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HGD homogentisate 1,2-dioxygenase [ Homo sapiens (human) ]

Gene ID: 3081, updated on 3-Apr-2024

Summary

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Official Symbol
HGDprovided by HGNC
Official Full Name
homogentisate 1,2-dioxygenaseprovided by HGNC
Primary source
HGNC:HGNC:4892
See related
Ensembl:ENSG00000113924 MIM:607474; AllianceGenome:HGNC:4892
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AKU; HGO
Summary
This gene encodes the enzyme homogentisate 1,2 dioxygenase. This enzyme is involved in the catabolism of the amino acids tyrosine and phenylalanine. Mutations in this gene are the cause of the autosomal recessive metabolism disorder alkaptonuria.[provided by RefSeq, May 2010]
Expression
Biased expression in liver (RPKM 82.5), kidney (RPKM 39.4) and 7 other tissues See more
Orthologs
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Genomic context

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Location:
3q13.33
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (120628172..120682239, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (123348044..123402117, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (120347019..120401086, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L34 pseudogene 9 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:120283490-120283693 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20335 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:120360644-120361843 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:120395854-120396804 Neighboring gene RAB, member of RAS oncogene family like 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:120438328-120438887 Neighboring gene MT-CO1 pseudogene 29 Neighboring gene MT-CO2 pseudogene 29

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A novel mutation in the homogentisate 1,2 dioxygenase gene identified in Chinese Hani pediatric patients with Alkaptonuria. Tao L, et al. Clin Chim Acta, 2022 Jul 1. PMID 35550814
  2. Alkaptonuria in Russia: mutational spectrum and novel variants. Bychkov I, et al. Eur J Med Genet, 2021 Apr. PMID 33621656
  3. Founder effects of the homogentisate 1,2-dioxygenase (HGD) gene in a gypsy population and mutation spectrum in the gene among alkaptonuria patients from India. Danda S, et al. Clin Rheumatol, 2020 Sep. PMID 32212000
  4. Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase. Sen Gupta PS, et al. J Biomol Struct Dyn, 2021 Mar. PMID 32107984
  5. Presentation of 14 alkaptonuria patients from Turkey. Akbaba AI, et al. J Pediatr Endocrinol Metab, 2020 Feb 25. PMID 31927521

See all (49) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structure-Function Relationship of Homogentisate 1,2-dioxygenase: Understanding the Genotype-Phenotype Correlations in the Rare Genetic Disease Alkaptonuria.
    Title: Structure-Function Relationship of Homogentisate 1,2-dioxygenase: Understanding the Genotype-Phenotype Correlations in the Rare Genetic Disease Alkaptonuria.
  2. Homogentisate 1,2-dioxygenase (HGD) gene variants in young Egyptian patients with alkaptonuria.
    Title: Homogentisate 1,2-dioxygenase (HGD) gene variants in young Egyptian patients with alkaptonuria.
  3. A novel mutation in the homogentisate 1,2 dioxygenase gene identified in Chinese Hani pediatric patients with Alkaptonuria.
    Title: A novel mutation in the homogentisate 1,2 dioxygenase gene identified in Chinese Hani pediatric patients with Alkaptonuria.
  4. Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase.
    Title: Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase.
  5. Alkaptonuria in Russia: mutational spectrum and novel variants.
    Title: Alkaptonuria in Russia: mutational spectrum and novel variants.
  6. Founder effects of the homogentisate 1,2-dioxygenase (HGD) gene in a gypsy population and mutation spectrum in the gene among alkaptonuria patients from India.
    Title: Founder effects of the homogentisate 1,2-dioxygenase (HGD) gene in a gypsy population and mutation spectrum in the gene among alkaptonuria patients from India.
  7. Presentation of 14 alkaptonuria patients from Turkey.
    Title: Presentation of 14 alkaptonuria patients from Turkey.
  8. Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.
    Title: Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.
  9. Twelve novel HGD gene variants have been identified in 99 alkaptonuria patients affecting the bones.
    Title: Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy.
  10. A novel alkaptonuria mutation, c.87 + 1G > A, shows a significant founder effect and high prevalence in a nomadic Indian population.
    Title: Mutation screening of the HGD gene identifies a novel alkaptonuria mutation with significant founder effect and high prevalence.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Alkaptonuria
MedGen: C0002066 OMIM: 203500 GeneReviews: Alkaptonuria
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ94126

