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

    Gene ID: 23743, updated on 9-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See BHMT2 in Genome Data Viewer
    Location:
    5q14.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (79069767..79090069)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (79550871..79571174)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20001

    General protein information

    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)

    NEW Try the new Transcript table

    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_001178005.2NP_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:23241
      S-methyl_trans; Homocysteine S-methyltransferase
    2. NM_017614.5NP_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:23303
      S-methyl_trans; Homocysteine S-methyltransferase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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)