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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	2653
Gene name	Glycine cleavage system protein H
Gene symbol	GCSH
Synonyms (NCBI Gene)	GCEMMDS7NKH
Chromosome	16
Chromosome location	16q23.2
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

Show/Hide all (4)

SNP ID	Visualize variation	Clinical significance	Consequence
rs386833859	C>A	Likely-pathogenic	Splice acceptor variant, coding sequence variant, missense variant
rs540997326	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant
rs769222264	G>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs886039730	T>C	Pathogenic	Missense variant, initiator codon variant, genic upstream transcript variant, non coding transcript variant

118

Show/Hide all (118)

miRTarBase ID	miRNA	Experiments	Reference
MIRT039361	hsa-miR-421	CLASH	23622248
MIRT1015152	hsa-miR-1244	CLIP-seq
MIRT1015153	hsa-miR-1264	CLIP-seq
MIRT1015154	hsa-miR-132	CLIP-seq
MIRT1015155	hsa-miR-145	CLIP-seq
MIRT1015156	hsa-miR-199a-3p	CLIP-seq
MIRT1015157	hsa-miR-199b-3p	CLIP-seq
MIRT1015158	hsa-miR-200b	CLIP-seq
MIRT1015159	hsa-miR-200c	CLIP-seq
MIRT1015160	hsa-miR-208a	CLIP-seq
MIRT1015161	hsa-miR-208b	CLIP-seq
MIRT1015162	hsa-miR-212	CLIP-seq
MIRT1015163	hsa-miR-2355-5p	CLIP-seq
MIRT1015164	hsa-miR-3117-5p	CLIP-seq
MIRT1015165	hsa-miR-3129-5p	CLIP-seq
MIRT1015166	hsa-miR-3617	CLIP-seq
MIRT1015167	hsa-miR-3658	CLIP-seq
MIRT1015168	hsa-miR-3660	CLIP-seq
MIRT1015169	hsa-miR-3688-3p	CLIP-seq
MIRT1015170	hsa-miR-380	CLIP-seq
MIRT1015171	hsa-miR-3924	CLIP-seq
MIRT1015172	hsa-miR-3978	CLIP-seq
MIRT1015173	hsa-miR-4263	CLIP-seq
MIRT1015174	hsa-miR-4274	CLIP-seq
MIRT1015175	hsa-miR-429	CLIP-seq
MIRT1015176	hsa-miR-4495	CLIP-seq
MIRT1015177	hsa-miR-4519	CLIP-seq
MIRT1015178	hsa-miR-4524	CLIP-seq
MIRT1015179	hsa-miR-4526	CLIP-seq
MIRT1015180	hsa-miR-4735-5p	CLIP-seq
MIRT1015181	hsa-miR-4761-3p	CLIP-seq
MIRT1015182	hsa-miR-4775	CLIP-seq
MIRT1015183	hsa-miR-499-5p	CLIP-seq
MIRT1015184	hsa-miR-548n	CLIP-seq
MIRT1015185	hsa-miR-548t	CLIP-seq
MIRT1015186	hsa-miR-549	CLIP-seq
MIRT1015187	hsa-miR-561	CLIP-seq
MIRT1015188	hsa-miR-590-3p	CLIP-seq
MIRT1015189	hsa-miR-641	CLIP-seq
MIRT2000559	hsa-miR-1208	CLIP-seq
MIRT1015152	hsa-miR-1244	CLIP-seq
MIRT2000560	hsa-miR-1246	CLIP-seq
MIRT1015153	hsa-miR-1264	CLIP-seq
MIRT1015154	hsa-miR-132	CLIP-seq
MIRT1015155	hsa-miR-145	CLIP-seq
MIRT1015156	hsa-miR-199a-3p	CLIP-seq
MIRT1015157	hsa-miR-199b-3p	CLIP-seq
