Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	3176
Gene name	Histamine N-methyltransferase
Gene symbol	HNMT
Synonyms (NCBI Gene)	HMTHNMT-S1HNMT-S2MRT51
Chromosome	2
Chromosome location	2q22.1
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-methioni

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SNP ID	Visualize variation	Clinical significance	Consequence
rs758252808	G>A	Pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant, intron variant

Show/Hide all (71)

miRTarBase ID	miRNA	Experiments	Reference
MIRT756045	hsa-miR-33a-5p	MicroarrayqRT-PCR	35899934
MIRT1050600	hsa-miR-1273f	CLIP-seq
MIRT1050601	hsa-miR-143	CLIP-seq
MIRT1050602	hsa-miR-2113	CLIP-seq
MIRT1050603	hsa-miR-221	CLIP-seq
MIRT1050604	hsa-miR-222	CLIP-seq
MIRT1050605	hsa-miR-323-3p	CLIP-seq
MIRT1050606	hsa-miR-4461	CLIP-seq
MIRT1050607	hsa-miR-4708-5p	CLIP-seq
MIRT1050608	hsa-miR-4770	CLIP-seq
MIRT1050609	hsa-miR-520f	CLIP-seq
MIRT1050610	hsa-miR-758	CLIP-seq
MIRT2011621	hsa-miR-3663-5p	CLIP-seq
MIRT2011622	hsa-miR-371-5p	CLIP-seq
MIRT2011623	hsa-miR-371b-5p	CLIP-seq
MIRT2243798	hsa-miR-129-5p	CLIP-seq
MIRT2243799	hsa-miR-21	CLIP-seq
MIRT2243800	hsa-miR-218	CLIP-seq
MIRT2243801	hsa-miR-300	CLIP-seq
MIRT2243802	hsa-miR-3160-3p	CLIP-seq
MIRT2243803	hsa-miR-3616-3p	CLIP-seq
MIRT2243804	hsa-miR-381	CLIP-seq
MIRT2243805	hsa-miR-4282	CLIP-seq
MIRT2243806	hsa-miR-4437	CLIP-seq
MIRT2243807	hsa-miR-4487	CLIP-seq
MIRT2243808	hsa-miR-450b-5p	CLIP-seq
MIRT2243809	hsa-miR-4666-3p	CLIP-seq
MIRT2243810	hsa-miR-4694-3p	CLIP-seq
MIRT2243811	hsa-miR-4704-3p	CLIP-seq
MIRT2243812	hsa-miR-4721	CLIP-seq
MIRT2243813	hsa-miR-4735-5p	CLIP-seq
MIRT2243814	hsa-miR-4775	CLIP-seq
MIRT2243815	hsa-miR-4781-3p	CLIP-seq
MIRT2243816	hsa-miR-4789-5p	CLIP-seq
MIRT2243817	hsa-miR-507	CLIP-seq
MIRT2243818	hsa-miR-556-5p	CLIP-seq
MIRT2243819	hsa-miR-557	CLIP-seq
MIRT2243820	hsa-miR-558	CLIP-seq
MIRT2243821	hsa-miR-590-3p	CLIP-seq
MIRT2243822	hsa-miR-590-5p	CLIP-seq
MIRT2243823	hsa-miR-596	CLIP-seq
MIRT2243824	hsa-miR-636	CLIP-seq
MIRT2546935	hsa-miR-1286	CLIP-seq
MIRT2546936	hsa-miR-148a	CLIP-seq
MIRT2546937	hsa-miR-148b	CLIP-seq
MIRT2546938	hsa-miR-152	CLIP-seq
MIRT2243802	hsa-miR-3160-3p	CLIP-seq
MIRT2243803	hsa-miR-3616-3p	CLIP-seq
MIRT2243806	hsa-miR-4437	CLIP-seq
MIRT2243807	hsa-miR-4487	CLIP-seq
MIRT2546939	hsa-miR-4493	CLIP-seq
MIRT2243812	hsa-miR-4721	CLIP-seq
MIRT2546940	hsa-miR-4722-5p	CLIP-seq
MIRT2546941	hsa-miR-485-3p	CLIP-seq
MIRT2546942	hsa-miR-487a	CLIP-seq
MIRT2546943	hsa-miR-516a-3p	CLIP-seq
MIRT2546944	hsa-miR-548aa	CLIP-seq
MIRT2243818	hsa-miR-556-5p	CLIP-seq
MIRT2243820	hsa-miR-558	CLIP-seq
MIRT2546945	hsa-miR-602	CLIP-seq
MIRT2243802	hsa-miR-3160-3p	CLIP-seq
MIRT2243803	hsa-miR-3616-3p	CLIP-seq
MIRT2243806	hsa-miR-4437	CLIP-seq
MIRT2243807	hsa-miR-4487	CLIP-seq
MIRT2546939	hsa-miR-4493	CLIP-seq
MIRT2243812	hsa-miR-4721	CLIP-seq
MIRT2546943	hsa-miR-516a-3p	CLIP-seq
MIRT2243818	hsa-miR-556-5p	CLIP-seq
MIRT2243820	hsa-miR-558	CLIP-seq
MIRT2546945	hsa-miR-602	CLIP-seq
MIRT1050610	hsa-miR-758	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0001692	Process	Histamine metabolic process	IMP	23505051
GO:0001695	Process	Histamine catabolic process	IDA	26206890
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	26206890
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA
GO:0005829	Component	Cytosol	IDA	23505051
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006548	Process	L-histidine catabolic process	TAS
GO:0007585	Process	Respiratory gaseous exchange by respiratory system	TAS	7943261
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008170	Function	N-methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IDA	26206890
GO:0032259	Process	Methylation	IEA
GO:0046539	Function	Histamine N-methyltransferase activity	IDA	26206890
GO:0046539	Function	Histamine N-methyltransferase activity	IEA
GO:0046539	Function	Histamine N-methyltransferase activity	TAS
GO:0070062	Component	Extracellular exosome	HDA	19056867

