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GLDC glycine decarboxylase [ Homo sapiens (human) ]

Gene ID: 2731, updated on 1-Jun-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
109.20200522 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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