Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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

Show/Hide all(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
rs121964979	G>A,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs121964980	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs140877566	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs144090917	C>G,T	Conflicting-interpretations-of-pathogenicity, benign	Missense variant, coding sequence variant
rs149070244	C>G,T	Pathogenic-likely-pathogenic, pathogenic	Splice donor variant
rs150171524	G>A,C	Conflicting-interpretations-of-pathogenicity, pathogenic	Missense variant, coding sequence variant
rs151163582	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs151268759	C>A,G,T	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs188269735	A>C	Pathogenic	Missense variant, coding sequence variant
rs191905539	C>A	Pathogenic	Coding sequence variant, stop gained
rs201135624	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs367781728	G>A,C	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs373618804	T>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833516	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833517	G>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant
rs386833518	T>-	Pathogenic-likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs386833519	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833520	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833521	G>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs386833522	->TTTG	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833523	A>G,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833524	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833525	C>G	Likely-pathogenic	Splice acceptor variant
rs386833526	->C	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833527	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833528	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833529	T>C	Pathogenic	Missense variant, coding sequence variant
rs386833530	C>G,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833531	G>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs386833532	GTCATAACCTG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833533	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833534	C>T	Likely-pathogenic	Splice donor variant
rs386833535	C>A,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833536	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833537	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833538	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833539	G>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833540	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833541	GAT>TAAACCAGGA	Likely-pathogenic	Stop gained, inframe indel, coding sequence variant
rs386833542	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833543	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs386833544	A>T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833545	T>C	Pathogenic	Splice acceptor variant
rs386833546	CA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833547	T>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833549	C>G,T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs386833550	C>T	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833551	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833552	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833553	C>T	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833554	C>T	Pathogenic	Splice acceptor variant
rs386833555	T>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833556	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs386833557	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs386833558	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833559	A>C,G	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833560	G>A	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833563	C>T	Likely-pathogenic	Splice donor variant
rs386833564	A>C,G	Likely-pathogenic	Stop gained, synonymous variant, coding sequence variant
rs386833565	G>T	Pathogenic	Synonymous variant, coding sequence variant
rs386833566	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833567	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833568	C>T	Likely-pathogenic	Intron variant
rs386833569	C>G	Likely-pathogenic	Splice acceptor variant
rs386833570	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833571	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833572	->T	Likely-pathogenic	Stop gained, coding sequence variant
rs386833573	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833574	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833575	C>G,T	Pathogenic	Splice donor variant
rs386833576	G>A,C,T	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs386833577	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833578	T>C,G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833579	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833580	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833581	C>G	Likely-pathogenic	Synonymous variant, coding sequence variant
rs386833582	G>A,C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833583	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833584	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833585	G>A,C	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs386833586	G>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant
rs386833587	G>A	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833588	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833589	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833590	C>A	Likely-pathogenic	Splice donor variant
rs386833591	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833592	C>A,G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833593	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs542056100	C>T	Pathogenic	Splice donor variant
rs570097430	G>A,T	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs751025203	G>A	Pathogenic	Coding sequence variant, stop gained
rs751822565	C>A	Pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs755313904	->GAAC	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant
rs759133707	C>T	Pathogenic	Coding sequence variant, missense variant
rs762989914	G>A	Pathogenic	Coding sequence variant, stop gained
rs763517274	C>G,T	Likely-pathogenic	Coding sequence variant, missense variant
rs765906340	C>G,T	Pathogenic	Splice donor variant
rs766762760	GTTT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs768091555	C>A	Likely-pathogenic	Intron variant
rs769625871	TGC>-	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe deletion
rs772068893	->AT	Pathogenic-likely-pathogenic	Coding sequence variant, frameshift variant
rs772574530	T>C	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs772871471	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs774099283	C>A,G	Likely-pathogenic	Splice donor variant
rs777365335	C>A,G	Likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs906049409	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs925908885	C>T	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs978795483	C>A,G	Likely-pathogenic, pathogenic	Splice donor variant
rs1114167353	A>T	Pathogenic	Coding sequence variant, missense variant
rs1163356968	C>G,T	Pathogenic	Coding sequence variant, missense variant, stop gained
rs1183976692	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1196401015	ATGATAGC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1207147043	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1211616091	C>T	Likely-pathogenic	Splice donor variant
rs1226098656	G>A,T	Likely-pathogenic	Synonymous variant, stop gained, coding sequence variant
rs1251443902	T>-	Pathogenic-likely-pathogenic	Coding sequence variant, frameshift variant
rs1259354298	T>C	Likely-pathogenic	Splice acceptor variant
rs1345599468	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1368757896	C>G,T	Likely-pathogenic	Splice donor variant
rs1399754800	C>-	Likely-pathogenic	Splice donor variant, coding sequence variant
rs1406713104	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1429861000	C>T	Likely-pathogenic	Splice acceptor variant
rs1430968530	T>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs1477860542	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs1554641737	->G	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554641887	A>G	Pathogenic-likely-pathogenic	Splice donor variant
rs1554642300	->G	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554643354	G>C	Pathogenic	Coding sequence variant, stop gained
rs1554643360	G>A	Pathogenic	Coding sequence variant, stop gained
rs1554643370	C>A	Likely-pathogenic	Splice acceptor variant
rs1554643619	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1554643738	A>T	Likely-pathogenic	Splice donor variant
rs1554644678	C>T	Likely-pathogenic	Intron variant
rs1554646529	C>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs1554646653	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1554646710	A>C	Pathogenic	Splice donor variant
rs1554648060	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1554649675	C>G	Likely-pathogenic	Splice acceptor variant
rs1554652870	G>A,T	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs1563834980	->G	Pathogenic	Coding sequence variant, frameshift variant
rs1563849699	CTG>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1563864784	->TATT	Pathogenic	Coding sequence variant, frameshift variant
rs1587922096	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1587950355	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1587951033	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1587958061	C>A	Pathogenic	Splice acceptor variant
rs1587959976	A>T	Pathogenic	Splice donor variant

