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Aliases for HNMT Gene

Aliases for HNMT Gene

  • Histamine N-Methyltransferase 2 3 3 5
  • HMT 3 4
  • EC 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 Mental Retardation, Autosomal Recessive 51 and Asthma. Among its related pathways are Cytochrome P450 - arranged by substrate type and Metabolism. Gene Ontology (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.

Additional gene information for HNMT Gene

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

Genomics for HNMT Gene

GeneHancer (GH) Regulatory Elements for HNMT Gene

Promoters and enhancers for HNMT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J137962 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 656.5 +0.8 821 3.9 PKNOX1 CLOCK FOXA2 MLX ARID4B DMAP1 YY1 DEK PAF1 ZNF263 HNMT ENSG00000260059 LOC105373637 SPOPL LOC105373636
GH02J137939 Enhancer 1 ENCODE 20.7 -21.3 -21312 6.7 FOXA2 MLX DMAP1 ZNF48 ETS1 YY1 TCF12 FOS PAF1 RXRA HNMT SPOPL LOC101928273
GH02J138028 Enhancer 0.9 Ensembl ENCODE 10.5 +64.4 64447 0.9 HDAC1 BATF YY1 TCF12 VEZF1 ETV6 SMARCE1 PHF21A CBFA2T3 JUNB HNMT LOC105373636
GH02J138071 Enhancer 0.9 ENCODE 10.3 +108.2 108212 2 PKNOX1 NEUROD1 SIN3A FEZF1 ZNF2 BRCA1 FOS SP3 TSHZ1 ZNF623 HNMT LOC105373636 LINC01832
GH02J137951 Enhancer 1.2 FANTOM5 Ensembl ENCODE 7.6 -11.5 -11480 1.7 HDAC1 ELF3 ZBTB40 ZNF766 FOS IKZF2 NCOA1 ELF1 ZNF592 SP1 HNMT SPOPL LOC101928273
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HNMT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HNMT gene promoter:
  • Cdc5
  • ATF-2
  • Hand1
  • E47
  • SRF (504 AA)
  • SRF
  • HFH-1
  • POU2F1
  • POU2F1a
  • POU2F1b

Genomic Locations for HNMT Gene

Genomic Locations for HNMT Gene
52,345 bases
Plus strand
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

Post-translational modifications for HNMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • R&D Systems Antibodies for HNMT (Histamine N-Methyltransferase/HNMT)
  • Boster Bio Antibodies for HNMT
  • Santa Cruz Biotechnology (SCBT) Antibodies for HNMT

No data available for DME Specific Peptides for HNMT Gene

Domains & Families for HNMT Gene

Gene Families for HNMT Gene

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

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

Function for HNMT Gene

Molecular function for HNMT Gene

UniProtKB/Swiss-Prot Function:
Inactivates histamine by N-methylation. Plays an important role in degrading histamine and in regulating the airway response to histamine.
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + histamine = S-adenosyl-L-homocysteine + N(tau)-methylhistamine.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=5.47 uM for histamine (at pH 8.0 and 25 degrees Celsius) {ECO:0000269 PubMed:26206890};
GENATLAS Biochemistry:
histamine N-methyltransferase,S-adenosyl-L-methionine dependent cytosolic enzyme

Enzyme Numbers (IUBMB) for HNMT Gene

Gene Ontology (GO) - Molecular Function for HNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0008170 N-methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0046539 histamine N-methyltransferase activity TAS --
genes like me logo Genes that share ontologies with HNMT: view
genes like me logo Genes that share phenotypes with HNMT: view

Human Phenotype Ontology for HNMT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HNMT Gene

MGI Knock Outs for HNMT:
  • Hnmt Hnmt<tm1a(KOMP)Wtsi>

Animal Model Products

Clone Products

No data available for Phenotypes From GWAS Catalog , 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

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 HNMT gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 4
mitochondrion 1

Gene Ontology (GO) - Cellular Components for HNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 26206890
GO:0005829 cytosol TAS --
GO:0043005 neuron projection IBA --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with HNMT: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HNMT Gene

Pathways & Interactions for HNMT Gene

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

Gene Ontology (GO) - Biological Process for HNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001695 histamine catabolic process IDA 26206890
GO:0006548 histidine catabolic process TAS --
GO:0007420 brain development IBA --
GO:0007585 respiratory gaseous exchange TAS 7943261
GO:0032259 methylation IDA,IEA 26206890
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Amodiaquine Approved, Investigational Pharma Target, inhibitor 101
Histamine Approved, Investigational Pharma Full agonist, Agonist, Enzyme, substrate 1105
Quinacrine Approved, Investigational Pharma Enzyme, inhibitor 6
Chlorhexidine Approved, Vet_approved Pharma Enzyme, inhibitor 545
Aspirin Approved, Vet_approved Pharma Channel blocker 1232

