Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
2731
Gene name Gene Name - the full gene name approved by the HGNC.
Glycine decarboxylase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
GLDC
Synonyms (NCBI Gene) Gene synonyms aliases
GCE, GCE1, GCSP, HYGN1
Chromosome Chromosome number
9
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
9p24.1
Summary Summary of gene provided in NCBI Entrez Gene.
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.
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.
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 information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0004375 Function Glycine dehydrogenase (decarboxylating) activity IBA 21873635
GO:0004375 Function Glycine dehydrogenase (decarboxylating) activity IDA 28244183
GO:0005654 Component Nucleoplasm IDA
GO:0005739 Component Mitochondrion IBA 21873635
GO:0005739 Component Mitochondrion IDA 28244183
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
238300 4313 ENSG00000178445
Protein
UniProt ID 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 information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Agenesis of corpus callosum Agenesis of corpus callosum rs754914260, rs1057519053, rs1057519056, rs1057519054, rs1057519055, rs1057519057, rs1384496494, rs1599017933
Epilepsy Epilepsy, Generalized rs113994140, rs28937874, rs1589762127, rs104894166, rs28939075, rs2134001459, rs104894167, rs119488099, rs119488100, rs387906420, rs121917752, rs121918622, rs281865564, rs387907313, rs397514670
View all (165 more)
10873393
Epileptic encephalopathy Encephalopathies rs587776508, rs121918334, rs121918317, rs121918321, rs74315390, rs28939684, rs74315391, rs74315392, rs118192244, rs121918622, rs121918623, rs121917953, rs121917955, rs121918624, rs121918625
View all (860 more)
Glycine encephalopathy Atypical glycine encephalopathy, Neonatal glycine encephalopathy, Infantile glycine encephalopathy rs121964983, rs121964984, rs121964985, rs121964986, rs181134220, rs386833679, rs386833682, rs386833683, rs386833684, rs386833686, rs1057519313, rs1057519314, rs1057519315, rs781466698, rs757918826
View all (3 more)
Unknown
Disease term Disease name Evidence References Source
Asthma Asthma 31619474 ClinVar, GWAS
Hyperglycinuria HYPERGLYCINURIA (disorder) ClinVar
Glycine Encephalopathy glycine encephalopathy, glycine encephalopathy 1, neonatal glycine encephalopathy, infantile glycine encephalopathy, atypical glycine encephalopathy GenCC
Associations from Text Mining
Disease Name Relationship Type References
Anti N Methyl D Aspartate Receptor Encephalitis Associate 31279534
Breast Neoplasms Associate 25496516
Carcinogenesis Associate 22225612
Carcinoma Ductal Associate 25053597
Carcinoma Hepatocellular Inhibit 30804330
Carcinoma Hepatocellular Associate 35508111
Carcinoma Lobular Associate 25053597
Carcinoma Non Small Cell Lung Associate 22225612
Cerebral Infarction Associate 26352407
Colorectal Neoplasms Associate 25117815