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Aliases for BHMT2 Gene

Aliases for BHMT2 Gene

  • Betaine--Homocysteine S-Methyltransferase 2 2 3 4 5
  • SMM-Hcy Methyltransferase 3 4
  • S-Methylmethionine--Homocysteine S-Methyltransferase BHMT2 3
  • Betaine-Homocysteine Methyltransferase 2 3
  • EC 4

External Ids for BHMT2 Gene

Previous GeneCards Identifiers for BHMT2 Gene

  • GC05P077171
  • GC05P078602
  • GC05P078404
  • GC05P078449
  • GC05P078401
  • GC05P073571
  • GC05P078366

Summaries for BHMT2 Gene

Entrez Gene Summary for BHMT2 Gene

  • Homocysteine is a sulfur-containing amino acid that plays a crucial role in methylation reactions. Transfer of the methyl group from betaine to homocysteine creates methionine, which donates the methyl group to methylate DNA, proteins, lipids, and other intracellular metabolites. The protein encoded by this gene is one of two methyl transferases that can catalyze the transfer of the methyl group from betaine to homocysteine. Anomalies in homocysteine metabolism have been implicated in disorders ranging from vascular disease to neural tube birth defects such as spina bifida. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

GeneCards Summary for BHMT2 Gene

BHMT2 (Betaine--Homocysteine S-Methyltransferase 2) is a Protein Coding gene. Diseases associated with BHMT2 include Orofacial Cleft. Among its related pathways are Metabolism and One carbon pool by folate. Gene Ontology (GO) annotations related to this gene include S-adenosylmethionine-homocysteine S-methyltransferase activity and S-methylmethionine-homocysteine S-methyltransferase activity. An important paralog of this gene is BHMT.

UniProtKB/Swiss-Prot for BHMT2 Gene

  • Involved in the regulation of homocysteine metabolism. Converts homocysteine to methionine using S-methylmethionine (SMM) as a methyl donor.

Additional gene information for BHMT2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BHMT2 Gene

Genomics for BHMT2 Gene

GeneHancer (GH) Regulatory Elements for BHMT2 Gene

Promoters and enhancers for BHMT2 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
GH05J079069 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 668 +0.2 235 1.5 BRD4 SAP130 BACH1 KMT2B ZNF48 YY1 ZNF316 POLR2A EGR1 IKZF5 BHMT2 DMGDH BHMT
GH05J079020 Enhancer 1 Ensembl ENCODE 7.6 -48.7 -48655 1.1 ELF3 CTCF MZF1 ZNF2 RAD21 GATA3 ZNF213 ZBTB48 SCRT2 ZNF143 ARSB BHMT BHMT2 LOC100505796 GC05M079042 DMGDH
GH05J078646 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 4.4 -421.1 -421060 4.3 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ETS1 SLC30A9 GLIS2 ZNF213 BHMT2 HMGB1P21 ENSG00000254170 LHFPL2
GH05J079030 Enhancer 0.9 ENCODE 7.9 -38.3 -38309 2.4 FOXA2 MLX DMAP1 YY1 RXRA NFYC REST PPARG KAT8 NFIL3 BHMT LHFPL2 BHMT2 GC05M079042 LOC100505796 DMGDH
GH05J079025 Enhancer 0.7 Ensembl 7.9 -44.3 -44316 0.4 CTCF MZF1 CEBPG ZNF384 KDM3A RAD21 RFX5 CC2D1A ZNF213 ZNF366 BHMT BHMT2 GC05M079042 LOC100505796 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 BHMT2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BHMT2 gene promoter:
  • POU3F1
  • Pax-5
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • FOXD1
  • LHX3b
  • Lhx3a
  • MZF-1

Genomic Locations for BHMT2 Gene

Genomic Locations for BHMT2 Gene
20,358 bases
Plus strand
20,358 bases
Plus strand

Genomic View for BHMT2 Gene

Genes around BHMT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BHMT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BHMT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BHMT2 Gene