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables homogentisate 1,2-dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables homogentisate 1,2-dioxygenase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-phenylalanine catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-phenylalanine catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in tyrosine catabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 

General protein information

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Preferred Names
homogentisate 1,2-dioxygenase
Names
homogentisate oxidase
homogentisate oxygenase
homogentisic acid oxidase
homogentisicase
NP_000178.2
XP_005247469.1
XP_005247470.1
XP_005247471.1
XP_011511048.1
XP_016861766.1
XP_047304014.1
XP_047304015.1
XP_054202370.1
XP_054202371.1
XP_054202372.1
XP_054202373.1
XP_054202374.1
XP_054202375.1
XP_054202376.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011957.1 RefSeqGene

    Range
    5243..59310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000187.4 → NP_000178.2  homogentisate 1,2-dioxygenase

    See identical proteins and their annotated locations for NP_000178.2

    Status: REVIEWED

    Source sequence(s)
    AA861603, AC133474, AK313563
    Consensus CDS
    CCDS3000.1
    UniProtKB/Swiss-Prot
    A8K417, B2R8Z0, Q93099
    Related
    ENSP00000283871.5, ENST00000283871.10
    Conserved Domains (1) summary
    TIGR01015
    Location:3 → 434
    hmgA; homogentisate 1,2-dioxygenase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    120628172..120682239 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247412.3 → XP_005247469.1  homogentisate 1,2-dioxygenase isoform X1

    Conserved Domains (1) summary
    cl21464
    Location:3 → 359
    cupin_like; Conserved domain found in cupin and related proteins

  2. XM_017006277.3 → XP_016861766.1  homogentisate 1,2-dioxygenase isoform X3

    UniProtKB/TrEMBL
    B3KW64
    Conserved Domains (1) summary
    cl21464
    Location:1 → 293
    cupin_like; Conserved domain found in cupin and related proteins

  3. XM_047448059.1 → XP_047304015.1  homogentisate 1,2-dioxygenase isoform X7

  4. XM_047448058.1 → XP_047304014.1  homogentisate 1,2-dioxygenase isoform X5

  5. XM_011512746.3 → XP_011511048.1  homogentisate 1,2-dioxygenase isoform X4

    UniProtKB/TrEMBL
    Q8WW71
    Conserved Domains (1) summary
    cl21464
    Location:3 → 293
    cupin_like; Conserved domain found in cupin and related proteins

  6. XM_005247413.3 → XP_005247470.1  homogentisate 1,2-dioxygenase isoform X2

    UniProtKB/TrEMBL
    Q8WW71
    Conserved Domains (1) summary
    cl21464
    Location:3 → 335
    cupin_like; Conserved domain found in cupin and related proteins

  7. XM_005247414.6 → XP_005247471.1  homogentisate 1,2-dioxygenase isoform X6

    See identical proteins and their annotated locations for XP_005247471.1

    Conserved Domains (1) summary
    cl21464
    Location:3 → 227
    cupin_like; Conserved domain found in cupin and related proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    123348044..123402117 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346395.1 → XP_054202370.1  homogentisate 1,2-dioxygenase isoform X1

  2. XM_054346397.1 → XP_054202372.1  homogentisate 1,2-dioxygenase isoform X3

    UniProtKB/TrEMBL
    B3KW64

  3. XM_054346401.1 → XP_054202376.1  homogentisate 1,2-dioxygenase isoform X7

  4. XM_054346399.1 → XP_054202374.1  homogentisate 1,2-dioxygenase isoform X5

  5. XM_054346398.1 → XP_054202373.1  homogentisate 1,2-dioxygenase isoform X4

  6. XM_054346396.1 → XP_054202371.1  homogentisate 1,2-dioxygenase isoform X2

  7. XM_054346400.1 → XP_054202375.1  homogentisate 1,2-dioxygenase isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q93099.2 GenPept UniProtKB/Swiss-Prot:Q93099

Gene LinkOut

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