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] See more...

Aliases for HDC Gene

Aliases for HDC Gene

  • Histidine Decarboxylase 2 3 4 5
  • EC 4.1.1.22 4 52
  • EC 4.1.1 52

External Ids for HDC Gene

Previous GeneCards Identifiers for HDC Gene

  • GC15M046091
  • GC15M043580
  • GC15M048113
  • GC15M048250
  • GC15M048321
  • GC15M050534
  • GC15M027365

Summaries for HDC Gene

Entrez Gene Summary for HDC Gene

  • 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]

GeneCards Summary for HDC Gene

HDC (Histidine Decarboxylase) is a Protein Coding gene. Diseases associated with HDC include Gilles De La Tourette Syndrome and Mastocytosis, Cutaneous. Among its related pathways are Metabolism and Amino Acid metabolism. Gene Ontology (GO) annotations related to this gene include pyridoxal phosphate binding and histidine decarboxylase activity. An important paralog of this gene is DDC.

UniProtKB/Swiss-Prot Summary for HDC Gene

Gene Wiki entry for HDC Gene

Additional gene information for HDC Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HDC Gene

Genomics for HDC Gene

GeneHancer (GH) Regulatory Elements for HDC Gene

Promoters and enhancers for HDC 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
GH15J050265 Promoter/Enhancer 0.5 EPDnew Ensembl 500.7 +0.3 291 0.8 HDC piR-32214-214
GH15J050264 Enhancer 0.2 Ensembl 500.7 +1.6 1590 0.2 HDC piR-32214-214
GH15J050256 Enhancer 1.4 FANTOM5 Ensembl ENCODE 21.7 +6.4 6390 8.2 ZNF217 CTCF TCF12 GTF2E2 PHB2 FOS ZBTB5 EP300 ZBTB11 AFF1 HDC GABPB1-AS1 ENSG00000259715 SLC27A2 ATP8B4 GABPB1 TRPM7 USP8 piR-32214-214 piR-45035-066
GH15J050349 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.4 -87.3 -87270 8.5 LARP7 ZBTB40 ZNF217 EP300 SIN3A NRF1 MYC TCF12 POLR2G GTF2E2 GABPB1-AS1 GABPB1 GABPB1-IT1 ENSG00000259715 USP8 TRPM7 ENSG00000259298 AP4E1 ENSG00000259618 ENSG00000242737
GH15J050226 Enhancer 0.8 Ensembl ENCODE 12.5 +39.5 39490 2 FOXA2 NR2F2 CEBPB ZNF316 CEBPG ZBTB33 JUND RXRA MAX HNF4A SLC27A2 HDC ENSG00000200605 RF00017-1783 lnc-GABPB1-2 RN7SL494P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HDC on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HDC

Top Transcription factor binding sites by QIAGEN in the HDC gene promoter:
  • FOXD3
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXO4
  • GR
  • GR-alpha
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • Sp1

Genomic Locations for HDC Gene

Genomic Locations for HDC Gene
chr15:50,241,945-50,266,091
(GRCh38/hg38)
Size:
24,147 bases
Orientation:
Minus strand
chr15:50,534,144-50,558,223
(GRCh37/hg19)
Size:
24,080 bases
Orientation:
Minus strand

Genomic View for HDC Gene

Genes around HDC on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HDC Gene

Proteins for HDC Gene

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

    Protein Symbol:
    P19113-DCHS_HUMAN
    Recommended name:
    Histidine decarboxylase
    Protein Accession:
    P19113
    Secondary Accessions:
    • A1L4G0
    • B7ZM01

    Protein attributes for HDC Gene

    Size:
    662 amino acids
    Molecular mass:
    74141 Da
    Cofactor:
    Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for HDC Gene

    Alternative splice isoforms for HDC Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDC Gene

Selected DME Specific Peptides for HDC Gene

P19113:
  • SDQAHSSVE
  • PSLLGDMLADAINCLGFTWASSPACTELE
  • QLPCCPL
  • SPACTELE
  • HWQSPHMHAY
  • NFSLRGEALQKAI
  • DFMHWQIPLSRRFR

Post-translational modifications for HDC Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for HDC Gene

Gene Families for HDC Gene

IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for HDC Gene

Blocks:
  • Pyridoxal-dependent decarboxylase
  • Aromatic-L-amino-acid decarboxylase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HDC Gene

