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

    Gene ID: 23743, updated on 10-Dec-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
    mouse all
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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_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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. 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
    3. Investigations of a common genetic variant in betaine-homocysteine methyltransferase (BHMT) in coronary artery disease. Weisberg IS, et al. Atherosclerosis, 2003 Apr. PMID 12818402
    4. 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
    5. Betaine-homocysteine methyltransferase-2: cDNA cloning, gene sequence, physical mapping, and expression of the human and mouse genes. Chadwick LH, et al. Genomics, 2000 Nov 15. PMID 11087663

    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)

    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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    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_001178005.2 → 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_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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H2M3.1 GenPept UniProtKB/Swiss-Prot:Q9H2M3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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