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
  • 1-Methyl-1H-imidazole-4-ethanamine
  • 1-Methyl-4-(2-aminoethyl)imidazole
  • 3-Methylhistamine
  • 4-(1-Aminoethyl)-1-methyl-1H-imidazole
  • Methylhistamine
Furamidine dihydrochloride
SGC 707
UNC 2327

(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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for HNMT Gene

Protein tissue co-expression partners for HNMT Gene

NURSA nuclear receptor signaling pathways regulating expression of HNMT Gene:


SOURCE GeneReport for Unigene cluster for HNMT Gene:


Evidence on tissue expression from TISSUES for HNMT Gene

  • Nervous system(4.6)
  • Kidney(4.5)
  • Liver(4.5)
  • Intestine(2.3)
  • Lung(2.3)
genes like me logo Genes that share expression patterns with HNMT: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia HNMT 34 33
  • 99.54 (n)
(Canis familiaris)
Mammalia HNMT 34 33
  • 90.53 (n)
(Bos Taurus)
Mammalia HNMT 34 33
  • 89.38 (n)
(Mus musculus)
Mammalia Hnmt 16 34 33
  • 86.76 (n)
(Rattus norvegicus)
Mammalia Hnmt 33
  • 86.3 (n)
(Monodelphis domestica)
Mammalia HNMT 34
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia HNMT 34
  • 56 (a)
(Gallus gallus)
Aves HNMT 34 33
  • 67.58 (n)
(Anolis carolinensis)
Reptilia HNMT 34
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hnmt 33
  • 61.4 (n)
African clawed frog
(Xenopus laevis)
Amphibia hnmt-prov 33
(Danio rerio)
Actinopterygii hnmt 34 33
  • 55.37 (n)
Dr.17340 33
Species where no ortholog for HNMT was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for HNMT: view image

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 Variation AA Info Type
rs11558538 risk-factor, Asthma, susceptibility to 138,002,079(+) C/T 5_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs745756308 pathogenic, Mental retardation, autosomal recessive 51, Mental retardation, autosomal recessive 51 (MRT51) [MIM:616739] 138,013,874(+) T/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs758252808 pathogenic, Mental retardation, autosomal recessive 51, Mental retardation, autosomal recessive 51 (MRT51) [MIM:616739] 137,970,206(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs765863580 likely-pathogenic, not provided 138,005,176(+) CC/C coding_sequence_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000046703 -- 137,976,053(+) G/T genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
esv2513921 CNV deletion 19546169
esv2671408 CNV deletion 23128226
esv34124 CNV loss 18971310
nsv583180 CNV gain 21841781
nsv583182 CNV loss 21841781
nsv7329 OTHER inversion 18451855

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)

Additional Variant Information for HNMT Gene

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

SNP Genotyping and Copy Number Assay Products

Disorders for HNMT Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
mental retardation, autosomal recessive 51
  • mrt51
  • asthma, susceptibility to
autosomal recessive non-syndromic intellectual disability
  • autosomal recessive mental retardation
mental retardation, x-linked, syndromic 13
  • mrxs13
heel spur
  • calcaneal spur
- elite association - COSMIC cancer census association via MalaCards
Search HNMT in MalaCards View complete list of genes associated with diseases


  • Mental retardation, autosomal recessive 51 (MRT51) [MIM:616739]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:26206890}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry.

Additional Disease Information for HNMT

Genetic Association Database
Human Genome Epidemiology 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 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 RM (Pharmacogenetics 2000) 3 4 22 44 58
  2. Histamine-N-methyl transferase polymorphism and risk for multiple sclerosis. (PMID: 19538200) García-Martín E … Jiménez-Jiménez FJ (European journal of neurology 2010) 3 22 44 58
  3. Histamine N-methyltransferase Thr105Ile is not associated with Parkinson's disease or essential tremor. (PMID: 19773194) Keeling BH … Farrer MJ (Parkinsonism & related disorders 2010) 3 22 44 58
  4. Histamine N-methyltransferase 939A>G polymorphism affects mRNA stability in patients with acetylsalicylic acid-intolerant chronic urticaria. (PMID: 19178400) Kim SH … Park HS (Allergy 2009) 3 22 44 58
  5. Nonsynonymous polymorphisms of histamine-metabolising enzymes in patients with Parkinson's disease. (PMID: 17985251) Agúndez JA … García-Martín E (Neuromolecular medicine 2008) 3 22 44 58

Products for HNMT Gene

Sources for HNMT Gene

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