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GLDC glycine decarboxylase [ Homo sapiens (human) ]

Gene ID: 2731, updated on 5-Jul-2025
Official Symbol
GLDCprovided by HGNC
Official Full Name
glycine decarboxylaseprovided by HGNC
Primary source
HGNC:HGNC:4313
See related
Ensembl:ENSG00000178445 MIM:238300; AllianceGenome:HGNC:4313
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; GCE1; 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
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See GLDC in Genome Data Viewer
Location:
9p24.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (6532467..6645729, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (6537521..6650780, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (6532467..6645729, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene TPD52 like 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28186 Neighboring gene ubiquitin like with PHD and ring finger domains 2 Neighboring gene RNA, 7SL, cytoplasmic 25, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:6566198-6567397 Neighboring gene Sharpr-MPRA regulatory region 10661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28187 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6622908-6623703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6630771-6631613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:6635584-6636084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:6636085-6636585 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:6644939-6645496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28193 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:6647723-6648278 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:6648279-6648834 Neighboring gene ribosomal protein L23a pseudogene 57 Neighboring gene NANOG hESC enhancer GRCh37_chr9:6656576-6657082 Neighboring gene RNA, 7SL, cytoplasmic 123, pseudogene Neighboring gene RPS3A pseudogene 54

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Associated conditions

Description Tests
Glycine encephalopathy
MedGen: C0751748 GeneReviews: Nonketotic Hyperglycinemia
Compare labs
Glycine encephalopathy 1
MedGen: CN376801 OMIM: 605899 GeneReviews: Nonketotic Hyperglycinemia
not available

EBI GWAS Catalog

Description
Genome-wide association study of periodontal pathogen colonization.
EBI GWAS Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Clone Names

  • MGC138198, MGC138200

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables electron transfer activity TAS
Traceable Author Statement
more info
PubMed 
enables glycine binding IBA
Inferred from Biological aspect of Ancestor
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
enables glycine dehydrogenase (decarboxylating) activity TAS
Traceable Author Statement
more info
PubMed 
enables lyase activity IEA
Inferred from Electronic Annotation
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
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
 
Process Evidence Code Pubs
involved_in amino acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
involved_in glycine catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in glycine catabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in glycine catabolic process TAS
Traceable Author Statement
more info
PubMed 
involved_in glycine decarboxylation via glycine cleavage system IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in glycine metabolic process IEA
Inferred from Electronic Annotation
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
 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
 
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
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

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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.

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, Q2M2F8
    UniProtKB/TrEMBL
    A0A1J0GNC2
    Related
    ENSP00000370737.4, ENST00000321612.8
    Conserved Domains (1) summary
    PRK05367
    Location:571009
    PRK05367; glycine dehydrogenase; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    6537521..6650780 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)