Proteins for BHMT2 Gene

  • Protein details for BHMT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    S-methylmethionine--homocysteine S-methyltransferase BHMT2
    Protein Accession:
    Secondary Accessions:
    • B7Z516
    • Q9NXX7

    Protein attributes for BHMT2 Gene

    363 amino acids
    Molecular mass:
    40354 Da
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Homotetramer (By similarity). May interact with PRNP.
    • Sequence=BAA90880.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for BHMT2 Gene


neXtProt entry for BHMT2 Gene

Post-translational modifications for BHMT2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BHMT2 Gene

No data available for DME Specific Peptides for BHMT2 Gene

Domains & Families for BHMT2 Gene

Gene Families for BHMT2 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for BHMT2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with BHMT2: view

No data available for UniProtKB/Swiss-Prot for BHMT2 Gene

Function for BHMT2 Gene

Molecular function for BHMT2 Gene

UniProtKB/Swiss-Prot Function:
Involved in the regulation of homocysteine metabolism. Converts homocysteine to methionine using S-methylmethionine (SMM) as a methyl donor.
UniProtKB/Swiss-Prot CatalyticActivity:
S-methyl-L-methionine + L-homocysteine = 2 L-methionine.

Enzyme Numbers (IUBMB) for BHMT2 Gene

Phenotypes From GWAS Catalog for BHMT2 Gene

Gene Ontology (GO) - Molecular Function for BHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0008270 zinc ion binding IDA 18230605
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047150 NOT betaine-homocysteine S-methyltransferase activity IDA,IEA 18230605
genes like me logo Genes that share ontologies with BHMT2: view
genes like me logo Genes that share phenotypes with BHMT2: view

Animal Model Products

miRNA for BHMT2 Gene

miRTarBase miRNAs that target BHMT2

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BHMT2 Gene

Localization for BHMT2 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 BHMT2 gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 2

Gene Ontology (GO) - Cellular Components for BHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with BHMT2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for BHMT2 Gene

Pathways & Interactions for BHMT2 Gene

genes like me logo Genes that share pathways with BHMT2: view

Pathways by source for BHMT2 Gene

2 BioSystems pathways for BHMT2 Gene
1 GeneGo (Thomson Reuters) pathway for BHMT2 Gene

UniProtKB/Swiss-Prot Q9H2M3-BHMT2_HUMAN

  • 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 BHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000096 sulfur amino acid metabolic process TAS --
GO:0006577 NOT amino-acid betaine metabolic process IDA 18230605
GO:0009086 methionine biosynthetic process IEA --
GO:0032259 methylation IEA --
GO:0033477 S-methylmethionine metabolic process IDA 18230605
genes like me logo Genes that share ontologies with BHMT2: view

No data available for SIGNOR curated interactions for BHMT2 Gene

Drugs & Compounds for BHMT2 Gene

(6) Drugs for BHMT2 Gene - From: DrugBank and HMDB

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

(4) Additional Compounds for BHMT2 Gene - From: 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 BHMT2: view

Transcripts for BHMT2 Gene

mRNA/cDNA for BHMT2 Gene

Unigene Clusters for BHMT2 Gene

Betaine--homocysteine S-methyltransferase 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BHMT2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10
SP1: - -
SP2: -
SP4: -

Relevant External Links for BHMT2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BHMT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BHMT2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BHMT2 Gene

This gene is overexpressed in Liver (x16.1) and Kidney - Cortex (x9.6).

Protein differential expression in normal tissues from HIPED for BHMT2 Gene

This gene is overexpressed in Liver, secretome (42.2), Kidney (11.3), and Liver (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BHMT2 Gene

Protein tissue co-expression partners for BHMT2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BHMT2 Gene:


SOURCE GeneReport for Unigene cluster for BHMT2 Gene:


mRNA Expression by UniProt/SwissProt for BHMT2 Gene:

Tissue specificity: Expressed in liver and kidney and at reduced levels in the brain, heart, and skeletal muscle.

