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Gldc glycine decarboxylase [ Rattus norvegicus (Norway rat) ]

Gene ID: 309312, updated on 3-Apr-2024

Summary

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Symbol
Gldcprovided by RGD
Full Name
glycine decarboxylaseprovided by RGD
Primary source
RGD:1308660
See related
Ensembl:ENSRNOG00000011599 AllianceGenome:RGD:1308660
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables anion binding activity; enzyme binding activity; and glycine dehydrogenase (decarboxylating) activity. Involved in glycine decarboxylation via glycine cleavage system and protein-containing complex assembly. Located in mitochondrion. Part of glycine cleavage complex. Human ortholog(s) of this gene implicated in glycine encephalopathy. Orthologous to human GLDC (glycine decarboxylase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Liver (RPKM 189.6), Kidney (RPKM 170.4) and 4 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
1q52
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (237296753..237375620, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (227883249..227962119, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (248295140..248377122, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 beta 2, pseudogene 3 Neighboring gene ubiquitin like with PHD and ring finger domains 2 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4, pseudogene 1 Neighboring gene cytochrome c, somatic, pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Epigenetic Silencing of the Putative Tumor Suppressor Gene GLDC (Glycine Dehydrogenase) in Gastric Carcinoma. Min HL, et al. Anticancer Res, 2016 Jan. PMID 26722042
  2. Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease. Bravo-Alonso I, et al. Hum Mutat, 2017 Jun. PMID 28244183
  3. Glycine decarboxylase deficiency causes neural tube defects and features of non-ketotic hyperglycinemia in mice. Pai YJ, et al. Nat Commun, 2015 Mar 4. PMID 25736695, Free PMC Article
  4. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. Kanno J, et al. J Med Genet, 2007 Mar. PMID 17361008, Free PMC Article
  5. Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. Flusser H, et al. Neurology, 2005 Apr 26. PMID 15851735

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables glycine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycine dehydrogenase (decarboxylating) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine dehydrogenase (decarboxylating) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycine dehydrogenase (decarboxylating) activity ISO
Inferred from Sequence Orthology
more info
  
enables lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pyridoxal phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine decarboxylation via glycine cleavage system IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycine decarboxylation via glycine cleavage system IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein-containing complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of glycine cleavage complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of glycine cleavage complex IDA
Inferred from Direct Assay
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 ISO
Inferred from Sequence Orthology
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 decarboxylase, glycine cleavage system protein P)
glycine dehydrogenase (decarboxylating)
glycine dehydrogenase (decarboxylating), mitochondrial-like
glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)
glycine dehydrogenase [decarboxylating], mitochondrial
glycine dehydrogenase [decarboxylating], mitochondrial-like
NP_001402873.1
XP_006231273.1

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)

  1. NM_001415944.1 → NP_001402873.1  glycine dehydrogenase (decarboxylating), mitochondrial

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    Related
    ENSRNOP00000069291.2, ENSRNOT00000089073.2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    237296753..237375620 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006231211.5 → XP_006231273.1  glycine dehydrogenase (decarboxylating), mitochondrial isoform X1

    UniProtKB/TrEMBL
    A0A0G2JUZ5
    Conserved Domains (3) summary
    PRK05367
    Location:61 → 823
    PRK05367; glycine dehydrogenase; Provisional
    pfam02347
    Location:69 → 492
    GDC-P; Glycine cleavage system P-protein
    cl18945
    Location:522 → 837
    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 ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001107583.1: Suppressed sequence

    Description
    NM_001107583.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

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