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HNMT histamine N-methyltransferase [ Homo sapiens (human) ]

Gene ID: 3176, updated on 17-Sep-2024

Summary

Official Symbol
HNMTprovided by HGNC
Official Full Name
histamine N-methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:5028
See related
Ensembl:ENSG00000150540 MIM:605238; AllianceGenome:HGNC:5028
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
Also known as
HMT; MRT51; HNMT-S1; HNMT-S2
Summary
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]
Expression
Ubiquitous expression in liver (RPKM 20.0), fat (RPKM 16.4) and 24 other tissues See more
Orthologs
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Genomic context

See HNMT in Genome Data Viewer
Location:
2q22.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (137964473..138016364)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (138410245..138462150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (138722043..138773934)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene thrombospondin type 1 domain containing 7B Neighboring gene RNA, 5S ribosomal pseudogene 105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:138464785-138465284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:138465941-138466440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16592 Neighboring gene uncharacterized LOC101928273 Neighboring gene uncharacterized LOC107985948 Neighboring gene uncharacterized LOC105373636 Neighboring gene NANOG hESC enhancer GRCh37_chr2:138829640-138830141 Neighboring gene long intergenic non-protein coding RNA 1832

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General protein information

Preferred Names
histamine N-methyltransferase
NP_001019245.1
NP_001019246.1
NP_008826.1
XP_011509366.1
XP_016859437.1
XP_016859438.1
XP_054197622.1
XP_054197623.1
XP_054197624.1

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_012966.1 RefSeqGene

    Range
    5236..57127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001024074.3NP_001019245.1  histamine N-methyltransferase isoform 2

    See identical proteins and their annotated locations for NP_001019245.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compared to isoform 1. This transcript is supported by multiple mRNAs and ESTs, but the predicted ORF has not yet been experimentally confirmed.
    Source sequence(s)
    AC093674
    Consensus CDS
    CCDS33297.1
    UniProtKB/Swiss-Prot
    P50135
    Related
    ENSP00000280096.5, ENST00000280096.5
  2. NM_001024075.3NP_001019246.1  histamine N-methyltransferase isoform 3

    See identical proteins and their annotated locations for NP_001019246.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also called HNMT-S, includes an alternate exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF523357
    Consensus CDS
    CCDS33296.1
    UniProtKB/Swiss-Prot
    P50135
    Related
    ENSP00000333259.4, ENST00000329366.8
  3. NM_006895.3NP_008826.1  histamine N-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_008826.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest protein (isoform 1).
    Source sequence(s)
    AA935821, AC093674, AF523358, AF523360
    Consensus CDS
    CCDS2181.1
    UniProtKB/Swiss-Prot
    B2R9J3, P50135, Q546Z6, Q7Z7I2, Q8IU56, Q8WW98, Q9BRW6
    Related
    ENSP00000280097.3, ENST00000280097.5
    Conserved Domains (1) summary
    pfam13489
    Location:32217
    Methyltransf_23; Methyltransferase 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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    137964473..138016364
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511064.3XP_011509366.1  histamine N-methyltransferase isoform X2

    Conserved Domains (1) summary
    pfam13489
    Location:191
    Methyltransf_23; Methyltransferase domain
  2. XM_017003949.3XP_016859438.1  histamine N-methyltransferase isoform X3

    UniProtKB/TrEMBL
    B4DWC1
    Conserved Domains (1) summary
    cl17173
    Location:32148
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
  3. XM_017003948.2XP_016859437.1  histamine N-methyltransferase isoform X1

    Conserved Domains (1) summary
    pfam13489
    Location:2183
    Methyltransf_23; Methyltransferase domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    138410245..138462150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341648.1XP_054197623.1  histamine N-methyltransferase isoform X2

  2. XM_054341649.1XP_054197624.1  histamine N-methyltransferase isoform X3

    UniProtKB/TrEMBL
    B4DWC1
  3. XM_054341647.1XP_054197622.1  histamine N-methyltransferase isoform X1