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2026β†’ Residue 161
NM_000187.4(HGD):c.158G>A (p.Arg53Gln)Pathogenic
Alkaptonuria|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 53
NM_000187.4(HGD):c.175del (p.Ser59fs)Pathogenic
Alkaptonuria|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 59
NM_000187.4(HGD):c.1102A>G (p.Met368Val)Pathogenic
Alkaptonuria|not provided|See cases
β˜…β˜…β˜†β˜†2025β†’ Residue 368
NM_000187.4(HGD):c.15+1G>APathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025
NM_000187.4(HGD):c.360T>G (p.Cys120Trp)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 120
NM_000187.4(HGD):c.808G>A (p.Gly270Arg)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 270
NM_000187.4(HGD):c.189G>T (p.Arg63Ser)Pathogenic
Alkaptonuria|See cases
β˜…β˜…β˜†β˜†2025β†’ Residue 63
NM_000187.4(HGD):c.688C>T (p.Pro230Ser)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 230
NM_000187.4(HGD):c.342+3A>CPathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025
NM_000187.4(HGD):c.899T>G (p.Val300Gly)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 300
NM_000187.4(HGD):c.457dup (p.Asp153fs)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 153
NM_000187.4(HGD):c.481G>A (p.Gly161Arg)Pathogenic
Alkaptonuria|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 161
NM_000187.4(HGD):c.343G>C (p.Gly115Arg)Pathogenic
Alkaptonuria|Clear cell carcinoma of kidney
β˜…β˜…β˜†β˜†2025β†’ Residue 115
NM_000187.4(HGD):c.347T>C (p.Leu116Pro)Pathogenic
Alkaptonuria|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 116
NM_000187.4(HGD):c.11T>A (p.Leu4Ter)Pathogenic
Alkaptonuria|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 4
NM_000187.4(HGD):c.125A>C (p.Glu42Ala)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 42
NM_000187.4(HGD):c.680T>C (p.Phe227Ser)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025β†’ Residue 227
NM_000187.4(HGD):c.1188+1G>APathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2025
NM_000187.4(HGD):c.502G>A (p.Glu168Lys)Pathogenic
Alkaptonuria
β˜…β˜…β˜†β˜†2024β†’ Residue 168
View on ClinVar β†—
Related Genes
GSTZ1Protein interaction100%HPDLProtein interaction99%TPH2Protein interaction96%HPDProtein interaction81%F13BProtein interaction80%FAHProtein interaction78%
Tissue Expression6 tissues
Liver
100%
Bone Marrow
0%
Lung
0%
Ovary
0%
Heart
0%
Brain
0%
Gene Interaction Network
Click a node to explore
HGDGSTZ1HPDLTPH2HPDF13BFAH
PROTEIN STRUCTURE
Preparing viewer…
PDB1EYB Β· 1.90 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.20LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.93 [0.72–1.20]
RankingsWhere HGD stands among ~20K protein-coding genes
  • #8,562of 20,598
    Most Researched52
  • #231of 5,498
    Most Pathogenic Variants272 Β· top 5%
  • #12,599of 17,882
    Most Constrained (LOEUF)1.20
Genes detectedHGD
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A Brief Review of Handgrip Strength and Sport Performance.
PMID: 28820854
J Strength Cond Res Β· 2017
1.00
2
Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.
PMID: 30737480
Eur J Hum Genet Β· 2019
0.90
3
Mutation screening of the HGD gene identifies a novel alkaptonuria mutation with significant founder effect and high prevalence.
PMID: 24575791
Ann Hum Genet Β· 2014
0.80
4
Homogentisate 1,2-dioxygenase (HGD) gene variants in young Egyptian patients with alkaptonuria.
PMID: 37658095
Sci Rep Β· 2023
0.70
5
Molecular Analysis of the HGD Gene in 9 Families With Alkaptonuric Ochronosis in Iran and Identification of Two Novel Variants.
PMID: 41236909
Mol Genet Genomic Med Β· 2025
0.60