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Aliases for HNMT Gene

Aliases for HNMT Gene

  • Histamine N-Methyltransferase 2 3 5
  • EC 4 63
  • HMT 3 4
  • HNMT-S1 3
  • HNMT-S2 3
  • MRT51 3

External Ids for HNMT Gene

Previous GeneCards Identifiers for HNMT Gene

  • GC02P136386
  • GC02P137029
  • GC02P138744
  • GC02P138932
  • GC02P138555
  • GC02P138438
  • GC02P130713

Summaries for HNMT Gene

Entrez Gene Summary for HNMT Gene

  • In mammals, histamine is metabolized by two major pathways: N(tau)-methylation via histamine N-methyltransferase and oxidative deamination via diamine oxidase. This gene encodes the first enzyme which is found in the cytosol and uses S-adenosyl-L-methionine as the methyl donor. In the mammalian brain, the neurotransmitter activity of histamine is controlled by N(tau)-methylation as diamine oxidase is not found in the central nervous system. A common genetic polymorphism affects the activity levels of this gene product in red blood cells. Multiple alternatively spliced transcript variants that encode different proteins have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for HNMT Gene

HNMT (Histamine N-Methyltransferase) is a Protein Coding gene. Diseases associated with HNMT include Asthma and Autosomal Recessive Non-Syndromic Intellectual Disability. Among its related pathways are Histidine metabolism and Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism. GO annotations related to this gene include N-methyltransferase activity and histamine N-methyltransferase activity.

UniProtKB/Swiss-Prot for HNMT Gene

  • Inactivates histamine by N-methylation. Plays an important role in degrading histamine and in regulating the airway response to histamine.

Tocris Summary for HNMT Gene

  • Protein arginine methyltransferases are enyzmes that catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the arginine residues on histones and other proteins. The dysregulation of this methylation is critical in the development of certain cancers.

No data available for Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HNMT Gene

Genomics for HNMT Gene

Regulatory Elements for HNMT Gene

Enhancers for HNMT Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around HNMT on UCSC Golden Path with GeneCards custom track

Promoters for HNMT Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HNMT on UCSC Golden Path with GeneCards custom track

Genomic Location for HNMT Gene

137,964,020 bp from pter
138,016,364 bp from pter
52,345 bases
Plus strand

Genomic View for HNMT Gene

Genes around HNMT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HNMT Gene

Proteins for HNMT Gene

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

    Protein Symbol:
    Recommended name:
    Histamine N-methyltransferase
    Protein Accession:
    Secondary Accessions:
    • B2R9J3
    • Q546Z6
    • Q7Z7I2
    • Q8IU56
    • Q8WW98
    • Q9BRW6

    Protein attributes for HNMT Gene

    292 amino acids
    Molecular mass:
    33295 Da
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for HNMT Gene

    Alternative splice isoforms for HNMT Gene


neXtProt entry for HNMT Gene

Proteomics data for HNMT Gene at MOPED

Post-translational modifications for HNMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HNMT Gene

Antibody Products

  • R&D Systems Antibodies for HNMT (Histamine N-Methyltransferase/HNMT)
  • Abcam antibodies for HNMT

Domains & Families for HNMT Gene

Protein Domains for HNMT Gene


Suggested Antigen Peptide Sequences for HNMT Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the class I-like SAM-binding methyltransferase superfamily. HNMT family.
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. HNMT family.
genes like me logo Genes that share domains with HNMT: view

No data available for Gene Families for HNMT Gene

Function for HNMT Gene

Molecular function for HNMT Gene

GENATLAS Biochemistry:
histamine N-methyltransferase,S-adenosyl-L-methionine dependent cytosolic enzyme
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + histamine = S-adenosyl-L-homocysteine + N(tau)-methylhistamine.
UniProtKB/Swiss-Prot Function:
Inactivates histamine by N-methylation. Plays an important role in degrading histamine and in regulating the airway response to histamine.

Enzyme Numbers (IUBMB) for HNMT Gene

genes like me logo Genes that share phenotypes with HNMT: view

Animal Model Products

No data available for Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HNMT Gene

Localization for HNMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for HNMT Gene


Subcellular locations from

Jensen Localization Image for HNMT Gene COMPARTMENTS Subcellular localization image for HNMT gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for HNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with HNMT: view

Pathways & Interactions for HNMT Gene

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

Interacting Proteins for HNMT Gene

Gene Ontology (GO) - Biological Process for HNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002347 response to tumor cell IEA --
GO:0006548 histidine catabolic process TAS --
GO:0006972 hyperosmotic response IEA --
GO:0014075 response to amine IEA --
GO:0032259 methylation IBA --
genes like me logo Genes that share ontologies with HNMT: view

No data available for SIGNOR curated interactions for HNMT Gene

Drugs & Compounds for HNMT Gene

(17) Drugs for HNMT Gene - From: DrugBank, PharmGKB, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Amodiaquine Approved Pharma Target, inhibitor 94
Quinacrine Approved Pharma Enzyme, inhibitor 6
Chlorhexidine Approved Pharma Enzyme, inhibitor 438
Histamine Phosphate Approved Pharma Enzyme, substrate 998
S-Adenosylmethionine Approved Nutra 0

(11) Additional Compounds for HNMT Gene - From: Tocris, Novoseek, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 1-Methyl-1H-imidazole-4-ethanamine
  • 1-Methyl-4-(2-aminoethyl)imidazole
  • 1-Methyl-4-(b-aminoethyl)imidazole
  • 1-Methyl-4-(beta-aminoethyl)imidazole
  • 1-Methyl-4-histamine
C 21
Furamidine dihydrochloride
SGC 707
TC-E 5003

