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Aliases for BHMT Gene

Aliases for BHMT Gene

  • Betaine--Homocysteine S-Methyltransferase 2 3 5
  • Epididymis Secretory Sperm Binding Protein Li 61p 3
  • Betaine--Homocysteine S-Methyltransferase 1 3
  • Betaine Homocysteine Methyltransferase 2
  • EC 4
  • HEL-S-61p 3
  • 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 Homocysteinemia and Choline Deficiency Disease. Among its related pathways are Glycine, serine and threonine metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include 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.

Additional gene information for BHMT Gene

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

Genomics for BHMT Gene

GeneHancer (GH) Regulatory Elements for BHMT Gene

Promoters and enhancers for BHMT 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
GH05J079111 Promoter 0.9 EPDnew 650.7 +0.0 12 0.1 TAF1 RXRA MAX RAD21 YY1 SP1 JUND ATF3 EGR1 POLR2A BHMT GC05M079171 RNY3P1 DMGDH
GH05J079133 Enhancer 1.2 Ensembl ENCODE 25.1 +22.1 22066 1.7 HDGF FOXA2 ARNT SIN3A ZNF2 ARID2 ZNF143 ATF7 SP3 MXD4 BHMT TENT2 RPS3AP20 RNY3P1 GC05M079171 DMGDH
GH05J078979 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 7.7 -128.9 -128927 7.4 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 ARSB GC05P078984 TENT2 JMY BHMT LHFPL2
GH05J079234 Promoter/Enhancer 1.5 Ensembl ENCODE 11 +125.3 125285 4.3 SMAD1 FOXA2 ARNT ARID4B SIN3A FEZF1 ZNF2 IRF4 YY1 POLR2B DMGDH JMY TENT2 BHMT GC05M079243
GH05J079020 Enhancer 1 Ensembl ENCODE 11.6 -90.7 -90717 1.1 ELF3 CTCF MZF1 ZNF2 RAD21 GATA3 ZNF213 ZBTB48 SCRT2 ZNF143 ARSB BHMT BHMT2 LOC100505796 GC05M079042 DMGDH
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BHMT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BHMT gene promoter:
  • GATA-2
  • Sox9
  • Hlf
  • AP-4
  • NF-kappaB1
  • NF-kappaB
  • S8
  • FOXF2
  • Evi-1
  • Tal-1

Genomic Locations for BHMT Gene

Genomic Locations for BHMT Gene
20,512 bases
Plus strand
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

Post-translational modifications for BHMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BHMT Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BHMT Gene

Domains & Families for BHMT Gene

Gene Families for BHMT Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for BHMT Gene

Graphical View of Domain Structure for InterPro Entry

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

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

Function for BHMT Gene

Molecular function for BHMT Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Trimethylammonioacetate + L-homocysteine = dimethylglycine + L-methionine.
GENATLAS Biochemistry:
betaine-homocysteine methyltransferase,expressed in liver and kidney,sulfur aminoacid metabolism

Enzyme Numbers (IUBMB) for BHMT Gene

Phenotypes From GWAS Catalog for BHMT Gene

Gene Ontology (GO) - Molecular Function for BHMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0008270 zinc ion binding IEA,IDA 18230605
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047150 betaine-homocysteine S-methyltransferase activity IEA,TAS --
genes like me logo Genes that share ontologies with BHMT: view
genes like me logo Genes that share phenotypes with BHMT: view

Animal Models for BHMT Gene

MGI Knock Outs for BHMT:
  • Bhmt Bhmt<tm1.2Zei>
  • Bhmt Bhmt<tm1b(EUCOMM)Hmgu>

Animal Model Products

Clone Products

  • Addgene plasmids for BHMT

No data available for 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

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 BHMT gene
Compartment Confidence
extracellular 5
cytosol 5
mitochondrion 2
nucleus 2
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for BHMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 21082674
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:0006479 protein methylation NAS 10075673
GO:0006577 amino-acid betaine metabolic process IDA 18230605
GO:0006579 amino-acid betaine catabolic process IEA --
GO:0009086 methionine biosynthetic process IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Methionine Approved Nutra Target, product of 102
Citric Acid Approved, Vet_approved Nutra Agonist, Activator, Target 1243
Betaine Approved Nutra 36
spermine Approved Nutra Full agonist, Agonist, Antagonist, Pore Blocker, Channel blocker 0
dimethylglycine Experimental Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 2-amino-4-Mercaptobutyric acid
  • Hcy
  • 2-amino-4-Mercaptobutyrate
  • (+-)-Homocysteine
  • (S)-2-amino-4-mercapto-Butanoate
  • N'-acetylspermine
  • N'-monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-acetamide
  • N-Acetylspermine
  • 1,7-diamino-4-Azaheptane
  • 3,3'-Iminobis(propylamine)
  • 3,3'-Iminobispropylamine
  • 3,3'-Iminodi(propylamine)
  • 3,3-Diaminodipropylamine
  • TRIMETHYL glycine
  • Trimethylammonioacetic acid
  • AcidinPepsin
  • Betaine hydrochloride
  • Betaine orphan brand
genes like me logo Genes that share compounds with BHMT: view

