GLDC glycine decarboxylase [Homo sapiens (human)] - Gene

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: mouse all

Genomic context

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_000009.12 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GLDC overexpression significantly induced cell autophagy, whereas GLDC downregulation reduced cell autophagy. Of note, GLDC is the post-transcriptional target of miR-30d-5p. GLDC overexpression could rescue miR-30d-5p-mediated cell metastasis and increase autophagy.
Title: Glycine decarboxylase induces autophagy and is downregulated by miRNA-30d-5p in hepatocellular carcinoma.
we identified a new alternative splicing isoform of GLDC, truncated GLDCV1, and demonstrated that GLDCV1 possesses similar biological activities to GLDCfl on regulating CSCs and tumorigenesis.
Title: Identification of a new <i>GLDC</i> gene alternative splicing variant and its protumorigenic roles in lung cancer.
These findings reveal a critical role of GLDC in sustaining the proliferation of neuroblastoma cells with high-level GLDC expression and suggest that MYCN amplification is a biomarker for GLDC-based therapeutic strategies against high-risk neuroblastoma.
Title: Glycine decarboxylase is a transcriptional target of MYCN required for neuroblastoma cell proliferation and tumorigenicity.
Collectively, GLDC regulates cellular antiviral response and orchestrates viral growth. GLDC is a functional susceptibility gene to severe influenza in humans.
Title: Identification and characterization of GLDC as host susceptibility gene to severe influenza.
these findings suggest that GLDC-mediated regulation of glycolysis and controlling AGE accumulation is related to maintenance and induction of pluripotency.
Title: Glycine decarboxylase regulates the maintenance and induction of pluripotency via metabolic control.
Our data indicate that GLDC downregulation decreases reactive oxygen species mediated ubiquitination of cofilin to enhance hepatocellular carcinoma progression and intrahepatic metastasis
Title: Downregulation of glycine decarboxylase enhanced cofilin-mediated migration in hepatocellular carcinoma cells.
A novel compound heterozygous variant was identified in the GLDC gene in a Chinese family with non-ketotic hyperglycinemia
Title: A novel compound heterozygous variant identified in GLDC gene in a Chinese family with non-ketotic hyperglycinemia.
it was concluded that elevated serum GLDC may increase lung cancer risk, and that smoking, GLDC, the miR29 family and DNMT signaling pathways may serve an important role in early malignant transformation during the development of lung cancer.
Title: Serum glycine dehydrogenase is associated with increased risk of lung cancer and promotes malignant transformation by regulating DNA methyltransferases expression.
a comprehensive functional and structural analysis of 19 GLDC missense variants identified in a cohort of 26 nonketotic hyperglycinemia patients was performed
Title: Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease.
The position and frequency of the breakpoint for CNVs correlated with intron size and presence of Alu elements. Missense mutations, most often recurring, were the most common type of disease-causing mutation in AMT
Title: The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Non-ketotic hyperglycinemia MedGen: C0751748 OMIM: 605899 GeneReviews: Nonketotic Hyperglycinemia	Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of periodontal pathogen colonization. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9S937 (e-PCR)
- UniSTS:54357

STS-AA009796 (e-PCR)
- UniSTS:24670

WI-20011 (e-PCR)
- UniSTS:32352

SHGC-14149 (e-PCR)
- UniSTS:12730

D9S2017 (e-PCR)
- UniSTS:4036

D9S324 (e-PCR)
- UniSTS:61911

SHGC-67420 (e-PCR)
- UniSTS:84724

Homology

Homologs of the GLDC gene: The GLDC gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, C.elegans, S.cerevisiae, K.lactis, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 316 organisms have orthologs with human gene GLDC
Orthologs

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

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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

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.