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HGD Gene(Protein Coding)

Homogentisate 1,2-Dioxygenase

GCID:
GC03M120628
GIFtS:
53
Genes Participants
UDN Logo

Aliases for HGD Gene

Aliases for HGD Gene

  • Homogentisate 1,2-Dioxygenase 2 3 5
  • Homogentisic Acid Oxidase 3 4
  • Homogentisate Oxygenase 3 4
  • Homogentisate Oxidase 2 3
  • Homogentisicase 3 4
  • EC 1.13.11.5 4 56
  • HGO 3 4
  • Homogentisate 1,2-Dioxygenase (Homogentisate Oxidase) 2
  • AKU 3

External Ids for HGD Gene

Previous HGNC Symbols for HGD Gene

  • AKU

Previous GeneCards Identifiers for HGD Gene

  • GC03M116980
  • GC03M119987
  • GC03M121628
  • GC03M121667
  • GC03M121829
  • GC03P9I0013
  • GC03M120347
  • GC03M117720

Summaries for HGD Gene

Entrez Gene Summary for HGD Gene

  • 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]

GeneCards Summary for HGD Gene

HGD (Homogentisate 1,2-Dioxygenase) is a Protein Coding gene. Diseases associated with HGD include Alkaptonuria and Ochronosis. Among its related pathways are Phenylalanine metabolism and Viral mRNA Translation. Gene Ontology (GO) annotations related to this gene include homogentisate 1,2-dioxygenase activity.

Additional gene information for HGD Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HGD Gene

Genomics for HGD Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for HGD Gene

Promoters and enhancers for HGD Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH03I120677 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 550.8 +2.0 1955 5.8 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 ETS1 YY1 SLC30A9 ATF7 HGD RABL3 PIR48626
GH03I120641 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.1 +39.9 39942 1.4 HDAC1 ATF1 TAF9B NFRKB ZBTB40 ZNF766 EGR1 ATF7 CREM NCOA1 HGD GTF2E1 RABL3 PIR48626
GH03I120719 Enhancer 0.9 Ensembl ENCODE 11.1 -37.2 -37166 1.2 FOXA2 NFIB SIN3A MTA3 CTBP1 GATA3 FOXK2 EGR1 ZNF444 RCOR1 HGD MTCO1P29 RABL3
GH03I120647 Enhancer 0.7 ENCODE dbSUPER 11.5 +35.3 35268 0.2 ZNF316 MAFG NFE2 EMSY HGD PIR48626
GH03I120691 Enhancer 1 Ensembl ENCODE 7.1 -10.7 -10746 3 ELF3 FOXA2 ARID4B ZBTB40 RARA YY1 SMARCC2 FOS MIXL1 CEBPB HGD GTF2E1 MTCO1P29 RABL3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HGD on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HGD gene promoter:

Genomic Locations for HGD Gene

Genomic Locations for HGD Gene
chr3:120,628,168-120,682,571
(GRCh38/hg38)
Size:
54,404 bases
Orientation:
Minus strand
chr3:120,347,015-120,401,418
(GRCh37/hg19)

Genomic View for HGD Gene

Genes around HGD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HGD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HGD Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HGD Gene

Proteins for HGD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HGD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q93099-HGD_HUMAN
    Recommended name:
    Homogentisate 1,2-dioxygenase
    Protein Accession:
    Q93099
    Secondary Accessions:
    • A8K417
    • B2R8Z0

    Protein attributes for HGD Gene

    Size:
    445 amino acids
    Molecular mass:
    49964 Da
    Cofactor:
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Quaternary structure:
    • Homohexamer arranged as a dimer of trimers.

    Three dimensional structures from OCA and Proteopedia for HGD Gene

neXtProt entry for HGD Gene

Protein Expression for HGD Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for HGD Gene

Q93099:
  • VVAWHGN
  • DPSIFTVLT
  • LGPIGANGLA
  • LYAEQLSG
  • AFMFESSLSLAVTKWG
  • MSEFMGLI
  • EICVIQRG
  • DFVIFPPRW
  • PNEICVI
  • TFRPPYYHRNCMSE
  • TMAFMFE

Post-translational modifications for HGD Gene

No Post-translational modifications

Other Protein References for HGD Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for HGD Gene

Gene Families for HGD Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for HGD Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HGD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q93099

UniProtKB/Swiss-Prot:

HGD_HUMAN :
  • Belongs to the homogentisate dioxygenase family.
Family:
  • Belongs to the homogentisate dioxygenase family.
genes like me logo Genes that share domains with HGD: view

Function for HGD Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for HGD Gene

GENATLAS Biochemistry:
homogentisate 1,2 dioxygenase (49kDa),catalyzing the third step of tyrosine catabolism
UniProtKB/Swiss-Prot CatalyticActivity:
Homogentisate + O(2) = 4-maleylacetoacetate.