GenScript: Design optimal peptide antigens:
  • Histidine decarboxylase (DCHS_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P19113

UniProtKB/Swiss-Prot:

DCHS_HUMAN :
  • Belongs to the group II decarboxylase family.
Family:
  • Belongs to the group II decarboxylase family.
genes like me logo Genes that share domains with HDC: view

Function for HDC Gene

Molecular function for HDC Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the biosynthesis of histamine from histidine.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H(+) + L-histidine = CO2 + histamine; Xref=Rhea:RHEA:20840, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57595, ChEBI:CHEBI:58432; EC=4.1.1.22; Evidence=. ;.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.1 mM for histidine {ECO:0000269 PubMed:22767596}; Vmax=1880 nmol/min/mg enzyme {ECO:0000269 PubMed:22767596};
GENATLAS Biochemistry:
histidine decarboxylase,brain,catalyzing the histidine synthesis

Enzyme Numbers (IUBMB) for HDC Gene

Phenotypes From GWAS Catalog for HDC Gene

Gene Ontology (GO) - Molecular Function for HDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004398 histidine decarboxylase activity TAS,IDA 22767596
GO:0005515 protein binding IPI 25416956
GO:0016829 lyase activity IEA --
GO:0016831 carboxy-lyase activity IEA --
genes like me logo Genes that share ontologies with HDC: view
genes like me logo Genes that share phenotypes with HDC: view

Human Phenotype Ontology for HDC Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HDC Gene

MGI Knock Outs for HDC:
  • Hdc Hdc<tm1Nagy>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDC

No data available for miRNA , Transcription Factor Targets and HOMER Transcription for HDC Gene

Localization for HDC 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 HDC gene
Compartment Confidence
cytosol 5
nucleus 3
plasma membrane 2
extracellular 2
endoplasmic reticulum 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with HDC: view

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

Pathways & Interactions for HDC Gene

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

UniProtKB/Swiss-Prot P19113-DCHS_HUMAN

  • Pathway: Amine and polyamine biosynthesis; histamine biosynthesis; histamine from L-histidine: step 1/1.

Gene Ontology (GO) - Biological Process for HDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001694 histamine biosynthetic process TAS --
GO:0006520 cellular amino acid metabolic process IEA --
GO:0006547 histidine metabolic process TAS 1487235
GO:0006548 histidine catabolic process IDA 22767596
GO:0019752 carboxylic acid metabolic process IEA --
genes like me logo Genes that share ontologies with HDC: view

No data available for SIGNOR curated interactions for HDC Gene

Drugs & Compounds for HDC Gene

(28) Drugs for HDC Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 20
Histamine Approved, Investigational Pharma Full agonist, Agonist 1227
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0
Pyruvic acid Approved, Investigational Nutra 0
spermidine Experimental Pharma Antagonist, Pore Blocker 0

(24) Additional Compounds for HDC Gene - From: Novoseek, HMDB, and IUPHAR

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
SAM486A
Inhibition, Inhibitor
N1-acetylspermine
  • N'-acetylspermine
  • N'-monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-acetamide
  • N-Acetylspermine
25593-72-0
Norspermidine
  • 1,7-diamino-4-Azaheptane
  • 3,3'-Iminobis(propylamine)
  • 3,3'-Iminobispropylamine
  • 3,3'-Iminodi(propylamine)
  • 3,3-Diaminodipropylamine
56-18-8
genes like me logo Genes that share compounds with HDC: view

Transcripts for HDC Gene

mRNA/cDNA for HDC Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDC

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

No ASD Table

Relevant External Links for HDC Gene

GeneLoc Exon Structure for
HDC

Expression for HDC Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Hypothalamus (x28.0).

Protein differential expression in normal tissues from HIPED for HDC Gene

This gene is overexpressed in Urine (64.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HDC Gene



Protein tissue co-expression partners for HDC Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HDC

SOURCE GeneReport for Unigene cluster for HDC Gene:

Hs.1481

Evidence on tissue expression from TISSUES for HDC Gene

  • Stomach(3.3)
  • Nervous system(2.7)
  • Lung(2.2)
  • Bone marrow(2.1)
  • Skin(2)
genes like me logo Genes that share expression patterns with HDC: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDC Gene

Orthologs for HDC Gene

This gene was present in the common ancestor of animals.

