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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
    mouse all
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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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