Enzyme Numbers (IUBMB) for HGD Gene

Gene Ontology (GO) - Molecular Function for HGD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004411 homogentisate 1,2-dioxygenase activity EXP 8782815
GO:0005515 protein binding IPI 21044950
GO:0016491 oxidoreductase activity IEA --
GO:0042802 identical protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HGD: view
genes like me logo Genes that share phenotypes with HGD: view

Human Phenotype Ontology for HGD Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for HGD Gene

miRTarBase miRNAs that target HGD

Inhibitory RNA Products

No data available for Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for HGD Gene

Localization for HGD Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HGD gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HGD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA,HDA 19056867
genes like me logo Genes that share ontologies with HGD: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HGD Gene

Pathways & Interactions for HGD Gene

genes like me logo Genes that share pathways with HGD: view

UniProtKB/Swiss-Prot Q93099-HGD_HUMAN

  • Pathway: Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6.

Gene Ontology (GO) - Biological Process for HGD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006520 cellular amino acid metabolic process IEA --
GO:0006559 L-phenylalanine catabolic process TAS,IEA --
GO:0006570 tyrosine metabolic process IEA --
GO:0006572 tyrosine catabolic process TAS,IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with HGD: view

No data available for SIGNOR curated interactions for HGD Gene

Drugs & Compounds for HGD Gene

Products:

  1. Drug

(13) Drugs for HGD Gene - From: ClinicalTrials, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bevacizumab Approved, Investigational Pharma VEGF antagonist, Therapeutic Antibodies, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors 2087
acetic acid Approved Nutra Full agonist, Agonist 116
Vitamin A Approved, Vet_approved Nutra 529
Oxygen Approved, Vet_approved Pharma 0
Adjuvants, Immunologic Pharma 2702

(5) Additional Compounds for HGD Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Fe2+
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
 15438-31-0
Homogentisic acid
  • (2,5-dihydroxyphenyl)-Acetate
  • (2,5-dihydroxyphenyl)-Acetic acid
  • 2,5-Dihydroxy-a-toluate
  • 2,5-Dihydroxy-a-toluic acid
  • 2,5-Dihydroxy-alpha-toluate
 451-13-8
Maleylacetoacetic acid
  • 4-Maleylacetoacetate
  • 4-Maleylacetoacetic acid
  • Maleylacetoacetate
 5698-52-2
genes like me logo Genes that share compounds with HGD: view

Transcripts for HGD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HGD Gene

(6) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(140) Selected AceView cDNA sequences:
(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HGD Gene

Homogentisate 1,2-dioxygenase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HGD Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b
SP1: - - -
SP2: - - - - -
SP3: - - - - - - -
SP4:
SP5:
SP6:

Relevant External Links for HGD Gene

GeneLoc Exon Structure for
HGD
ECgene alternative splicing isoforms for
HGD

Expression for HGD Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HGD Gene

mRNA expression in normal human tissues for HGD Gene
mRNA expression by GTEx for HGD GenemRNA expression by BioGPS for HGD Gene

mRNA differential expression in normal tissues according to GTEx for HGD Gene

This gene is overexpressed in Liver (x31.7) and Kidney - Cortex (x8.5).

Protein differential expression in normal tissues from HIPED for HGD Gene

This gene is overexpressed in Liver, secretome (41.0) and Liver (11.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HGD Gene



NURSA nuclear receptor signaling pathways regulating expression of HGD Gene:

HGD

SOURCE GeneReport for Unigene cluster for HGD Gene:

Hs.368254

mRNA Expression by UniProt/SwissProt for HGD Gene:

Q93099-HGD_HUMAN
Tissue specificity: Highest expression in the prostate, small intestine, colon, kidney and liver.

Evidence on tissue expression from TISSUES for HGD Gene

  • Liver(4.7)
  • Kidney(4.6)
  • Blood(4.4)
  • Intestine(2.5)
  • Gall bladder(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HGD Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Thorax:
  • aorta
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
  • prostate
  • ureter
  • urethra
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with HGD: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for HGD Gene

