Shmt2 serine hydroxymethyltransferase 2 (mitochondrial) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Shmt2provided by MGI
Official Full Name: serine hydroxymethyltransferase 2 (mitochondrial)provided by MGI
Primary source: MGI:MGI:1277989
See related: Ensembl:ENSMUSG00000025403 AllianceGenome:MGI:1277989
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: SHMT; 2700043D08Rik
Summary: Enables glycine hydroxymethyltransferase activity. Involved in several processes, including formate biosynthetic process; regulation of oxidative phosphorylation; and tetrahydrofolate interconversion. Acts upstream of or within dTMP biosynthetic process. Located in mitochondrial inner membrane. Is active in mitochondrial matrix and nucleus. Is expressed in several structures, including future brain; hepatic primordium; placenta; skeleton; and submandibular gland primordium. Human ortholog(s) of this gene implicated in neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities. Orthologous to human SHMT2 (serine hydroxymethyltransferase 2). [provided by Alliance of Genome Resources, May 2025]
Expression: Ubiquitous expression in liver adult (RPKM 102.9), kidney adult (RPKM 81.2) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 D3; 10 74.51 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (127352992..127358313, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (127517123..127522444, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Serine Hydroxymethyltransferase 2 Deficiency in the Hematopoietic System Disrupts Erythropoiesis and Induces Anemia in Murine Models.
Title: Serine Hydroxymethyltransferase 2 Deficiency in the Hematopoietic System Disrupts Erythropoiesis and Induces Anemia in Murine Models.
Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2.
Title: Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2.
SHMT2 Mediates Small-Molecule-Induced Alleviation of Alzheimer Pathology Via the 5'UTR-dependent ADAM10 Translation Initiation.
Title: SHMT2 Mediates Small-Molecule-Induced Alleviation of Alzheimer Pathology Via the 5'UTR-dependent ADAM10 Translation Initiation.
SHMT2 reduces fatty liver but is necessary for liver inflammation and fibrosis in mice.
Title: SHMT2 reduces fatty liver but is necessary for liver inflammation and fibrosis in mice.
Serine synthesis via reversed SHMT2 activity drives glycine depletion and acetaminophen hepatotoxicity in MASLD.
Title: Serine synthesis via reversed SHMT2 activity drives glycine depletion and acetaminophen hepatotoxicity in MASLD.
The role of SHMT2 in modulating lipid metabolism in hepatocytes via glycine-mediated mTOR activation.
Title: The role of SHMT2 in modulating lipid metabolism in hepatocytes via glycine-mediated mTOR activation.
Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders.
Title: Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders.
Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
Title: Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
SHMT2 can contribute to liver regeneration after partial hepatectomy, and this is likely related to the activation of Akt/mTOR signaling pathway by its metabolic product, glycine, in hepatocytes.
Title: SHMT2 Promotes Liver Regeneration Through Glycine-activated Akt/mTOR Pathway.
Knockdown of SHMT2 worsens IR injury through the ROS/JNK/P53 signaling pathway.
Title: Downregulating Serine Hydroxymethyltransferase 2 Deteriorates Hepatic Ischemia-Reperfusion Injury through ROS/JNK/P53 Signaling in Mice.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (9) 1 citation
Gene trapped (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AA986903 (e-PCR)
- UniSTS:185857

PMC133987P1 (e-PCR)
- UniSTS:270699

Shmt2 (e-PCR), detects polymorphism
- UniSTS:546987

RH125781 (e-PCR)
- UniSTS:162528

Shmt2 (e-PCR), detects polymorphism
- UniSTS:526055

RH126912 (e-PCR)
- UniSTS:208629

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables L-allo-threonine aldolase activity	IEA Inferred from Electronic Annotation more info
enables L-allo-threonine aldolase activity	ISO Inferred from Sequence Orthology more info
enables amino acid binding	IEA Inferred from Electronic Annotation more info
enables amino acid binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables glycine hydroxymethyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine hydroxymethyltransferase activity	IGI Inferred from Genetic Interaction more info	PubMed
enables glycine hydroxymethyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables glycine hydroxymethyltransferase activity	ISO Inferred from Sequence Orthology more info
enables glycine hydroxymethyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables pyridoxal phosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info
enables pyridoxal phosphate binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in L-serine biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in L-serine biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in L-serine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in L-serine metabolic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within dTMP biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in formate biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glycine biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in glycine biosynthetic process from serine	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine biosynthetic process from serine	IEA Inferred from Electronic Annotation more info
involved_in glycine biosynthetic process from serine	ISO Inferred from Sequence Orthology more info
involved_in glycine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycine metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in one-carbon metabolic process	ISO Inferred from Sequence Orthology more info
involved_in one-carbon metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in protein K63-linked deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K63-linked deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein homotetramerization	ISO Inferred from Sequence Orthology more info
involved_in protein homotetramerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein tetramerization	ISO Inferred from Sequence Orthology more info
involved_in regulation of aerobic respiration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of aerobic respiration	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitochondrial translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitochondrial translation	ISO Inferred from Sequence Orthology more info
involved_in regulation of oxidative phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of oxidative phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in response to type I interferon	IEA Inferred from Electronic Annotation more info
involved_in response to type I interferon	ISO Inferred from Sequence Orthology more info
involved_in tetrahydrofolate interconversion	IEA Inferred from Electronic Annotation more info
involved_in tetrahydrofolate interconversion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tetrahydrofolate metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in tetrahydrofolate metabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of BRISC complex	IEA Inferred from Electronic Annotation more info
part_of BRISC complex	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in microtubule cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in microtubule cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in mitochondrial inner membrane	HDA more info	PubMed
located_in mitochondrial inner membrane	ISO Inferred from Sequence Orthology more info
is_active_in mitochondrial matrix	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial matrix	ISO Inferred from Sequence Orthology more info
located_in mitochondrial nucleoid	IEA Inferred from Electronic Annotation more info
located_in mitochondrial nucleoid	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	HDA more info	PubMed
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IGI Inferred from Genetic Interaction more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: serine hydroxymethyltransferase, mitochondrial

Names: glycine hydroxymethyltransferase; serine methylase

NP_001239245.1

EC 2.1.2.1

NP_082506.1

EC 2.1.2.1

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.

mRNA and Protein(s)

NM_001252316.1 → NP_001239245.1 serine hydroxymethyltransferase, mitochondrial isoform 2

See identical proteins and their annotated locations for NP_001239245.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses a different splice site in the 5' coding region, compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus when it is compared to isoform 1.

Source sequence(s)

AK162421, AK169192

Consensus CDS

CCDS88105.1

UniProtKB/TrEMBL

Q3TFD0, Q9CZN7

Related

ENSMUSP00000151616.2, ENSMUST00000219239.2

Conserved Domains (1) summary

PLN03226
Location:42 → 499

PLN03226; serine hydroxymethyltransferase; Provisional
NM_028230.4 → NP_082506.1 serine hydroxymethyltransferase, mitochondrial isoform 1

See identical proteins and their annotated locations for NP_082506.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).

Source sequence(s)

AK162421, BY760884

Consensus CDS

CCDS24244.1

UniProtKB/Swiss-Prot

Q3TFD0, Q99K87, Q9CZN7

Related

ENSMUSP00000026470.5, ENSMUST00000026470.6

Conserved Domains (1) summary

PLN03226
Location:45 → 502

PLN03226; serine hydroxymethyltransferase; Provisional