Human Gene HNMT (ENST00000280097.5_4) from GENCODE V47lift37
  Description: histamine N-methyltransferase, transcript variant 1 (from RefSeq NM_006895.3)
Gencode Transcript: ENST00000280097.5_4
Gencode Gene: ENSG00000150540.14_7
Transcript (Including UTRs)
   Position: hg19 chr2:138,722,043-138,773,934 Size: 51,892 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr2:138,722,062-138,771,700 Size: 49,639 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:138,722,043-138,773,934)mRNA (may differ from genome)Protein (292 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HNMT_HUMAN
DESCRIPTION: RecName: Full=Histamine N-methyltransferase; Short=HMT; EC=2.1.1.8;
FUNCTION: Inactivates histamine by N-methylation. Plays an important role in degrading histamine and in regulating the airway response to histamine.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + histamine = S- adenosyl-L-homocysteine + N(tau)-methylhistamine.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Cytoplasm.
POLYMORPHISM: Variant Ile-105 has a reduced activity and seems to be linked with a predisposition to asthma.
SIMILARITY: Belongs to the methyltransferase superfamily. HNMT family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HNMT
Diseases sorted by gene-association score: mental retardation, autosomal recessive 51* (1230), asthma* (228), asthma susceptibility, hnmt related* (100), autosomal recessive non-syndromic intellectual disability* (82), mental retardation, x-linked, syndromic 13 (11), heel spur (10), comedo carcinoma (10), suppression amblyopia (9), urticaria (8), eosinophilia-myalgia syndrome (7), angioedema (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.00 RPKM in Ovary
Total median expression: 304.36 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00190.000 Picture PostScript Text
3' UTR -463.102234-0.207 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016673 - Histamine_N-methyltransferase

Pfam Domains:
PF08242 - Methyltransferase domain
PF13489 - Methyltransferase domain

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1ICZ - Model 1JQD - X-ray MuPIT 1JQE - X-ray MuPIT 2AOT - X-ray MuPIT 2AOU - X-ray MuPIT 2AOV - X-ray MuPIT 2AOW - X-ray MuPIT 2AOX - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P50135
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008168 methyltransferase activity
GO:0008170 N-methyltransferase activity
GO:0016740 transferase activity
GO:0046539 histamine N-methyltransferase activity

Biological Process:
GO:0001695 histamine catabolic process
GO:0006548 histidine catabolic process
GO:0007420 brain development
GO:0007585 respiratory gaseous exchange
GO:0032259 methylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043005 neuron projection
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF523356 - Homo sapiens histamine N-methyltransferase short variant 1 (HNMT) mRNA, complete cds; alternatively spliced.
AF523357 - Homo sapiens histamine N-methyltransferase short variant 2 (HNMT) mRNA, complete cds; alternatively spliced.
AF523358 - Homo sapiens histamine N-methyltransferase variant 1 (HNMT) mRNA, complete cds; alternatively spliced.
AF523359 - Homo sapiens histamine N-methyltransferase variant 2 (HNMT) mRNA, complete cds; alternatively spliced.
AF523360 - Homo sapiens histamine N-methyltransferase variant 3 (HNMT) mRNA, complete cds; alternatively spliced.
U08092 - Human histamine N-methyltransferase (HNMT) mRNA, complete cds.
BC005907 - Homo sapiens histamine N-methyltransferase, mRNA (cDNA clone IMAGE:4249496), complete cds.
AK301462 - Homo sapiens cDNA FLJ51345 complete cds, highly similar to Histamine N-methyltransferase (EC 2.1.1.8).
AK313804 - Homo sapiens cDNA, FLJ94422, Homo sapiens histamine N-methyltransferase (HNMT), mRNA.
BC020677 - Homo sapiens histamine N-methyltransferase, mRNA (cDNA clone MGC:22386 IMAGE:4767331), complete cds.
D16224 - Homo sapiens mRNA for histamine N-methyltransferase, complete cds.
KJ905778 - Synthetic construct Homo sapiens clone ccsbBroadEn_15448 HNMT gene, encodes complete protein.
AB590282 - Synthetic construct DNA, clone: pFN21AE1447, Homo sapiens HNMT gene for histamine N-methyltransferase, without stop codon, in Flexi system.
DQ894348 - Synthetic construct Homo sapiens clone IMAGE:100008808; FLH176708.01L; RZPDo839G06121D histamine N-methyltransferase (HNMT) gene, encodes complete protein.
CU676632 - Synthetic construct Homo sapiens gateway clone IMAGE:100022174 5' read HNMT mRNA.
DQ891166 - Synthetic construct clone IMAGE:100003796; FLH176712.01X; RZPDo839G06122D histamine N-methyltransferase (HNMT) gene, encodes complete protein.
KJ896992 - Synthetic construct Homo sapiens clone ccsbBroadEn_06386 HNMT gene, encodes complete protein.
KR711254 - Synthetic construct Homo sapiens clone CCSBHm_00021502 HNMT (HNMT) mRNA, encodes complete protein.
JD229219 - Sequence 210243 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-6181 - histamine degradation

Reactome (by CSHL, EBI, and GO)

Protein P50135 (Reactome details) participates in the following event(s):

R-HSA-175993 HNMT transfers CH3 group from AdoMet to Hist
R-HSA-2408544 AdoSeMet is converted to AdeSeHCys by MetTrans(1)
R-HSA-70921 Histidine catabolism
R-HSA-2408508 Metabolism of ingested SeMet, Sec, MeSec into H2Se
R-HSA-6788656 Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
R-HSA-2408522 Selenoamino acid metabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9J3, ENST00000280097.1, ENST00000280097.2, ENST00000280097.3, ENST00000280097.4, HNMT_HUMAN, NM_006895, P50135, Q546Z6, Q7Z7I2, Q8IU56, Q8WW98, Q9BRW6, uc317jsw.1, uc317jsw.2
UCSC ID: ENST00000280097.5_4
RefSeq Accession: NM_006895.3
Protein: P50135 (aka HNMT_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.