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    HDC histidine decarboxylase [ Homo sapiens (human) ]

    Gene ID: 3067, updated on 28-Oct-2024

    Summary

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    Official Symbol
    HDCprovided by HGNC
    Official Full Name
    histidine decarboxylaseprovided by HGNC
    Primary source
    HGNC:HGNC:4855
    See related
    Ensembl:ENSG00000140287 MIM:142704; AllianceGenome:HGNC:4855
    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
    Summary
    This gene encodes a member of the group II decarboxylase family and forms a homodimer that converts L-histidine to histamine in a pyridoxal phosphate dependent manner. Histamine regulates several physiologic processes, including neurotransmission, gastric acid secretion,inflamation, and smooth muscle tone.[provided by RefSeq, Aug 2010]
    Expression
    Broad expression in gall bladder (RPKM 9.0), stomach (RPKM 6.4) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HDC in Genome Data Viewer
    Location:
    15q21.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (50241947..50265726, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (48050179..48073964, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (50534144..50557923, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATPase phospholipid transporting 8B4 (putative) Neighboring gene RNA, 5S ribosomal pseudogene 394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9389 Neighboring gene Sharpr-MPRA regulatory region 771 Neighboring gene Sharpr-MPRA regulatory region 7155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9390 Neighboring gene NANOG hESC enhancer GRCh37_chr15:50408634-50409147 Neighboring gene ATP8B4 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:50502954-50503533 Neighboring gene solute carrier family 27 member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:50544247-50544748 Neighboring gene RNA, 7SL, cytoplasmic 494, pseudogene Neighboring gene GA binding protein transcription factor subunit beta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6426 Neighboring gene GABPB1 intronic transcript Neighboring gene GABPB1 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 94, pseudogene

    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 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. Detection of histamine and histidine decarboxylase in human platelets by flow cytometry. Váczi A, et al. Inflamm Res, 2001 Apr. PMID 11411619
    2. Expression of non-mast cell histidine decarboxylase in tumor-associated microvessels in human esophageal squamous cell carcinomas. Li Z, et al. APMIS, 2008 Dec. PMID 19133005
    3. HDC gene polymorphisms are associated with age at natural menopause in Caucasian women. Zhang F, et al. Biochem Biophys Res Commun, 2006 Oct 6. PMID 16919600, Free PMC Article
    4. Differential activity of histidine decarboxylase in normal and pre-eclamptic placentae. Brew O, et al. Placenta, 2007 May-Jun. PMID 16822545
    5. Histamine and histidine decarboxylase up-regulation in colorectal cancer: correlation with tumor stage. Masini E, et al. Inflamm Res, 2005 Apr. PMID 15928846

