HDC (histidine decarboxylase)

Gene

• Entrez ID: 3067
• Gene name: Histidine decarboxylase
• Gene symbol: HDC
• Synonyms (NCBI Gene): -
• Chromosome: 15
• Chromosome location: 15q21.2
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs267606861	C>T	Pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2241373	hsa-miR-4643	CLIP-seq
MIRT2241374	hsa-miR-466	CLIP-seq
MIRT2241375	hsa-miR-4789-3p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HDAC7	Repression	17827213
KAT5	Repression	17827213
KLF4	Repression	14670968;17827213

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001694	Process	Histamine biosynthetic process	IBA
GO:0001694	Process	Histamine biosynthetic process	IDA	22767596
GO:0001694	Process	Histamine biosynthetic process	IEA
GO:0001694	Process	Histamine biosynthetic process	IEA
GO:0004398	Function	Histidine decarboxylase activity	IBA
GO:0004398	Function	Histidine decarboxylase activity	IDA	22767596
GO:0004398	Function	Histidine decarboxylase activity	IEA
GO:0004398	Function	Histidine decarboxylase activity	TAS	1487235
GO:0005515	Function	Protein binding	IPI	25416956
GO:0005737	Component	Cytoplasm	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006520	Process	Amino acid metabolic process	IEA
GO:0006547	Process	L-histidine metabolic process	TAS	1487235
GO:0006548	Process	L-histidine catabolic process	IBA
GO:0006548	Process	L-histidine catabolic process	IDA	22767596
GO:0006548	Process	L-histidine catabolic process	IEA
GO:0016829	Function	Lyase activity	IEA
GO:0016830	Function	Carbon-carbon lyase activity	IEA
GO:0016831	Function	Carboxy-lyase activity	IEA
GO:0019752	Process	Carboxylic acid metabolic process	IEA
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0042401	Process	Biogenic amine biosynthetic process	IEA
GO:0042423	Process	Catecholamine biosynthetic process	IEA

Other IDs

• MIM: 142704
• HGNC: 4855
• e!Ensembl: ENSG00000140287

Protein

• UniProt ID: P19113
• Protein name: Histidine decarboxylase (HDC) (EC 4.1.1.22)
• Protein function: Catalyzes the biosynthesis of histamine from histidine.
• PDB: 4E1O, 7EIW, 7EIX, 7EIY
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00282	Pyridoxal_deC	36 → 414	Pyridoxal-dependent decarboxylase conserved domain	Domain

• Sequence:

  MMEPEEYRERGREMVDYICQYLSTVRERRVTPDVQPGYLRAQLPESAPEDPDSWDSIFGD
  IERIIMPGVVHWQSPHMHAYYPALTSWPSLLGDMLADAINCLGFTWASSPACTELEMNVM
  DWLAKMLGLPEHFLHHHPSSQGGGVLQSTVSESTLIALLAARKNKILEMKTSEPDADESC
  LNARLVAYASDQAHSSVEKAGLISLVKMKFLPVDDNFSLRGEALQKAIEEDKQRGLVPVF
  VCATLGTTGVCAFDCLSELGPICAREGLWLHIDAAYAGTAFLCPEFRGFLKGIEYADSFT
  FNPSKWMMVHFDCTGFWVKDKYKLQQTFSVNPIYLRHANSGVATDFMHWQIPLSRRFRSV
  KLWFVIRSFGVKNLQAHVRHGTEMAKYFESLVRNDPSFEIPAKRHLGLVVFRLKGPNCLT
  ENVLKEIAKAGRLFLIPATIQDKLIIRFTVTSQFTTRDDILRDWNLIRDAATLILSQHCT
  SQPSPRVGNLISQIRGARAWACGTSLQSVSGAGDDPVQARKIIKQPQRVGAGPMKRENGL
  HLETLLDPVDDCFSEEAPDATKHKLSSFLFSYLSVQTKKKTVRSLSCNSVPVSAQKPLPT
  EASVKNGGSSRVRIFSRFPEDMMMLKKSAFKKLIKFYSVPSFPECSSQCGLQLPCCPLQA
  MV

• Sequence length: 662

Pathways

KEGG:

Histidine metabolism
Metabolic pathways

Reactome:

Histidine catabolism

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Tourette syndrome	Pathogenic; Likely pathogenic	rs267606861, rs2509380645	RCV000016047 RCV003993575	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GILLES DE LA TOURETTE SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HDC-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEPATOMEGALY	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHINITIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations