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    GLDC glycine decarboxylase [ Homo sapiens (human) ]

    Gene ID: 2731, updated on 15-Mar-2020

    Summary

    Official Symbol
    GLDCprovided by HGNC
    Official Full Name
    glycine decarboxylaseprovided by HGNC
    Primary source
    HGNC:HGNC:4313
    See related
    Ensembl:ENSG00000178445 MIM:238300
    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
    GCE; GCSP; HYGN1
    Summary
    Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase). The protein encoded by this gene is the P protein, which binds to glycine and enables the methylamine group from glycine to be transferred to the T protein. Defects in this gene are a cause of nonketotic hyperglycinemia (NKH).[provided by RefSeq, Jan 2010]
    Expression
    Biased expression in kidney (RPKM 25.8), placenta (RPKM 17.4) and 4 other tissues See more
    Orthologs

    Genomic context

    See GLDC in Genome Data Viewer
    Location:
    9p24.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (6532467..6645729, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (6532464..6645692, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene TPD52 like 3 Neighboring gene ubiquitin like with PHD and ring finger domains 2 Neighboring gene RNA, 7SL, cytoplasmic 25, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10661 Neighboring gene ribosomal protein L23a pseudogene 57 Neighboring gene HNF4 motif-containing MPRA enhancer 135 Neighboring gene RNA, 7SL, cytoplasmic 123, pseudogene

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC138198, MGC138200

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    electron transfer activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enzyme binding IEA
    Inferred from Electronic Annotation
    more info
     
    glycine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glycine dehydrogenase (decarboxylating) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glycine dehydrogenase (decarboxylating) activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lyase activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    pyridoxal binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    pyridoxal phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular response to leukemia inhibitory factor IEA
    Inferred from Electronic Annotation
    more info
     
    electron transport chain IEA
    Inferred from Electronic Annotation
    more info
     
    glycine catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    glycine decarboxylation via glycine cleavage system IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    response to lipoic acid ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    response to methylamine ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    glycine cleavage complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    glycine dehydrogenase (decarboxylating), mitochondrial
    Names
    glycine cleavage system protein P
    glycine decarboxylase P-protein
    glycine dehydrogenase (aminomethyl-transferring)
    glycine dehydrogenase [decarboxylating], mitochondrial
    nonketotic hyperglycinemia
    NP_000161.2

    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_016397.1 RefSeqGene

      Range
      5001..118229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_643

    mRNA and Protein(s)

    1. NM_000170.3NP_000161.2  glycine dehydrogenase (decarboxylating), mitochondrial precursor

      See identical proteins and their annotated locations for NP_000161.2

      Status: REVIEWED

      Source sequence(s)
      AI480362, AL162411, AW593954, BC111993, DA741442, DR002916
      Consensus CDS
      CCDS34987.1
      UniProtKB/Swiss-Prot
      P23378
      Related
      ENSP00000370737.3, ENST00000321612.7
      Conserved Domains (1) summary
      PRK05367
      Location:571009
      PRK05367; glycine dehydrogenase; Provisional

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

      Range
      6532467..6645729 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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