Show/Hide all(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
MIRT2235287	hsa-miR-671-5p	CLIP-seq
MIRT2539021	hsa-miR-1304	CLIP-seq
MIRT2539022	hsa-miR-143	CLIP-seq
MIRT2539023	hsa-miR-2467-5p	CLIP-seq
MIRT2539024	hsa-miR-3188	CLIP-seq
MIRT2539025	hsa-miR-342-5p	CLIP-seq
MIRT2539026	hsa-miR-3975	CLIP-seq
MIRT2539027	hsa-miR-4505	CLIP-seq
MIRT2539028	hsa-miR-4651	CLIP-seq
MIRT2539029	hsa-miR-4664-5p	CLIP-seq
MIRT2539030	hsa-miR-4731-5p	CLIP-seq
MIRT2539031	hsa-miR-4770	CLIP-seq
MIRT2539032	hsa-miR-485-5p	CLIP-seq
MIRT2539033	hsa-miR-608	CLIP-seq
MIRT2539021	hsa-miR-1304	CLIP-seq
MIRT2539022	hsa-miR-143	CLIP-seq
MIRT2539023	hsa-miR-2467-5p	CLIP-seq
MIRT2539024	hsa-miR-3188	CLIP-seq
MIRT2539025	hsa-miR-342-5p	CLIP-seq
MIRT2539026	hsa-miR-3975	CLIP-seq
MIRT2539027	hsa-miR-4505	CLIP-seq
MIRT2539028	hsa-miR-4651	CLIP-seq
MIRT2539029	hsa-miR-4664-5p	CLIP-seq
MIRT2539030	hsa-miR-4731-5p	CLIP-seq
MIRT2539031	hsa-miR-4770	CLIP-seq
MIRT2539032	hsa-miR-485-5p	CLIP-seq
MIRT2539033	hsa-miR-608	CLIP-seq

Show/Hide all(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
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	28244183
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005886	Component	Plasma membrane	IDA
GO:0005960	Component	Glycine cleavage complex	IBA
GO:0006520	Process	Amino acid metabolic process	IEA
GO:0006544	Process	Glycine metabolic process	IEA
GO:0006546	Process	Glycine catabolic process	IDA	28244183
GO:0006546	Process	Glycine catabolic process	IEA
GO:0006546	Process	Glycine catabolic process	TAS	1996985
GO:0009055	Function	Electron transfer activity	TAS	2268343
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0016594	Function	Glycine binding	IBA
GO:0016829	Function	Lyase activity	IEA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0036255	Process	Response to methylamine	ISS
GO:0042803	Function	Protein homodimerization activity	ISS
GO:0070280	Function	Pyridoxal binding	ISS
GO:1903442	Process	Response to lipoic acid	ISS
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA

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
LDDLLWIFGCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKK
LENKDISLVHSMIPLGSCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEK
DLCELTGYDQVCFQPNSGAQGEYAGLATIRAYLNQKGEGHRTVCLIPKSAHGTNPASAHM
AGMKIQPVEVDKYGNIDAVHLKAMVDKHKENLAAIMITYPSTNGVFEENISDVCDLIHQH
GGQVYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHGGGGPGMGPIGVKKHLAPFL
PNHPVISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILNANYM
AKRLETHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVA
GTLMVEPTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCVTSSHW
DRPYSREVAAFPLPFVKPENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS

Sequence length

1020

Interactions

View interactions

	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

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Asthma	Asthma in any disease, Asthma, Asthma (childhood onset), Atopic asthma	N/A	N/A	GWAS
Glycine Encephalopathy	glycine encephalopathy, glycine encephalopathy 1, neonatal glycine encephalopathy, infantile glycine encephalopathy, atypical glycine encephalopathy	N/A	N/A	GenCC

Show/Hide Text Mining Associations (33)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
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
Corticobasal Degeneration	Associate	28271184
Endometrial Neoplasms	Associate	31692912
Heredodegenerative Disorders Nervous System	Associate	32421718
Hyperglycinemia Nonketotic	Associate	17361008, 24334290, 26947380, 27362913, 28416785, 28737873, 29232014, 29304759, 31349202, 32421718
Hypertension Pulmonary	Associate	26352407
Lung Neoplasms	Associate	22225612
Neoplasm Metastasis	Associate	30575323, 37781511
Neoplasm Metastasis	Inhibit	30804330
Neoplasms	Associate	22225612, 24979213, 32055850, 35508111, 36275705
Neural Tube Defects	Associate	29232014
Neuroblastoma	Associate	37545226
Neurodegenerative Diseases	Associate	22121227
Osteosarcoma	Associate	29210060
Periodontitis	Associate	27531006
Primary hyperoxaluria type 1	Inhibit	31279534
Prostatic Neoplasms	Associate	37781511
Psychotic Disorders	Associate	31279534
Renal Insufficiency Chronic	Associate	26352407
Schizophrenia	Associate	29232014
Squamous Cell Carcinoma of Head and Neck	Associate	37245006
Supranuclear Palsy Progressive	Associate	28271184
Thyroid Neoplasms	Associate	27277113
Triple Negative Breast Neoplasms	Associate	24390667, 40217479

GLDC (glycine decarboxylase)