MIM	HGNC	e!Ensembl
605238	5028	ENSG00000150540

P50135

Protein name

Histamine N-methyltransferase (HMT) (EC 2.1.1.8)

Protein function

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

PDB

1JQD , 1JQE , 2AOT , 2AOU , 2AOV , 2AOW , 2AOX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13489	Methyltransf_23	27 → 217		Domain

Sequence

MASSMRSLFSDHGKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIG
GGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKTSNLENVKFAWHKETS
SEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWD
KLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLL
WDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA

Sequence length

292

Interactions

View interactions

	KEGG		Reactome
	Histidine metabolism Metabolic pathways		Histidine catabolism

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Intellectual disability, autosomal recessive 51	Pathogenic; Likely pathogenic	rs758252808, rs745756308	RCV000203518 RCV000203542

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Uncertain significance	rs186485844	RCV005930789
HNMT-related disorder	Benign; risk factor; Likely benign	rs11558538, rs113138471, rs11569725, rs200508858	RCV003974798 RCV003904751 RCV003922200 RCV003968165
Inherited susceptibility to asthma	Benign; risk factor; Uncertain significance; Conflicting classifications of pathogenicity	rs11558538, rs186485844, rs765863580	RCV000005467 RCV003228596 RCV003227774
Ovarian serous cystadenocarcinoma	Uncertain significance	rs186485844	RCV005930790
Pulmonary arterial hypertension	Uncertain significance	rs767467449	RCV005863870
Thymoma	Benign; Likely benign	rs529181997	RCV005903082

Show/Hide Text Mining Associations (24)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Asthma	Associate	19025430, 25295384, 25909280
Autistic Disorder	Associate	33310825
Carcinoma Renal Cell	Associate	29099276
Colitis Ulcerative	Associate	16489678
Deafness	Associate	33524580
Deafness autosomal recessive 51	Associate	33310825
Dermatitis Atopic	Associate	19025430
Developmental Disabilities	Associate	33310825
Drug Hypersensitivity	Stimulate	25909280
Dyskinesia Drug Induced	Associate	25768024
Endometrial Neoplasms	Associate	32894095, 39326337
Esophageal Squamous Cell Carcinoma	Associate	26004606
Intellectual Disability	Associate	26206890, 33310825
Intestinal Diseases	Associate	33310825
Language Development Disorders	Associate	33310825
Migraine Disorders	Associate	27130307
Neoplasms	Associate	36057625, 37883365
Pancreatic Neoplasms	Associate	23807219
Parkinson Disease	Associate	25768024, 38027039
Personality Disorders	Associate	33310825
Progeria	Associate	30565836
Rhinitis Allergic	Associate	19025430
Schizophrenia	Associate	25768024
Sleep Wake Disorders	Associate	33310825

HNMT (histamine N-methyltransferase)