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

Gene ID: 23743, updated on 23-Nov-2023

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
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Genomic context

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

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)

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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_001178005.2NP_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_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)