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    SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) [ Homo sapiens (human) ]

    Gene ID: 6472, updated on 7-Feb-2016
    Official Symbol
    SHMT2provided by HGNC
    Official Full Name
    serine hydroxymethyltransferase 2 (mitochondrial)provided by HGNC
    Primary source
    HGNC:HGNC:10852
    See related
    Ensembl:ENSG00000182199; HPRD:00717; MIM:138450; Vega:OTTHUMG00000171246
    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
    Also known as
    GLYA; SHMT; HEL-S-51e
    Summary
    This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
    Orthologs
    See SHMT2 in Epigenomics, MapViewer
    Location:
    12q12-q14
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 12 NC_000012.12 (57229573..57234935)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57623356..57628718)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene LDL receptor related protein 1 Neighboring gene microRNA 1228 Neighboring gene neurexophilin 4 Neighboring gene NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 Neighboring gene SH3 and cysteine rich domain 3 Neighboring gene R3H domain containing 2

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    L-allo-threonine aldolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    amino acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    glycine hydroxymethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    glycine hydroxymethyltransferase activity TAS
    Traceable Author Statement
    more info
     
    identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    pyridoxal phosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    L-serine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    L-serine metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    folic acid metabolic process TAS
    Traceable Author Statement
    more info
     
    glycine biosynthetic process from serine IEA
    Inferred from Electronic Annotation
    more info
     
    glycine metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    glycine metabolic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    one-carbon metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    protein K63-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein homotetramerization IEA
    Inferred from Electronic Annotation
    more info
     
    protein tetramerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    response to type I interferon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    small molecule metabolic process TAS
    Traceable Author Statement
    more info
     
    tetrahydrofolate interconversion IEA
    Inferred from Electronic Annotation
    more info
     
    tetrahydrofolate metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    vitamin metabolic process TAS
    Traceable Author Statement
    more info
     
    water-soluble vitamin metabolic process TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    BRISC complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
     
    mitochondrial intermembrane space IEA
    Inferred from Electronic Annotation
    more info
     
    mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrial nucleoid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    serine hydroxymethyltransferase, mitochondrial
    Names
    GLY A+
    epididymis secretory sperm binding protein Li 51e
    glycine auxotroph A, human complement for hamster
    glycine hydroxymethyltransferase
    serine aldolase
    serine hydroxymethylase
    serine methylase
    threonine aldolase
    NP_001159828.1
    NP_001159829.1
    NP_001159830.1
    NP_001159831.1
    NP_005403.2

    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_029163.1 RefSeqGene

      Range
      5001..10363
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001166356.1NP_001159828.1  serine hydroxymethyltransferase, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159828.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      BC032584, BC091501, DC386590
      Consensus CDS
      CCDS55837.1
      UniProtKB/Swiss-Prot
      P34897
      UniProtKB/TrEMBL
      Q5BJF5
      Related
      ENSP00000452315, OTTHUMP00000245570, ENST00000557487, OTTHUMT00000412539
      Conserved Domains (1) summary
      cd00378
      Location:51455
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    2. NM_001166357.1NP_001159829.1  serine hydroxymethyltransferase, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001159829.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) is the longest transcript. It differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform 3. Translation efficiency is uncertain from this alternative start codon, and there is rapid turnover of the mitochondrial protein in the cytoplasm prior to mitochondrial import due to its shortened import presequence (PMID 8999870).
      Source sequence(s)
      AK315916, BC091501, DC339924
      Consensus CDS
      CCDS53805.1
      UniProtKB/TrEMBL
      A0A024RB99
      UniProtKB/Swiss-Prot
      P34897
      UniProtKB/TrEMBL
      Q5BJF5
      Related
      ENSP00000413770, OTTHUMP00000245566, ENST00000449049, OTTHUMT00000412534
      Conserved Domains (1) summary
      cd00378
      Location:30444
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    3. NM_001166358.1NP_001159830.1  serine hydroxymethyltransferase, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001159830.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform 3. Translation efficiency is uncertain from this alternative start codon, and there is rapid turnover of the mitochondrial protein in the cytoplasm prior to mitochondrial import due to its shortened import presequence (PMID 8999870).
      Source sequence(s)
      AC137834, BC091501, BX647711, DA052422
      Consensus CDS
      CCDS53805.1
      UniProtKB/TrEMBL
      A0A024RB99
      UniProtKB/Swiss-Prot
      P34897
      UniProtKB/TrEMBL
      Q5BJF5
      UniProtKB/TrEMBL
      Q5HYG8
      Related
      ENSP00000406881, OTTHUMP00000245562, ENST00000414700, OTTHUMT00000412529
      Conserved Domains (1) summary
      cd00378
      Location:30444
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    4. NM_001166359.1NP_001159831.1  serine hydroxymethyltransferase, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001159831.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform 3. Translation efficiency is uncertain from this alternative start codon, and there is rapid turnover of the mitochondrial protein in the cytoplasm prior to mitochondrial import due to its shortened import presequence (PMID 8999870).
      Source sequence(s)
      AC137834, AK296183, BC091501, CN395976
      Consensus CDS
      CCDS53805.1
      UniProtKB/TrEMBL
      A0A024RB99
      UniProtKB/TrEMBL
      B4DJQ3
      UniProtKB/Swiss-Prot
      P34897
      UniProtKB/TrEMBL
      Q5BJF5
      Related
      ENSP00000452419, OTTHUMP00000245565, ENST00000553474, OTTHUMT00000412533
      Conserved Domains (1) summary
      cd00378
      Location:30444
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    5. NM_005412.5NP_005403.2  serine hydroxymethyltransferase, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_005403.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC011911, BC091501, DC386590
      Consensus CDS
      CCDS8934.1
      UniProtKB/Swiss-Prot
      P34897
      UniProtKB/TrEMBL
      Q5BJF5
      UniProtKB/TrEMBL
      V9HW06
      Related
      ENSP00000333667, OTTHUMP00000245559, ENST00000328923, OTTHUMT00000412525
      Conserved Domains (1) summary
      cd00378
      Location:51465
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...

    RNA

    1. NR_029415.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate 5' exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region and is likely a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC137834, AK297173, BC091501, CN395976
    2. NR_029416.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) contains an alternate 5' exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region and is likely a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC137834, AK301443, BC091501, DA052422
    3. NR_029417.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC091501, DC386590
    4. NR_048562.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) contains an alternate 5' exon, lacks an internal exon, and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC008711
      Related
      ENST00000553837, OTTHUMT00000412536

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p2 Primary Assembly

      Range
      57229573..57234935
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538675.1XP_011536977.1  

      See identical proteins and their annotated locations for XP_011536977.1

      UniProtKB/TrEMBL
      B4DLV4
      Conserved Domains (1) summary
      cd00378
      Location:101369
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    2. XM_011538677.1XP_011536979.1  

      See identical proteins and their annotated locations for XP_011536979.1

      UniProtKB/TrEMBL
      B4DLV4
      Conserved Domains (1) summary
      cd00378
      Location:101369
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    3. XM_011538676.1XP_011536978.1  

      See identical proteins and their annotated locations for XP_011536978.1

      UniProtKB/TrEMBL
      B4DLV4
      Conserved Domains (1) summary
      cd00378
      Location:101369
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
    4. XM_011538678.1XP_011536980.1  

      See identical proteins and their annotated locations for XP_011536980.1

      UniProtKB/TrEMBL
      B4DLV4
      Conserved Domains (1) summary
      cd00378
      Location:101369
      SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

      Range
      57591454..57596816
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)