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Aliases for BHMT Gene

Aliases for BHMT Gene

  • Betaine--Homocysteine S-Methyltransferase 2 3 5
  • EC 4 63
  • Epididymis Secretory Sperm Binding Protein Li 61p 3
  • Betaine Homocysteine Methyltransferase 2
  • HEL-S-61p 3
  • EC 2.1.1 63
  • BHMT1 3

External Ids for BHMT Gene

Previous GeneCards Identifiers for BHMT Gene

  • GC05P077213
  • GC05P078644
  • GC05P078446
  • GC05P078491
  • GC05P078443
  • GC05P073615

Summaries for BHMT Gene

Entrez Gene Summary for BHMT Gene

  • This gene encodes a cytosolic enzyme that catalyzes the conversion of betaine and homocysteine to dimethylglycine and methionine, respectively. Defects in this gene could lead to hyperhomocyst(e)inemia, but such a defect has not yet been observed. [provided by RefSeq, Jul 2008]

GeneCards Summary for BHMT Gene

BHMT (Betaine--Homocysteine S-Methyltransferase) is a Protein Coding gene. Diseases associated with BHMT include Hyperhomocysteinemia and Choline Deficiency Disease. Among its related pathways are One carbon pool by folate and Metabolism. GO annotations related to this gene include protein complex binding and S-adenosylmethionine-homocysteine S-methyltransferase activity. An important paralog of this gene is BHMT2.

UniProtKB/Swiss-Prot for BHMT Gene

  • Involved in the regulation of homocysteine metabolism. Converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline.

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

Genomics for BHMT Gene

Regulatory Elements for BHMT Gene

Enhancers for BHMT 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 BHMT on UCSC Golden Path with GeneCards custom track

Genomic Location for BHMT Gene

79,111,779 bp from pter
79,132,290 bp from pter
20,512 bases
Plus strand

Genomic View for BHMT Gene

Genes around BHMT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for BHMT Gene

Proteins for BHMT Gene

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

    Protein Symbol:
    Recommended name:
    Betaine--homocysteine S-methyltransferase 1
    Protein Accession:
    Secondary Accessions:
    • Q9UNI9

    Protein attributes for BHMT Gene

    406 amino acids
    Molecular mass:
    44998 Da
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Homotetramer.

    Three dimensional structures from OCA and Proteopedia for BHMT Gene

neXtProt entry for BHMT Gene

Proteomics data for BHMT Gene at MOPED

Post-translational modifications for BHMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BHMT Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for BHMT Gene

Protein Domains for BHMT Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 Hcy-binding domain.
  • Contains 1 Hcy-binding domain.
genes like me logo Genes that share domains with BHMT: view

No data available for Gene Families for BHMT Gene

Function for BHMT Gene

Molecular function for BHMT Gene

GENATLAS Biochemistry:
betaine-homocysteine methyltransferase,expressed in liver and kidney,sulfur aminoacid metabolism
UniProtKB/Swiss-Prot CatalyticActivity:
Trimethylammonioacetate + L-homocysteine = dimethylglycine + L-methionine.
UniProtKB/Swiss-Prot Function:
Involved in the regulation of homocysteine metabolism. Converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline.

Enzyme Numbers (IUBMB) for BHMT Gene

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

Animal Models for BHMT Gene

MGI Knock Outs for BHMT:

Animal Model Products

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

Localization for BHMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for BHMT Gene


Subcellular locations from

Jensen Localization Image for BHMT Gene COMPARTMENTS Subcellular localization image for BHMT gene
Compartment Confidence
cytosol 5
extracellular 5
mitochondrion 2
nucleus 2
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for BHMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA --
genes like me logo Genes that share ontologies with BHMT: view

Pathways & Interactions for BHMT Gene

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

UniProtKB/Swiss-Prot Q93088-BHMT1_HUMAN

  • Pathway: Amine and polyamine degradation; betaine degradation; sarcosine from betaine: step 1/2.
  • Pathway: Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (BhmT route): step 1/1.

Gene Ontology (GO) - Biological Process for BHMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000096 sulfur amino acid metabolic process TAS --
GO:0006577 amino-acid betaine metabolic process IDA 18230605
GO:0006579 amino-acid betaine catabolic process IEA --
GO:0009086 methionine biosynthetic process IEA --
GO:0042426 choline catabolic process TAS --
genes like me logo Genes that share ontologies with BHMT: view

No data available for SIGNOR curated interactions for BHMT Gene

Drugs & Compounds for BHMT Gene

(18) Drugs for BHMT Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Methionine Approved Nutra Target, product of 0
spermine Approved Nutra Full agonist, Agonist 0
Dimethylglycine Experimental Pharma 0
S-(D-Carboxybutyl)-L-Homocysteine Experimental Pharma Target 0
putrescine Experimental Pharma Antagonist, Pore Blocker 0

(6) Additional Compounds for BHMT Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (+-)-homocysteine
  • (S)-2-amino-4-mercapto-Butanoate
  • (S)-2-amino-4-mercapto-Butanoic acid
  • 2-Amino-4-mercapto-Butanoate
  • 2-Amino-4-mercapto-Butanoic acid
  • N'-Acetylspermine
  • N'-Monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-Acetamide
  • N-Acetylspermine
  • -1,3-propanediamine
  • 1,7-Diamino-4-azaheptane
  • 3, 3'-Diaminodipropylamine
  • 3, {3'-Iminobis[propylamine]}
  • 3,3'-Diamino-Dipropylamine
genes like me logo Genes that share compounds with BHMT: view

Transcripts for BHMT Gene

Unigene Clusters for BHMT Gene

Betaine--homocysteine S-methyltransferase:
Representative Sequences:

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

No ASD Table

Relevant External Links for BHMT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BHMT Gene

mRNA expression in normal human tissues for BHMT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BHMT Gene

This gene is overexpressed in Liver (x30.7) and Kidney - Cortex (x19.0).