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis.
      Title: The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis.
    2. Correlation between histidine decarboxylase expression of keratinocytes and visual analogue scale in patients with atopic dermatitis.
      Title: Correlation between histidine decarboxylase expression of keratinocytes and visual analogue scale in patients with atopic dermatitis.
    3. Expression of histidine decarboxylase in melanocytes of the human skin.
      Title: Expression of histidine decarboxylase in melanocytes of the human skin.
    4. Study of the antitumour effects and the modulation of immune response by histamine in breast cancer.
      Title: Study of the antitumour effects and the modulation of immune response by histamine in breast cancer.
    5. Human histidine decarboxylase (HDC) and dopa decarboxilase (DDC) are highly homologous enzymes responsible for the synthesis of biogenic amines (BA) like histamine, and serotonin and dopamine, respectively. This review summarizes the analogies and differences in their origin as well as their common pathophysiological scenarios. [review]
      Title: Structural and functional analogies and differences between histidine decarboxylase and aromatic l-amino acid decarboxylase molecular networks: Biomedical implications.
    6. a Possible Role for the Histidine Decarboxylase Gene in Tourette Syndrome in the Chinese Han Population
      Title: Investigation of a Possible Role for the Histidine Decarboxylase Gene in Tourette Syndrome in the Chinese Han Population: A Family-Based Study.
    7. Human enterochromaffin-like cells appear to partially co-express VMAT-2 and HDC. Co-expression of VMAT-2 and HDC might be required for increased histamine production in patients with gastric neuroendocrine tumors.
      Title: Histidine decarboxylase and urinary methylimidazoleacetic acid in gastric neuroendocrine cells and tumours.
    8. The findings indicate that polymorphisms of HDC gene were significantly associated with breast cancer in Chinese Han population and may be novel diagnostic or therapeutic targets for breast cancer.
      Title: Associations of polymorphisms in histidine decarboxylase, histamine N-methyltransferase and histamine receptor H3 genes with breast cancer.
    9. HDC rs17740607 polymorphism is at least a partial loss-of-function variant and acts as a protective factor against chronic heart failure
      Title: Relation of polymorphism of the histidine decarboxylase gene to chronic heart failure in Han Chinese.
    10. Investigated variation across the HDC (histidine decarboxylase) gene for association with Tourette Syndrome.
      Title: Support of the histaminergic hypothesis in Tourette syndrome: association of the histamine decarboxylase gene in a large sample of families.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    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
    Tourette syndrome
    MedGen: C0040517 OMIM: 137580 GeneReviews: Not available
    		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

    • MGC163399

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histidine decarboxylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histidine decarboxylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in L-histidine catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in L-histidine catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in L-histidine metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in catecholamine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in histamine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in histamine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in histamine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    histidine decarboxylase
    NP_001293075.1
    NP_002103.2
    XP_016877583.1
    XP_016877584.1
    XP_016877586.1
    XP_016877587.1
    XP_016877588.1
    XP_054233733.1
    XP_054233734.1
    XP_054233735.1
    XP_054233736.1
    XP_054233737.1

    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_027487.1 RefSeqGene

      Range
      5240..29019
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001306146.2 → NP_001293075.1  histidine decarboxylase isoform 2

      See identical proteins and their annotated locations for NP_001293075.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC022087, AK027221, BC144173
      Consensus CDS
      CCDS76754.1
      UniProtKB/Swiss-Prot
      P19113
      Related
      ENSP00000440252.1, ENST00000543581.5
      Conserved Domains (1) summary
      pfam00282
      Location:36 → 381
      Pyridoxal_deC; Pyridoxal-dependent decarboxylase conserved domain

    2. NM_002112.4 → NP_002103.2  histidine decarboxylase isoform 1

      See identical proteins and their annotated locations for NP_002103.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL041199, M60445
      Consensus CDS
      CCDS10134.1
      UniProtKB/Swiss-Prot
      A1L4G0, B7ZM01, P19113
      Related
      ENSP00000267845.3, ENST00000267845.8
      Conserved Domains (1) summary
      pfam00282
      Location:36 → 414
      Pyridoxal_deC; Pyridoxal-dependent decarboxylase conserved domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      50241947..50265726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022097.2 → XP_016877586.1  histidine decarboxylase isoform X3

    2. XM_017022095.2 → XP_016877584.1  histidine decarboxylase isoform X2

    3. XM_017022094.2 → XP_016877583.1  histidine decarboxylase isoform X1

    4. XM_017022098.2 → XP_016877587.1  histidine decarboxylase isoform X4

    5. XM_017022099.2 → XP_016877588.1  histidine decarboxylase isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      48050179..48073964 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377760.1 → XP_054233735.1  histidine decarboxylase isoform X3

    2. XM_054377759.1 → XP_054233734.1  histidine decarboxylase isoform X2

    3. XM_054377758.1 → XP_054233733.1  histidine decarboxylase isoform X1

    4. XM_054377761.1 → XP_054233736.1  histidine decarboxylase isoform X4

    5. XM_054377762.1 → XP_054233737.1  histidine decarboxylase isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P19113.2 GenPept UniProtKB/Swiss-Prot:P19113

    Gene LinkOut

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

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