Gldc glycine decarboxylase [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Gldcprovided by MGI
Official Full Name: glycine decarboxylaseprovided by MGI
Primary source: MGI:MGI:1341155
See related: Ensembl:ENSMUSG00000024827 AllianceGenome:MGI:1341155
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: D19Wsu57e; b2b2679Clo; D030049L12Rik
Summary: Predicted to enable several functions, including glycine binding activity; glycine dehydrogenase (decarboxylating) activity; and vitamin B6 binding activity. Acts upstream of or within cellular response to leukemia inhibitory factor. Located in mitochondrion. Is expressed in several structures, including central nervous system; integumental system; limb; sensory organ; and urinary system. Used to study glycine encephalopathy. Human ortholog(s) of this gene implicated in glycine encephalopathy. Orthologous to human GLDC (glycine decarboxylase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in liver adult (RPKM 46.0), kidney adult (RPKM 27.4) and 15 other tissues See more
Orthologs: human all
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Genomic context

Location:: 19 C1; 19 24.87 cM

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (30075847..30152829, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (30098441..30175441, complement)

Chromosome 19 - NC_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Regulation of glycine metabolism by the glycine cleavage system and conjugation pathway in mouse models of non-ketotic hyperglycinemia.
Title: Regulation of glycine metabolism by the glycine cleavage system and conjugation pathway in mouse models of non-ketotic hyperglycinemia.
Genomic analyses of glycine decarboxylase neurogenic mutations yield a large-scale prediction model for prenatal disease.
Title: Genomic analyses of glycine decarboxylase neurogenic mutations yield a large-scale prediction model for prenatal disease.
Impaired folate 1-carbon metabolism causes formate-preventable hydrocephalus in glycine decarboxylase-deficient mice.
Title: Impaired folate 1-carbon metabolism causes formate-preventable hydrocephalus in glycine decarboxylase-deficient mice.
Exencephaly and ventriculomegaly were detectable by High-frequency ultrasound in homozygous Gldc-deficient mouse embryos indicating this to be an effective tool to study CNS development.
Title: Use of high-frequency ultrasound to study the prenatal development of cranial neural tube defects and hydrocephalus in Gldc-deficient mice.
These studies support a direct relationship between p53 mutations and GLDC expression in B cell lymphoma.
Title: Glycine Decarboxylase Expression Increased in p53-Mutated B Cell Lymphoma Mice.
Glycine decarboxylase deficiency causes neural tube defects and features of non-ketotic hyperglycinemia in mice through limiting supply of one-carbon units from mitochondrial folate metabolism.
Title: Glycine decarboxylase deficiency causes neural tube defects and features of non-ketotic hyperglycinemia in mice.
Results suggest that there is a direct correlation between ischemic injury and extracellular glycine concentration maintained by glycine decarboxylase and the glycine cleavage multienzyme system.
Title: Direct correlation between ischemic injury and extracellular glycine concentration in mice with genetically altered activities of the glycine cleavage multienzyme system.

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Variation

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Alleles

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

Chemically induced (ENU) (1)
Endonuclease-mediated (4)
Gene trapped (1)
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI194796 (e-PCR)
- UniSTS:209454

D9Mit34.1 (e-PCR), detects polymorphism
- UniSTS:131903

Gldc (e-PCR), detects polymorphism
- UniSTS:143217

RH125989 (e-PCR)
- UniSTS:162701

RH125877 (e-PCR)
- UniSTS:142227

Gldc (e-PCR), detects polymorphism
- UniSTS:546794

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables enzyme binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables glycine binding	IBA Inferred from Biological aspect of Ancestor more info
enables glycine binding	IEA Inferred from Electronic Annotation more info
enables glycine binding	ISO Inferred from Sequence Orthology more info
enables glycine dehydrogenase (decarboxylating) activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine dehydrogenase (decarboxylating) activity	ISO Inferred from Sequence Orthology more info	PubMed
enables glycine dehydrogenase (decarboxylating) activity	ISS Inferred from Sequence or Structural Similarity more info
enables lyase activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables pyridoxal binding	ISS Inferred from Sequence or Structural Similarity 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
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in glycine catabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycine catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycine decarboxylation via glycine cleavage system	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within glycine decarboxylation via glycine cleavage system	ISO Inferred from Sequence Orthology more info
involved_in glycine decarboxylation via glycine cleavage system	ISO Inferred from Sequence Orthology more info
involved_in protein-containing complex assembly	IEA Inferred from Electronic Annotation more info
involved_in protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in response to lipoic acid	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to methylamine	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of glycine cleavage complex	IBA Inferred from Biological aspect of Ancestor more info
part_of glycine cleavage complex	IEA Inferred from Electronic Annotation more info
part_of glycine cleavage complex	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
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: glycine dehydrogenase (decarboxylating), mitochondrial

Names: glycine cleavage system P protein; glycine dehydrogenase (aminomethyl-transferring); glycine dehydrogenase [decarboxylating], mitochondrial

NP_613061.1

EC 1.4.4.2

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_138595.3 → NP_613061.1 glycine dehydrogenase (decarboxylating), mitochondrial precursor

See identical proteins and their annotated locations for NP_613061.1

Status: VALIDATED

Source sequence(s)

AC157986, AC162613

Consensus CDS

CCDS37956.1

UniProtKB/Swiss-Prot

Q91W43

UniProtKB/TrEMBL

Q8BJQ7

Related

ENSMUSP00000025778.8, ENSMUST00000025778.9

Conserved Domains (3) summary

COG1003
Location:509 → 982

GcvP2; Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]

PRK05367
Location:62 → 1014

PRK05367; glycine dehydrogenase; Provisional

pfam02347
Location:70 → 493

GDC-P; Glycine cleavage system P-protein