Shmt1 serine hydroxymethyltransferase 1 (soluble) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Shmt1provided by MGI
Official Full Name: serine hydroxymethyltransferase 1 (soluble)provided by MGI
Primary source: MGI:MGI:98299
See related: Ensembl:ENSMUSG00000020534 AllianceGenome:MGI:98299
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; mshmt; mshmt1; mshmt2
Summary: Enables glycine hydroxymethyltransferase activity. Involved in tetrahydrofolate interconversion. Acts upstream of or within cellular response to leukemia inhibitory factor and dTMP biosynthetic process. Located in mitochondrion. Is active in nucleus. Is expressed in several structures, including alimentary system; brain ventricular layer; genitourinary system; liver and biliary system; and skin. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1). [provided by Alliance of Genome Resources, Jul 2025]
Expression: Broad expression in liver adult (RPKM 76.7), kidney adult (RPKM 33.5) and 15 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B2; 11 37.84 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (60679723..60702062, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (60788897..60811265, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

HOXD8 suppresses renal cell carcinoma growth by upregulating SHMT1 expression.
Title: HOXD8 suppresses renal cell carcinoma growth by upregulating SHMT1 expression.
Shmt1 and dietary folate deficiency influence metabolic markers of homocysteine remethylation in mice.
Title: Disruption of shmt1 impairs hippocampal neurogenesis and mnemonic function in mice.
SHMT1 and TYMS localization to the nucleus is essential to prevent uracil accumulation in DNA
Title: Nuclear localization of de novo thymidylate biosynthesis pathway is required to prevent uracil accumulation in DNA.
Data show that Shmt1 hemizygosity was associated with increased risk for intestinal cancer in Apc(min)(/+) mice through a gene-by-diet interaction.
Title: Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apc(min)-mediated intestinal cancer risk.
These results provide evidence that disruption of Shmt1 expression causes NTDs by impairing thymidylate biosynthesis and shows that changes in the expression of genes that encode folate-dependent enzymes may be key determinates of NTD risk.
Title: Shmt1 and de novo thymidylate biosynthesis underlie folate-responsive neural tube defects in mice.
It is one of the genetic components regulating PPI in mice and is relevant to schizophrenia susceptibility in humans. (review)
Title: [Analysis of mouse strain-dependent prepulse inhibition points to a role for Shmt1 (SHMT1) in mice and in schizophrenia].
Shmt1 (SHMT1), but not Srr, is likely to be one of the genetic components regulating prepulse inhibition in mice and possibly relevant to human schizophrenia.
Title: Analysis of strain-dependent prepulse inhibition points to a role for Shmt1 (SHMT1) in mice and in schizophrenia.
SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis
Title: SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis.
mitochondrial SHMT-derived one-carbon units are essential for folate-mediated one-carbon metabolism in the cytoplasm
Title: Cytoplasmic serine hydroxymethyltransferase regulates the metabolic partitioning of methylenetetrahydrofolate but is not essential in mice.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (3)
Gene trapped (2)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:224581

AI324848 (e-PCR)
- UniSTS:160102

RH127015 (e-PCR)
- UniSTS:209774

Shmt1 (e-PCR), detects polymorphism
- UniSTS:546986

AI385541 (e-PCR)
- UniSTS:180217

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables L-allo-threonine aldolase activity	ISO Inferred from Sequence Orthology more info
enables aldehyde-lyase activity	ISO Inferred from Sequence Orthology more info
enables amino acid 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	IEA Inferred from Electronic Annotation 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 mRNA 5'-UTR binding	IEA Inferred from Electronic Annotation more info
enables mRNA 5'-UTR binding	ISO Inferred from Sequence Orthology more info
enables mRNA regulatory element binding translation repressor activity	IEA Inferred from Electronic Annotation more info
enables mRNA regulatory element binding translation repressor activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	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
enables pyridoxal phosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables serine binding	IEA Inferred from Electronic Annotation more info
enables serine binding	ISO Inferred from Sequence Orthology more info
enables small molecule binding	IEA Inferred from Electronic Annotation more info
enables small molecule binding	ISO Inferred from Sequence Orthology more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in L-serine catabolic process	IEA Inferred from Electronic Annotation more info
involved_in L-serine catabolic process	ISO Inferred from Sequence Orthology more info
involved_in L-serine metabolic process	IEA Inferred from Electronic Annotation 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 cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to tetrahydrofolate	IEA Inferred from Electronic Annotation more info
involved_in cellular response to tetrahydrofolate	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dTMP biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in dTMP biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in folic acid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in folic acid metabolic process	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation 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 negative regulation of translation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in one-carbon metabolic process	IC Inferred by Curator more info	PubMed
involved_in one-carbon metabolic process	IEA Inferred from Electronic Annotation more info
involved_in protein homotetramerization	IEA Inferred from Electronic Annotation 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 purine nucleobase biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in purine nucleobase biosynthetic process	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 interconversion	ISO Inferred from Sequence Orthology more info
involved_in tetrahydrofolate metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in tetrahydrofolate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in tetrahydrofolate metabolic process	ISO Inferred from Sequence Orthology more info
involved_in tetrahydrofolate metabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	HDA more info	PubMed
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IGI Inferred from Genetic Interaction more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: serine hydroxymethyltransferase, cytosolic

Names: glycine hydroxymethyltransferase; serine methylase

NP_001412339.1

EC 2.1.2.1

NP_001412340.1

EC 2.1.2.1

NP_001412341.1

EC 2.1.2.1

NP_001412342.1

EC 2.1.2.1

NP_001412343.1

EC 2.1.2.1

NP_033197.2

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_001425410.1 → NP_001412339.1 serine hydroxymethyltransferase, cytosolic isoform 1

Status: VALIDATED

Source sequence(s)

AL596215

UniProtKB/Swiss-Prot

P50431, Q64508, Q8R0X9

UniProtKB/TrEMBL

Q9CWR5

Related

ENSMUSP00000134269.2, ENSMUST00000174214.2
NM_001425411.1 → NP_001412340.1 serine hydroxymethyltransferase, cytosolic isoform 2

Status: VALIDATED

Source sequence(s)

AL596215

UniProtKB/TrEMBL

G3UZ26

Related

ENSMUSP00000134318.2, ENSMUST00000174719.8
NM_001425412.1 → NP_001412341.1 serine hydroxymethyltransferase, cytosolic isoform 3

Status: VALIDATED

Source sequence(s)

AL596215

UniProtKB/TrEMBL

Q9CWR5
NM_001425413.1 → NP_001412342.1 serine hydroxymethyltransferase, cytosolic isoform 3

Status: VALIDATED

Source sequence(s)

AL596215

UniProtKB/TrEMBL

Q9CWR5
NM_001425414.1 → NP_001412343.1 serine hydroxymethyltransferase, cytosolic isoform 4

Status: VALIDATED

Source sequence(s)

AL596215
NM_009171.3 → NP_033197.2 serine hydroxymethyltransferase, cytosolic isoform 1

See identical proteins and their annotated locations for NP_033197.2

Status: VALIDATED

Source sequence(s)

AL596215

Consensus CDS

CCDS24799.1

UniProtKB/Swiss-Prot

P50431, Q64508, Q8R0X9

UniProtKB/TrEMBL

Q9CWR5

Related

ENSMUSP00000018744.9, ENSMUST00000018744.15

Conserved Domains (1) summary

PLN03226
Location:13 → 475

PLN03226; serine hydroxymethyltransferase; Provisional