Orthologs for HGD Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HGD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HGD 33 34
  • 99.78 (n)
cow
(Bos Taurus)
 Mammalia HGD 33 34
  • 91.24 (n)
dog
(Canis familiaris)
 Mammalia HGD 33 34
  • 91.16 (n)
oppossum
(Monodelphis domestica)
 Mammalia HGD 34
  • 90 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Hgd 33 16 34
  • 88.44 (n)
rat
(Rattus norvegicus)
 Mammalia Hgd 33
  • 88.44 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia HGD 34
  • 76 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HGD 33 34
  • 76.92 (n)
lizard
(Anolis carolinensis)
 Reptilia HGD 34
  • 75 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hgd 33
  • 72.95 (n)
Str.8815 33
zebrafish
(Danio rerio)
 Actinopterygii hgd 33 34
  • 72.54 (n)
fruit fly
(Drosophila melanogaster)
 Insecta hgo 35 33 34
  • 65.59 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP009609 33
  • 61.03 (n)
worm
(Caenorhabditis elegans)
 Secernentea hgo-1 33 34
  • 61.83 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons HGO 33
  • 60.27 (n)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.12262 33
rice
(Oryza sativa)
 Liliopsida Os06g0103300 33
  • 58.14 (n)
Os.11622 33
barley
(Hordeum vulgare)
 Liliopsida Hv.8867 33
wheat
(Triticum aestivum)
 Liliopsida Ta.6319 33
corn
(Zea mays)
 Liliopsida Zm.8772 33
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 66 (a)
 OneToOne
bread mold
(Neurospora crassa)
 Ascomycetes NCU05499 33
  • 55.27 (n)
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.14034 33
Species where no ortholog for HGD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for HGD Gene

ENSEMBL:
Gene Tree for HGD (if available)
TreeFam:
Gene Tree for HGD (if available)

Paralogs for HGD Gene

No data available for Paralogs for HGD Gene

Variants for HGD Gene

Sequence variations from dbSNP and Humsavar for HGD Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1049246177 (AKU) [MIM:203500] 120,674,947(-) G/A 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1057516307 likely-pathogenic, Alkaptonuria 120,646,265(-) A/G intron_variant, splice_donor_variant
rs1057516352 likely-pathogenic, Alkaptonuria 120,650,818(-) CCC/CC 5_prime_UTR_variant, coding_sequence_variant, frameshift
rs1057516355 likely-pathogenic, Alkaptonuria 120,682,109(-) C/G genic_upstream_transcript_variant, initiator_codon_variant, missense_variant
rs1057516362 likely-pathogenic, Alkaptonuria 120,675,847(-) CC/AAT 5_prime_UTR_variant, coding_sequence_variant, frameshift

Structural Variations from Database of Genomic Variants (DGV) for HGD Gene

Variant ID Type Subtype PubMed ID
nsv829699 CNV loss 17160897

Variation tolerance for HGD Gene

Residual Variation Intolerance Score: 21.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.13; 51.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HGD Gene

Human Gene Mutation Database (HGMD)
HGD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HGD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HGD Gene

Disorders for HGD Gene

MalaCards: The human disease database

(9) MalaCards diseases for HGD Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
alkaptonuria
  • aku
ochronosis
arthropathy
  • ankylosis of ankle and foot joint
prostate calculus
  • calculus of prostate
lower urinary tract calculus
  • calculus of lower urinary tract
- elite association - COSMIC cancer census association via MalaCards
Search HGD in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HGD_HUMAN
  • Alkaptonuria (AKU) [MIM:203500]: An autosomal recessive error of metabolism characterized by an increase in the level of homogentisic acid. The clinical manifestations are urine that turns dark on standing and alkalinization, black ochronotic pigmentation of cartilage and collagenous tissues, and spine arthritis. {ECO:0000269 PubMed:10205262, ECO:0000269 PubMed:10340975, ECO:0000269 PubMed:10482952, ECO:0000269 PubMed:10594001, ECO:0000269 PubMed:19862842, ECO:0000269 PubMed:21437689, ECO:0000269 PubMed:23353776, ECO:0000269 PubMed:23430897, ECO:0000269 PubMed:25681086, ECO:0000269 PubMed:8782815, ECO:0000269 PubMed:9154114, ECO:0000269 PubMed:9529363, ECO:0000269 PubMed:9630082}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HGD

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HGD: view

No data available for Genatlas for HGD Gene

Publications for HGD Gene

  1. Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria. (PMID: 19862842) Vilboux T … Gahl WA (Human mutation 2009) 3 4 22 58
  2. Crystal structure of human homogentisate dioxygenase. (PMID: 10876237) Titus GP … Timm DE (Nature structural biology 2000) 3 4 22 58
  3. Mutational analysis of the HGO gene in Finnish alkaptonuria patients. (PMID: 10594001) Beltrán-Valero de Bernabé D … Ranki A (Journal of medical genetics 1999) 3 4 22 58
  4. Allelic heterogeneity of alkaptonuria in Central Europe. (PMID: 10482952) Müller CR … Kress W (European journal of human genetics : EJHG 1999) 3 4 22 58
  5. Ocular ochronosis in alkaptonuria patients carrying mutations in the homogentisate 1,2-dioxygenase gene. (PMID: 10340975) Felbor U … Kress W (The British journal of ophthalmology 1999) 3 4 22 58

Products for HGD Gene

Sources for HGD Gene

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