Gene Gene information from NCBI Gene database.
Entrez ID 2731
Gene name Glycine decarboxylase
Gene symbol GLDC
Synonyms (NCBI Gene)
GCEGCE1GCSPHYGN1
Chromosome 9
Chromosome location 9p24.1
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
SNPs SNP information provided by dbSNP.
152
SNP ID Visualize variation Clinical significance Consequence
rs121964974 C>A Pathogenic Coding sequence variant, missense variant
rs121964975 AAG>- Pathogenic-likely-pathogenic Coding sequence variant, inframe deletion
rs121964976 C>G,T Pathogenic, benign Coding sequence variant, synonymous variant, missense variant
rs121964977 G>A Pathogenic Coding sequence variant, missense variant
rs121964978 A>G Pathogenic Initiator codon variant, missense variant
miRNA miRNA information provided by mirtarbase database.
32
miRTarBase ID miRNA Experiments Reference
MIRT042509 hsa-miR-423-3p CLASH 23622248
MIRT042509 hsa-miR-423-3p CLASH 23622248
MIRT2235284 hsa-miR-3190 CLIP-seq
MIRT2235285 hsa-miR-4491 CLIP-seq
MIRT2235286 hsa-miR-4657 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
28
GO ID Ontology Definition Evidence Reference
GO:0004375 Function Glycine dehydrogenase (decarboxylating) activity IBA
GO:0004375 Function Glycine dehydrogenase (decarboxylating) activity IDA 28244183
GO:0004375 Function Glycine dehydrogenase (decarboxylating) activity IEA
GO:0004375 Function Glycine dehydrogenase (decarboxylating) activity TAS 1996985
GO:0005654 Component Nucleoplasm IDA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
238300 4313 ENSG00000178445
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P23378
Protein name Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) (Glycine cleavage system P protein) (Glycine decarboxylase) (Glycine dehydrogenase (aminomethyl-transferring))
Protein function The glycine cleavage system catalyzes the degradation of glycine. The P protein (GLDC) binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to
PDB 6I33 , 6I34 , 6I35
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02347 GDC-P 65 488 Glycine cleavage system P-protein Domain
PF01212 Beta_elim_lyase 584 743 Beta-eliminating lyase Domain
Sequence
MQSCARAWGLRLGRGVGGGRRLAGGSGPCWAPRSRDSSSGGGDSAAAGASRLLERLLPRH
DDFARRHIGPGDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATL
HAISSKNQIWRSYIGMGYYNCSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQ
TMVCDITGLDMANASLLDEGTAAAEALQLCYRHNKRRKFLVDPRCHPQTIAVVQTRAKYT
GVLTELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTELVERAHQSGSLACCATDLLALC
ILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRMVGVTRDATGKEV
YRLALQTREQHIRRDKATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLILSE
GLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKD
LDDLLWIF
GCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKK
LENKDISLVHSMIPLGSCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEK
DLCELTGYDQVCFQPNSGAQGEYAGLATIRAYLNQKGEGHRTVCLIPKSAHGTNPASAHM
AGMKIQPVEVDKYGNIDAVHLKAMVDKHKENLAAIMITYPSTNGVFEENISDVCDLIHQH
GGQVYLDGANMNAQVGICRPGDF
GSDVSHLNLHKTFCIPHGGGGPGMGPIGVKKHLAPFL
PNHPVISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILNANYM
AKRLETHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVA
GTLMVEPTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCVTSSHW
DRPYSREVAAFPLPFVKPENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS
Sequence length 1020
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Glycine, serine and threonine metabolism
Glyoxylate and dicarboxylate metabolism
One carbon pool by folate
Lipoic acid metabolism
Metabolic pathways
Carbon metabolism
  Glycine degradation
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
34
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Generalized epilepsy Pathogenic rs121964976 RCV000449527
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
GLDC-related disorder Pathogenic; Likely pathogenic rs121964976, rs191905539, rs1163356968, rs386833518, rs386833521, rs386833524, rs386833554, rs386833557, rs386833580 RCV003398490
RCV004745365
RCV003983163
RCV003415813
RCV004745180
View all (4 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Global developmental delay Pathogenic rs121964976 RCV000449527
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycine encephalopathy Likely pathogenic; Pathogenic rs1818705322, rs2129898042, rs1818463608, rs758575745, rs367987650, rs2129719653, rs1818287644, rs2129663304, rs1447727878, rs2129725961, rs2129831711, rs959935793, rs2129896575, rs777632051, rs2129897960
View all (335 more)
RCV001325842
RCV001638060
RCV003511751
RCV001360323
RCV001377475
View all (384 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormal brain morphology Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATOPIC ASTHMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Agenesis of corpus callosum Agenesis Of Corpus Callosum HPO_DG
★☆☆☆☆
Found in Text Mining only
Asthma Asthma GWASCAT_DG 31619474
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atypical glycine encephalopathy Glycine Encephalopathy Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autistic Disorder Autism BEFREE 25667990
★☆☆☆☆
Found in Text Mining only
B-Cell Lymphomas B-Cell Lymphoma BEFREE 26599272
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 25496516 Associate
★☆☆☆☆
Found in Text Mining only
Carcinogenesis Carcinogenesis Pubtator 22225612 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Ductal Ductal carcinoma Pubtator 25053597 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 30804330 Inhibit
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 35508111 Associate
★☆☆☆☆
Found in Text Mining only