(5) Tocris Compounds for HNMT Gene

Compound Action Cas Number
C 21 Selective PRMT1 inhibitor 1229236-78-5
Furamidine dihydrochloride Selective PRMT1 inhibitor 55368-40-6
SGC 707 Potent and selective allosteric inhibitor of PRMT3
TC-E 5003 Selective PRMT1 inhibitor 17328-16-4
UNC 2327 Allosteric inhibitor of PRMT3 1426152-53-5
genes like me logo Genes that share compounds with HNMT: view

Transcripts for HNMT Gene

Unigene Clusters for HNMT Gene

Histamine N-methyltransferase:
Representative Sequences:

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

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: - - - -
SP2: -
SP3: - - -
SP4: -
SP5: - -

Relevant External Links for HNMT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HNMT Gene

mRNA expression in normal human tissues for HNMT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HNMT Gene

This gene is overexpressed in Uterus (9.8) and Spleen (6.6).

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

SOURCE GeneReport for Unigene cluster for HNMT Gene Hs.42151

genes like me logo Genes that share expression patterns with HNMT: view

Protein tissue co-expression partners for HNMT Gene

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HNMT Gene

Orthologs for HNMT Gene

This gene was present in the common ancestor of chordates.

Orthologs for HNMT Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia HNMT 35
  • 89.38 (n)
  • 87.33 (a)
  • 87 (a)
(Canis familiaris)
Mammalia HNMT 35
  • 90.53 (n)
  • 87.67 (a)
  • 83 (a)
(Mus musculus)
Mammalia Hnmt 35
  • 86.76 (n)
  • 83.9 (a)
Hnmt 16
Hnmt 36
  • 83 (a)
(Pan troglodytes)
Mammalia HNMT 35
  • 99.54 (n)
  • 98.97 (a)
  • 99 (a)
(Rattus norvegicus)
Mammalia Hnmt 35
  • 86.3 (n)
  • 84.25 (a)
(Monodelphis domestica)
Mammalia HNMT 36
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia HNMT 36
  • 56 (a)
(Gallus gallus)
Aves HNMT 35
  • 67.58 (n)
  • 60.14 (a)
  • 60 (a)
(Anolis carolinensis)
Reptilia HNMT 36
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hnmt 35
  • 61.4 (n)
  • 58.08 (a)
African clawed frog
(Xenopus laevis)
Amphibia hnmt-prov 35
(Danio rerio)
Actinopterygii Dr.17340 35
hnmt 35
  • 55.37 (n)
  • 43.84 (a)
hnmt 36
  • 38 (a)
Species with no ortholog for HNMT:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for HNMT Gene

Gene Tree for HNMT (if available)
Gene Tree for HNMT (if available)

Paralogs for HNMT Gene

No data available for Paralogs for HNMT Gene

Variants for HNMT Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HNMT Gene

Variant Ile-105 has a reduced activity and seems to be linked with a predisposition to asthma.

Sequence variations from dbSNP and Humsavar for HNMT Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
VAR_010252 -
rs1580111 -- 137,991,487(-) ataac(A/G)tgttt intron-variant
rs1580112 -- 137,991,320(-) TTTTC(A/G)TCCAA intron-variant
rs1580113 -- 137,991,273(-) cctat(C/T)caatg intron-variant
rs2737377 -- 138,006,328(+) TTGAT(G/T)ATATT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv7329 OTHER Inversion 18451855
nsv875159 CNV Gain 21882294
esv2671408 CNV Deletion 23128226
nsv875160 CNV Loss 21882294
esv34124 CNV Loss 18971310
nsv875161 CNV Loss 21882294
esv2513921 CNV Deletion 19546169

Variation tolerance for HNMT Gene

Residual Variation Intolerance Score: 59.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.01; 68.45% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HNMT Gene

Human Gene Mutation Database (HGMD)

Disorders for HNMT Gene

MalaCards: The human disease database

(11) MalaCards diseases for HNMT Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • asthma, protection against
autosomal recessive non-syndromic intellectual disability
  • autosomal recessive mental retardation
heel spur
  • calcaneal spur
suppression amblyopia
  • strabismic amblyopia
erythema multiforme
  • stevens-johnson syndrome
- elite association - COSMIC cancer census association via MalaCards
Search HNMT in MalaCards View complete list of genes associated with diseases

Relevant External Links for HNMT

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

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

Publications for HNMT Gene

  1. Histamine N-methyltransferase pharmacogenetics: association of a common functional polymorphism with asthma. (PMID: 10803682) Yan L. … Weinshilboum R.M. (Pharmacogenetics 2000) 3 4 23 48 67
  2. Histamine pharmacogenomics. (PMID: 19450133) GarcA-a-MartA-n E. … AgA_ndez J.A. (Pharmacogenomics 2009) 23 25 26
  3. Imidazole derivatives as a novel class of hybrid compounds with inhibitory histamine N-methyltransferase potencies and histamine hH3 receptor affinities. (PMID: 12713826) Grassmann S. … Stark H. (Bioorg. Med. Chem. 2003) 23 25 26
  4. The role of HMT (histamine N-methyltransferase) in airways: a review. (PMID: 8750789) Okinaga S. … Sasaki H. (Methods Find Exp Clin Pharmacol 1995) 23 25 26
  5. Histamine-N-methyl transferase polymorphism and risk for multiple sclerosis. (PMID: 19538200) GarcA-a-MartA-n E. … JimAcnez-JimAcnez F.J. (Eur. J. Neurol. 2010) 3 23

Products for HNMT Gene

Sources for HNMT Gene