MIRT1015162	hsa-miR-212	CLIP-seq
MIRT1015163	hsa-miR-2355-5p	CLIP-seq
MIRT2000561	hsa-miR-3065-5p	CLIP-seq
MIRT1015164	hsa-miR-3117-5p	CLIP-seq
MIRT1015165	hsa-miR-3129-5p	CLIP-seq
MIRT2000562	hsa-miR-3163	CLIP-seq
MIRT2000563	hsa-miR-338-5p	CLIP-seq
MIRT2000564	hsa-miR-33a	CLIP-seq
MIRT2000565	hsa-miR-33b	CLIP-seq
MIRT2000566	hsa-miR-3679-3p	CLIP-seq
MIRT1015169	hsa-miR-3688-3p	CLIP-seq
MIRT2000567	hsa-miR-3977	CLIP-seq
MIRT1015172	hsa-miR-3978	CLIP-seq
MIRT2000568	hsa-miR-410	CLIP-seq
MIRT2000569	hsa-miR-412	CLIP-seq
MIRT1015173	hsa-miR-4263	CLIP-seq
MIRT1015174	hsa-miR-4274	CLIP-seq
MIRT2000570	hsa-miR-4420	CLIP-seq
MIRT2000571	hsa-miR-4446-5p	CLIP-seq
MIRT2000572	hsa-miR-4452	CLIP-seq
MIRT1015177	hsa-miR-4519	CLIP-seq
MIRT1015178	hsa-miR-4524	CLIP-seq
MIRT2000573	hsa-miR-4733-5p	CLIP-seq
MIRT1015181	hsa-miR-4761-3p	CLIP-seq
MIRT2000574	hsa-miR-548c-3p	CLIP-seq
MIRT1015184	hsa-miR-548n	CLIP-seq
MIRT1015185	hsa-miR-548t	CLIP-seq
MIRT1015187	hsa-miR-561	CLIP-seq
MIRT2000575	hsa-miR-568	CLIP-seq
MIRT2000576	hsa-miR-656	CLIP-seq
MIRT2000559	hsa-miR-1208	CLIP-seq
MIRT2000560	hsa-miR-1246	CLIP-seq
MIRT1015155	hsa-miR-145	CLIP-seq
MIRT2000561	hsa-miR-3065-5p	CLIP-seq
MIRT1015164	hsa-miR-3117-5p	CLIP-seq
MIRT2234113	hsa-miR-320a	CLIP-seq
MIRT2234114	hsa-miR-320b	CLIP-seq
MIRT2234115	hsa-miR-320c	CLIP-seq
MIRT2234116	hsa-miR-320d	CLIP-seq
MIRT2234117	hsa-miR-3938	CLIP-seq
MIRT2000567	hsa-miR-3977	CLIP-seq
MIRT2000569	hsa-miR-412	CLIP-seq
MIRT2000570	hsa-miR-4420	CLIP-seq
MIRT2234118	hsa-miR-4429	CLIP-seq
MIRT2234119	hsa-miR-4436b-5p	CLIP-seq
MIRT2000573	hsa-miR-4733-5p	CLIP-seq
MIRT2234120	hsa-miR-518a-5p	CLIP-seq
MIRT2234121	hsa-miR-527	CLIP-seq
MIRT1015186	hsa-miR-549	CLIP-seq
MIRT2000575	hsa-miR-568	CLIP-seq
MIRT1015164	hsa-miR-3117-5p	CLIP-seq
MIRT2000560	hsa-miR-1246	CLIP-seq
MIRT1015155	hsa-miR-145	CLIP-seq
MIRT2000561	hsa-miR-3065-5p	CLIP-seq
MIRT1015164	hsa-miR-3117-5p	CLIP-seq
MIRT2000563	hsa-miR-338-5p	CLIP-seq
MIRT1015169	hsa-miR-3688-3p	CLIP-seq
MIRT1015172	hsa-miR-3978	CLIP-seq
MIRT2000568	hsa-miR-410	CLIP-seq
MIRT2000569	hsa-miR-412	CLIP-seq
MIRT2000573	hsa-miR-4733-5p	CLIP-seq
MIRT2000576	hsa-miR-656	CLIP-seq
MIRT2000560	hsa-miR-1246	CLIP-seq
MIRT1015155	hsa-miR-145	CLIP-seq
MIRT2000561	hsa-miR-3065-5p	CLIP-seq
MIRT1015164	hsa-miR-3117-5p	CLIP-seq
MIRT2000563	hsa-miR-338-5p	CLIP-seq
MIRT1015169	hsa-miR-3688-3p	CLIP-seq
MIRT1015172	hsa-miR-3978	CLIP-seq
MIRT2000569	hsa-miR-412	CLIP-seq
MIRT2000573	hsa-miR-4733-5p	CLIP-seq