Evidence on tissue expression from TISSUES for BHMT2 Gene

  • Kidney(4.8)
  • Liver(4.7)
genes like me logo Genes that share expression patterns with BHMT2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BHMT2 Gene

Orthologs for BHMT2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for BHMT2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BHMT2 34 33
  • 99.45 (n)
(Canis familiaris)
Mammalia BHMT2 34 33
  • 87.85 (n)
(Bos Taurus)
Mammalia BHMT2 34 33
  • 85.36 (n)
(Mus musculus)
Mammalia Bhmt2 16 34 33
  • 84.53 (n)
(Rattus norvegicus)
Mammalia Bhmt2 33
  • 83.79 (n)
(Monodelphis domestica)
Mammalia BHMT2 34
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia BHMT2 34
  • 79 (a)
(Gallus gallus)
Aves -- 34
  • 67 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 68 (a)
(Danio rerio)
Actinopterygii bhmt 34
  • 63 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SAM4 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
-- 34
  • 45 (a)
CSA.1410 34
  • 44 (a)
CSA.4075 34
  • 44 (a)
Species where no ortholog for BHMT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for BHMT2 Gene

Gene Tree for BHMT2 (if available)
Gene Tree for BHMT2 (if available)
Evolutionary constrained regions (ECRs) for BHMT2: view image

Paralogs for BHMT2 Gene

Paralogs for BHMT2 Gene

(1) SIMAP similar genes for BHMT2 Gene using alignment to 3 proteins:

  • E5RH96_HUMAN Pseudogenes for BHMT2 Gene

genes like me logo Genes that share paralogs with BHMT2: view

Variants for BHMT2 Gene

Sequence variations from dbSNP and Humsavar for BHMT2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs56774046 likely-pathogenic, not provided 79,069,518(+) A/G upstream_transcript_variant
rs556440039 likely-benign, not specified 79,069,543(+) C/A upstream_transcript_variant
rs57739060 likely-benign, not specified 79,069,632(+) G/C upstream_transcript_variant
rs1000004663 -- 79,071,837(+) A/C intron_variant
rs1000092160 -- 79,076,776(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BHMT2 Gene

Variant ID Type Subtype PubMed ID
esv2762527 CNV gain 21179565
esv3605521 CNV gain 21293372
nsv1022839 CNV gain 25217958
nsv462216 CNV loss 19166990
nsv519156 CNV gain 19592680
nsv598741 CNV loss 21841781

Variation tolerance for BHMT2 Gene

Residual Variation Intolerance Score: 68.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BHMT2 Gene

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 BHMT2 Gene

Disorders for BHMT2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for BHMT2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
orofacial cleft
- elite association - COSMIC cancer census association via MalaCards
Search BHMT2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BHMT2

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 BHMT2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BHMT2 Gene

Publications for BHMT2 Gene

  1. Betaine-homocysteine S-methyltransferase-2 is an S-methylmethionine-homocysteine methyltransferase. (PMID: 18230605) Szegedi SS … Garrow TA (The Journal of biological chemistry 2008) 2 3 4 22 58
  2. Betaine-homocysteine methyltransferase-2: cDNA cloning, gene sequence, physical mapping, and expression of the human and mouse genes. (PMID: 11087663) Chadwick LH … Nadeau JH (Genomics 2000) 2 3 4 22 58
  3. Associations of folate and choline metabolism gene polymorphisms with orofacial clefts. (PMID: 19737740) Mostowska A … Jagodzinski PP (Journal of medical genetics 2010) 3 44 58
  4. Early-onset ischaemic stroke: analysis of 58 polymorphisms in 17 genes involved in methionine metabolism. (PMID: 20458436) Giusti B … Abbate R (Thrombosis and haemostasis 2010) 3 44 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for BHMT2 Gene

Sources for BHMT2 Gene

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