Transcripts for BHMT Gene

mRNA/cDNA for BHMT Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(138) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BHMT Gene

Betaine--homocysteine S-methyltransferase:
Representative Sequences:

Clone Products

  • Addgene plasmids for BHMT

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for BHMT Gene

Protein tissue co-expression partners for BHMT Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BHMT Gene:


SOURCE GeneReport for Unigene cluster for BHMT Gene:


mRNA Expression by UniProt/SwissProt for BHMT Gene:

Tissue specificity: Found exclusively in liver and kidney.

Evidence on tissue expression from TISSUES for BHMT Gene

  • Kidney(4.9)
  • Liver(4.9)
  • Lung(4.1)
  • Eye(3.4)
genes like me logo Genes that share expression patterns with BHMT: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BHMT Gene

Orthologs for BHMT Gene

This gene was present in the common ancestor of chordates.

Orthologs for BHMT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BHMT 34 33
  • 99.43 (n)
(Mus musculus)
Mammalia Gm5096 34
  • 94 (a)
Bhmt 16 34 33
  • 88.07 (n)
(Monodelphis domestica)
Mammalia BHMT 34
  • 91 (a)
(Canis familiaris)
Mammalia BHMT 34 33
  • 90.62 (n)
(Bos Taurus)
Mammalia BHMT 34 33
  • 90.04 (n)
(Ornithorhynchus anatinus)
Mammalia BHMT 34
  • 89 (a)
(Rattus norvegicus)
Mammalia Bhmt 33
  • 86.42 (n)
(Gallus gallus)
Aves -- 34
  • 85 (a)
  • 78.96 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bhmt 33
  • 75.85 (n)
Str.8632 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.21139 33
(Danio rerio)
Actinopterygii bhmt 34 33
  • 70.59 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9438 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
CSA.1410 34
  • 46 (a)
-- 34
  • 45 (a)
CSA.4075 34
  • 45 (a)
Cin.5992 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5992 33
Species where no ortholog for BHMT 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)
  • 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)
Evolutionary constrained regions (ECRs) for BHMT: view image

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 Variation AA Info Type
rs763726268 not-provided, not provided 79,131,091(+) AAAAA/AAAA coding_sequence_variant, frameshift
rs1000192019 -- 79,113,474(+) G/A intron_variant
rs1000201978 -- 79,113,794(+) T/A intron_variant
rs1000441319 -- 79,120,175(+) T/C intron_variant
rs1000492775 -- 79,126,563(+) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
esv1010320 CNV insertion 20482838
esv2762527 CNV gain 21179565
esv3308186 CNV mobile element insertion 20981092
esv3408955 CNV insertion 20981092
esv3442711 CNV duplication 20981092
nsv1019727 CNV gain 25217958
nsv1022839 CNV gain 25217958
nsv4892 CNV insertion 18451855
nsv512853 CNV insertion 21212237
nsv519156 CNV gain 19592680
nsv525398 CNV gain 19592680

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)

Additional Variant Information for BHMT Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for BHMT Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
  • hyperhomocysteinemia
choline deficiency disease
  • choline deficiency
neural tube defects
  • neural tube defects, susceptibility to
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

Additional Disease Information for BHMT

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 BHMT: view

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

Publications for BHMT Gene

  1. Investigations of a common genetic variant in betaine-homocysteine methyltransferase (BHMT) in coronary artery disease. (PMID: 12818402) Weisberg IS … Rozen R (Atherosclerosis 2003) 3 4 22 44 58
  2. Betaine-homocysteine methyltransferase expression in porcine and human tissues and chromosomal localization of the human gene. (PMID: 9281325) Sunden SL … Garrow TA (Archives of biochemistry and biophysics 1997) 2 3 4 22 58
  3. Purification, kinetic properties, and cDNA cloning of mammalian betaine-homocysteine methyltransferase. (PMID: 8798461) Garrow TA (The Journal of biological chemistry 1996) 2 3 4 22 58
  4. 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. (PMID: 19493349) Shaw GM … Finnell RH (BMC medical genetics 2009) 3 22 44 58
  5. MALDI-TOF MS genotyping of polymorphisms related to 1-carbon metabolism using common and mass-modified terminators. (PMID: 18988749) Meyer K … Ueland PM (Clinical chemistry 2009) 3 22 44 58

Products for BHMT Gene

Sources for BHMT Gene

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