Protein differential expression in normal tissues from HIPED for BHMT Gene

This gene is overexpressed in Liver, secretome (38.9), Liver (16.5), and Kidney (9.0).

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

SOURCE GeneReport for Unigene cluster for BHMT Gene Hs.80756

mRNA Expression by UniProt/SwissProt for BHMT Gene

Tissue specificity: Found exclusively in liver and kidney.
genes like me logo Genes that share expression patterns with BHMT: view

Protein tissue co-expression partners for BHMT Gene

- Elite partner

Primer Products

Orthologs for BHMT Gene

This gene was present in the common ancestor of chordates.

Orthologs for BHMT Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia BHMT 35
  • 90.04 (n)
  • 94.07 (a)
  • 93 (a)
(Canis familiaris)
Mammalia BHMT 35
  • 90.62 (n)
  • 95.06 (a)
  • 95 (a)
(Mus musculus)
Mammalia Bhmt 35
  • 88.07 (n)
  • 94.57 (a)
Bhmt 16
Bhmt 36
  • 94 (a)
Gm5096 36
  • 94 (a)
(Pan troglodytes)
Mammalia BHMT 35
  • 99.43 (n)
  • 99.26 (a)
  • 99 (a)
(Rattus norvegicus)
Mammalia Bhmt 35
  • 86.42 (n)
  • 92.59 (a)
(Monodelphis domestica)
Mammalia BHMT 36
  • 91 (a)
(Ornithorhynchus anatinus)
Mammalia BHMT 36
  • 89 (a)
(Gallus gallus)
Aves BHMT 35
  • 78.96 (n)
  • 86.87 (a)
-- 36
  • 85 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bhmt 35
  • 75.85 (n)
  • 84.62 (a)
Str.8632 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.21139 35
(Danio rerio)
Actinopterygii bhmt 35
  • 70.59 (n)
  • 78.2 (a)
bhmt 36
  • 78 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9438 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5992 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 45 (a)
-- 36
  • 47 (a)
CSA.1410 36
  • 46 (a)
CSA.4075 36
  • 45 (a)
Species with no ortholog for BHMT:
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 BHMT Gene

Gene Tree for BHMT (if available)
Gene Tree for BHMT (if available)

Paralogs for BHMT Gene

Paralogs for BHMT Gene

(1) SIMAP similar genes for BHMT Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with BHMT: view

Variants for BHMT Gene

Sequence variations from dbSNP and Humsavar for BHMT Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs3733890 - 79,126,136(+) TGCCC(A/G)ACTGA reference, missense
rs59866108 - 79,121,335(+) CCCCC(A/C/G)GCGAG reference, missense
rs918417 -- 79,112,610(-) ATTTC(A/G)GATGA intron-variant
rs2909853 -- 79,129,924(+) GAAGC(C/T)GAGGC intron-variant
rs1002735 -- 79,132,200(+) GAGGT(C/T)ATGCA utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
nsv519156 CNV Gain 19592680
nsv525398 CNV Gain 19592680
esv1010320 CNV Insertion 20482838
nsv4892 CNV Insertion 18451855
esv272460 CNV Insertion 20981092
nsv512853 CNV Insertion 21212237

Variation tolerance for BHMT Gene

Residual Variation Intolerance Score: 46.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.95; 83.98% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for BHMT Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BHMT Gene

Disorders for BHMT Gene

MalaCards: The human disease database

(5) MalaCards diseases for BHMT Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
choline deficiency disease
  • choline deficiency
placental abruption
  • abruptio placenta
neural tube defects
  • spina bifida
vascular disease
  • vascular tissue disease
- elite association - COSMIC cancer census association via MalaCards
Search BHMT in MalaCards View complete list of genes associated with diseases

Relevant External Links for BHMT

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 BHMT: view

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

Publications for BHMT Gene

  1. Betaine-homocysteine methyltransferase expression in porcine and human tissues and chromosomal localization of the human gene. (PMID: 9281325) Sunden S.L.F. … Garrow T.A. (Arch. Biochem. Biophys. 1997) 2 3 4 23 67
  2. Twenty-four non-synonymous polymorphisms in the one-carbon metabolic pathway and risk of colorectal adenoma in the Nurses' Health Study. (PMID: 17389618) Hazra A. … Hunter D.J. (Carcinogenesis 2007) 23 25 26
  3. Purification, kinetic properties, and cDNA cloning of mammalian betaine-homocysteine methyltransferase. (PMID: 8798461) Garrow T.A. (J. Biol. Chem. 1996) 2 3 23
  4. MALDI-TOF MS genotyping of polymorphisms related to 1-carbon metabolism using common and mass-modified terminators. (PMID: 18988749) Meyer K. … Ueland P.M. (Clin. Chem. 2009) 3 23
  5. 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. (PMID: 19493349) Shaw G.M. … Finnell R.H. (BMC Med. Genet. 2009) 3 23

Products for BHMT Gene

Sources for BHMT Gene