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BHMT2 betaine--homocysteine S-methyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 23743, updated on 5-Mar-2024

Summary

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Official Symbol
BHMT2provided by HGNC
Official Full Name
betaine--homocysteine S-methyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:1048
See related
Ensembl:ENSG00000132840 MIM:605932; AllianceGenome:HGNC:1048
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Biased expression in kidney (RPKM 175.7), liver (RPKM 113.0) and 1 other tissue See more
Orthologs
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Genomic context

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See BHMT2 in Genome Data Viewer
Location:
5q14.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (79069767..79090069)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (79550871..79571174)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (78365590..78385892)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:78105507-78106007 Neighboring gene arylsulfatase B Neighboring gene Sharpr-MPRA regulatory region 14877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:78270456-78270975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:78270976-78271494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16127 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:78293710-78294909 Neighboring gene IMPACT pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr5:78317526-78318027 Neighboring gene dimethylglycine dehydrogenase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:78407958-78408802 Neighboring gene uncharacterized LOC124901012 Neighboring gene betaine--homocysteine S-methyltransferase Neighboring gene RNY3 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association of Maternal Betaine-Homocysteine Methyltransferase (BHMT) and BHMT2 Genes Polymorphisms with Congenital Heart Disease in Offspring. Luo M, et al. Reprod Sci, 2023 Jan. PMID 35835902
  2. Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes. Ganu RS, et al. PLoS One, 2015. PMID 26213999, Free PMC Article
  3. Human betaine-homocysteine methyltransferase (BHMT) and BHMT2: common gene sequence variation and functional characterization. Li F, et al. Mol Genet Metab, 2008 Jul. PMID 18457970, Free PMC Article
  4. Investigations of a common genetic variant in betaine-homocysteine methyltransferase (BHMT) in coronary artery disease. Weisberg IS, et al. Atherosclerosis, 2003 Apr. PMID 12818402
  5. Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft. Wang P, et al. Oral Dis, 2018 Jul. PMID 29356306

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association of Maternal Betaine-Homocysteine Methyltransferase (BHMT) and BHMT2 Genes Polymorphisms with Congenital Heart Disease in Offspring.
    Title: Association of Maternal Betaine-Homocysteine Methyltransferase (BHMT) and BHMT2 Genes Polymorphisms with Congenital Heart Disease in Offspring.
  2. Our study suggested markers in BHMT/BHMT2 and DMGDH might affect the risk of NSCL/P through pairwise interaction.
    Title: Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft.
  3. A three-way interaction among maternal and fetal variants in BHMT2, GSTP1 and GPX3 contribute to congenital heart defects
    Title: A Three-Way Interaction among Maternal and Fetal Variants Contributing to Congenital Heart Defects.
  4. The faster evolutionary rate of BHMT2 overall suggests that selective constraints were reduced relative to BHMT.
    Title: Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes.
  5. Multiple SNPs in BHMT and BHMT2 were identified to be associated with the occurrence of infant obstructive heart defects and interaction effects with maternal use of folic acid supplements.
    Title: Obstructive heart defects associated with candidate genes, maternal obesity, and folic acid supplementation.
  6. No significant level of association was found with cleft lip with or without cleft palate and BHMT2 variants.
    Title: New evidence for the role of cystathionine beta-synthase in non-syndromic cleft lip with or without cleft palate.
  7. gene-gene interaction analysis revealed a significant epistatic interaction of BHMT2 (rs673752), PEMT (rs12325817), and PCYT1A (rs712012) with maternal NCL/P susceptibility.
    Title: Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts.
  8. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  9. Observational study of gene-disease association, gene-gene interaction, gene-environment interaction, and genetic testing. (HuGE Navigator)
    Title: Integrative predictive model of coronary artery calcification in atherosclerosis.
  10. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
EBI GWAS Catalog
Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
EBI GWAS Catalog
Genome-wide association study of selenium concentrations.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20001

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables S-adenosylmethionine-homocysteine S-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables S-methylmethionine-homocysteine S-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables S-methylmethionine-homocysteine S-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables betaine-homocysteine S-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-methionine salvage IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-methionine salvage IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in S-adenosylmethionine metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in S-methylmethionine metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in amino-acid betaine metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 

General protein information

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Preferred Names
S-methylmethionine--homocysteine S-methyltransferase BHMT2
Names
SMM-hcy methyltransferase
betaine-homocysteine methyltransferase 2
NP_001171476.1
NP_060084.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029157.1 RefSeqGene

    Range
    5044..25346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001178005.2 → NP_001171476.1  S-methylmethionine--homocysteine S-methyltransferase BHMT2 isoform 2

    See identical proteins and their annotated locations for NP_001171476.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AC008502, AK298298, BC020665, CB140104
    Consensus CDS
    CCDS54871.1
    UniProtKB/TrEMBL
    B2RDF4
    Related
    ENSP00000430278.1, ENST00000521567.1
    Conserved Domains (1) summary
    cl22882
    Location:23 → 241
    S-methyl_trans; Homocysteine S-methyltransferase

  2. NM_017614.5 → NP_060084.2  S-methylmethionine--homocysteine S-methyltransferase BHMT2 isoform 1

    See identical proteins and their annotated locations for NP_060084.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC008502, BC020665, CB140104
    Consensus CDS
    CCDS4045.1
    UniProtKB/Swiss-Prot
    B7Z516, Q9H2M3, Q9NXX7
    UniProtKB/TrEMBL
    B2RDF4
    Related
    ENSP00000255192.3, ENST00000255192.8
    Conserved Domains (1) summary
    pfam02574
    Location:23 → 303
    S-methyl_trans; Homocysteine S-methyltransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    79069767..79090069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    79550871..79571174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H2M3.1 GenPept UniProtKB/Swiss-Prot:Q9H2M3

Gene LinkOut

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