Orthologs for HDC Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HDC 31 30
  • 99.7 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HDC 31 30
  • 91.39 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HDC 31 30
  • 89.87 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hdc 30
  • 86.15 (n)
mouse
(Mus musculus)
Mammalia Hdc 17 31 30
  • 85.9 (n)
oppossum
(Monodelphis domestica)
Mammalia HDC 31
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HDC 31
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves HDC 31 30
  • 73.03 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HDC 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hdc 30
  • 70.24 (n)
zebrafish
(Danio rerio)
Actinopterygii hdc 31 30
  • 66.86 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009001 30
  • 61.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta Hdc 31 32 30
  • 60.99 (n)
OneToOne
Ddc 32
  • 51 (a)
CG30446 32
  • 49 (a)
CG30445 32
  • 49 (a)
amd 32
  • 38 (a)
worm
(Caenorhabditis elegans)
Secernentea ZK829.2 32
  • 39 (a)
tdc-1 31 32
  • 36 (a)
ManyToMany
C05D2.3 32
  • 33 (a)
F12A10.3 32
  • 30 (a)
hdl-1 31
  • 22 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 22 (a)
ManyToMany
-- 31
  • 21 (a)
ManyToMany
Species where no ortholog for HDC was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HDC Gene

ENSEMBL:
Gene Tree for HDC (if available)
TreeFam:
Gene Tree for HDC (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HDC: view image

Paralogs for HDC Gene

Paralogs for HDC Gene

(2) SIMAP similar genes for HDC Gene using alignment to 3 proteins:

  • DCHS_HUMAN
  • B7ZM01_HUMAN
  • H0YLF0_HUMAN
genes like me logo Genes that share paralogs with HDC: view

Variants for HDC Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HDC Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
713554 Likely Benign: not provided 50,242,769(-) T/C MISSENSE_VARIANT
752661 Likely Benign: not provided 50,253,664(-) G/A SYNONYMOUS_VARIANT
773049 Benign: not provided 50,242,506(-) C/T SYNONYMOUS_VARIANT
776888 Benign: not provided 50,242,592(-) A/G MISSENSE_VARIANT
rs1353958864 A colorectal cancer sample p.Glu285Lys

Additional dbSNP identifiers (rs#s) for HDC Gene

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

Variant ID Type Subtype PubMed ID
nsv1531 CNV insertion 18451855

Variation tolerance for HDC Gene

Residual Variation Intolerance Score: 10.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.65; 72.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDC Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for HDC Gene

MalaCards: The human disease database

(14) MalaCards diseases for HDC Gene - From: ClinVar, GTR, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
gilles de la tourette syndrome
  • gts
mastocytosis, cutaneous
  • mastc
systemic mastocytosis
  • corneal dystrophy, subepithelial mucinous
mastocytosis
  • mast cell hyperplasia
stomach disease
  • gastric disease
- elite association - COSMIC cancer census association via MalaCards
Search HDC in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HDC

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 HDC: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HDC Gene

Publications for HDC Gene

  1. HDC gene polymorphisms are associated with age at natural menopause in Caucasian women. (PMID: 16919600) Zhang F … Deng HW (Biochemical and biophysical research communications 2006) 3 23 41 54
  2. Structure of the L-histidine decarboxylase gene. (PMID: 8288622) Yatsunami K … Yamamoto M (The Journal of biological chemistry 1994) 3 4 23 54
  3. Preparation of a rat brain histidine decarboxylase (HDC) cDNA probe by PCR and assignment of the human HDC gene to chromosome 15. (PMID: 1487235) Bruneau G … Thibault J (Human genetics 1992) 2 3 23 54
  4. Cloning of the cDNA encoding human histidine decarboxylase from an erythroleukemia cell line and mapping of the gene locus to chromosome 15. (PMID: 1768863) Zahnow CA … Joseph DR (DNA sequence : the journal of DNA sequencing and mapping 1991) 3 4 23 54
  5. Structural study reveals that Ser-354 determines substrate specificity on human histidine decarboxylase. (PMID: 22767596) Komori H … Higuchi Y (The Journal of biological chemistry 2012) 3 4 54

Products for HDC Gene

Sources for HDC Gene