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004047	Function	Aminomethyltransferase activity	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 32296183
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	TAS	3348809
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005960	Component	Glycine cleavage complex	IBA
GO:0005960	Component	Glycine cleavage complex	IEA
GO:0005960	Component	Glycine cleavage complex	TAS	3348809
GO:0006546	Process	Glycine catabolic process	IEA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IBA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IEA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	TAS	1671321

MIM	HGNC	e!Ensembl
238330	4208	ENSG00000140905

P23434

Protein name

Glycine cleavage system H protein, mitochondrial (Lipoic acid-containing protein)

Protein function

The glycine cleavage system catalyzes the degradation of glycine. The H protein (GCSH) shuttles the methylamine group of glycine from the P protein (GLDC) to the T protein (GCST). Has a pivotal role in the lipoylation of enzymes involved in cell

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01597	GCV_H	51 → 171	Glycine cleavage H-protein	Domain

Sequence

MALRVVRSVRALLCTLRAVPSPAAPCPPRPWQLGVGAVRTLRTGPALLSVRKFTEKHEWV
TTENGIGTVGISNFAQEALGDVVYCSLPEVGTKLNKQDEFGALESVKAASELYSPLSGEV
TEINEALAENPGLVNKSCYEDGWLIKMTLSNPSELDELMSEEAYEKYIKSIEE

Sequence length

173

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		Glyoxylate metabolism and glycine degradation Glycine degradation

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)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
GCSH-related disorder	Likely pathogenic; Pathogenic	rs769222264, rs886039730	RCV003417868 RCV003401220	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycine encephalopathy	Likely pathogenic; Pathogenic	rs769222264, rs886039730, rs386833859, rs1972233022	RCV001359426 RCV001804993 RCV000049828 RCV001296956	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Multiple mitochondrial dysfunctions syndrome 7	Likely pathogenic; Pathogenic	rs769222264, rs886039730, rs1165763082, rs2507679454, rs2507661713	RCV003236577 RCV003236578 RCV003236610 RCV003236611 RCV003236614	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
ATYPICAL GLYCINE ENCEPHALOPATHY	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCINE ENCEPHALOPATHY WITH NORMAL SERUM GLYCINE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (32)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Atypical glycine encephalopathy	Glycine Encephalopathy	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	30337557		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30337557	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36195876	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Ischemic stroke	Pubtator	34087973	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	36190515	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	37773841	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	36190515	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	40355831	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycinemia Nonketotic	Hyperglycemia	Pubtator	24334290, 33890291, 36190515	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycinemia, Nonketotic, Type I	Hyperglycinemia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycinemia, Nonketotic, Type II	Hyperglycinemia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycinemia, Nonketotic, Type III	Hyperglycinemia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycinemia, Transient Neonatal	Hyperglycinemia	BEFREE	12402263		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycinemia, Transient Neonatal	Hyperglycinemia	GENOMICS_ENGLAND_DG	16450403		★★★★★ ★☆☆☆☆ Found in Text Mining only
HYPERGLYCINURIA (disorder)	Hyperglycinuria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Infantile glycine encephalopathy	Glycine Encephalopathy	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	BEFREE	7532919		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	30337557		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30337557		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neonatal glycine encephalopathy	Glycine Encephalopathy	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nonketotic Hyperglycinemia	Nonketotic Hyperglycinemia	BEFREE	11450847, 16450403, 1695480, 17361008, 2013671, 21470805, 24334290, 25231368, 27481395		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nonketotic Hyperglycinemia	Nonketotic Hyperglycinemia	GENOMICS_ENGLAND_DG	16450403		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nonketotic Hyperglycinemia	Nonketotic Hyperglycinemia	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nonketotic Hyperglycinemia	Nonketotic Hyperglycinemia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Russell-Silver syndrome	Russell-Silver Syndrome	BEFREE	20082469		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	32084007	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	29232014		★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	33890291	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

GCSH (glycine cleavage system protein H)