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SHMT2 serine hydroxymethyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 6472, updated on 3-Nov-2019

Summary

Official Symbol
SHMT2provided by HGNC
Official Full Name
serine hydroxymethyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:10852
See related
Ensembl:ENSG00000182199 MIM:138450
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]
Expression
Ubiquitous expression in liver (RPKM 35.4), lymph node (RPKM 21.8) and 25 other tissues See more
Orthologs

Genomic context

See SHMT2 in Genome Data Viewer
Location:
12q13.3
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (57229685..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 Sharpr-MPRA regulatory region 225 Neighboring gene NDUFA4 mitochondrial complex associated like 2 Neighboring gene SH3 and cysteine rich domain 3

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?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
cobalt ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine hydroxymethyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine hydroxymethyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyridoxal phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
serine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
L-serine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
L-serine catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
L-serine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to tetrahydrofolate IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
folic acid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
folic acid metabolic process TAS
Traceable Author Statement
more info
 
glycine biosynthetic process from serine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
one-carbon metabolic process IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homotetramerization IDA
Inferred from Direct Assay
more info
PubMed 
protein tetramerization IDA
Inferred from Direct Assay
more info
PubMed 
regulation of aerobic respiration IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mitochondrial translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of oxidative phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of oxidative phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to type I interferon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to type I interferon IDA
Inferred from Direct Assay
more info
PubMed 
tetrahydrofolate interconversion IEA
Inferred from Electronic Annotation
more info
 
tetrahydrofolate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tetrahydrofolate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
BRISC complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
BRISC complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 
mitochondrial inner membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial matrix IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial nucleoid IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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 hydroxymethyltransferase 2 (mitochondrial)
serine methylase
threonine aldolase
NP_001159828.1
NP_001159829.1
NP_001159830.1
NP_001159831.1
NP_005403.2
XP_011536977.1
XP_011536978.1
XP_011536979.1
XP_011536980.1

NCBI Reference Sequences (RefSeq)

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
    5139..10363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166356.2NP_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
    Consensus CDS
    CCDS55837.1
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    Q5BJF5
    Related
    ENSP00000452315.1, ENST00000557487.5
    Conserved Domains (2) summary
    PLN03226
    Location:45492
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:49438
    SHMT; Serine hydroxymethyltransferase
  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/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    A0A024RB99, Q5BJF5
    Related
    ENSP00000413770.3, ENST00000449049.7
    Conserved Domains (2) summary
    PLN03226
    Location:24481
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:28427
    SHMT; Serine hydroxymethyltransferase
  3. NM_001166358.2NP_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
    Consensus CDS
    CCDS53805.1
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    A0A024RB99, Q5BJF5, Q5HYG8
    Related
    ENSP00000406881.3, ENST00000414700.7
    Conserved Domains (2) summary
    PLN03226
    Location:24481
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:28427
    SHMT; Serine hydroxymethyltransferase
  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/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    A0A024RB99, B4DJQ3, Q5BJF5
    Related
    ENSP00000452419.1, ENST00000553474.5
    Conserved Domains (2) summary
    PLN03226
    Location:24481
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:28427
    SHMT; Serine hydroxymethyltransferase
  5. NM_005412.6NP_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, V9HW06
    Related
    ENSP00000333667.3, ENST00000328923.8
    Conserved Domains (1) summary
    PLN03226
    Location:45502
    PLN03226; serine hydroxymethyltransferase; Provisional

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
    Related
    ENST00000555116.5
  2. NR_029416.2 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
  3. NR_029417.2 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
    Related
    ENST00000556825.5
  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
    ENST00000555774.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    57229685..57234935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538677.3XP_011536979.1  serine hydroxymethyltransferase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011536979.1

    UniProtKB/TrEMBL
    B4DLV4
    Conserved Domains (1) summary
    cl18945
    Location:101352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  2. XM_011538675.3XP_011536977.1  serine hydroxymethyltransferase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011536977.1

    UniProtKB/TrEMBL
    B4DLV4
    Conserved Domains (1) summary
    cl18945
    Location:101352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  3. XM_011538676.3XP_011536978.1  serine hydroxymethyltransferase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011536978.1

    UniProtKB/TrEMBL
    B4DLV4
    Conserved Domains (1) summary
    cl18945
    Location:101352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  4. XM_011538678.2XP_011536980.1  serine hydroxymethyltransferase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011536980.1

    UniProtKB/TrEMBL
    B4DLV4
    Conserved Domains (1) summary
    cl18945
    Location:101352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
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