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.	275
Gene name Gene Name - the full gene name approved by the HGNC.	Aminomethyltransferase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	AMT
Synonyms (NCBI Gene) Gene synonyms aliases	GCE, GCE2, GCST, GCVT, NKH
Disease Acronyms (UniProt) Disease acronyms from UniProt database	GCE2, NKH
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p21.31
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by

Show/Hide all(36)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1126422	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs116192290	C>G,T	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Non coding transcript variant, missense variant, coding sequence variant
rs121964981	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs121964984	C>G	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs121964985	C>A,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs121964986	G>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs181134220	C>G,T	Pathogenic	Splice acceptor variant
rs386833681	C>G	Likely-pathogenic	Splice acceptor variant
rs386833682	T>A,C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs386833683	GAGGGCCAAATCTTT>-	Pathogenic	Non coding transcript variant, coding sequence variant, inframe deletion, intron variant
rs386833684	A>G	Pathogenic	Splice donor variant, intron variant
rs386833685	G>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs386833689	T>C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs386833690	C>T	Uncertain-significance, pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs386833691	TCA>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, inframe deletion
rs386833692	GC>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs541594122	A>C,T	Likely-pathogenic	Splice donor variant
rs558998633	G>A	Likely-pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs753221440	C>A,T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs757918826	C>T	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs781466698	G>A	Pathogenic-likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs797045082	C>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs866625610	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs1056820947	G>A	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1238918084	->C	Likely-pathogenic	Splice acceptor variant, non coding transcript variant, coding sequence variant
rs1278265933	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1553638247	A>G	Pathogenic	Splice donor variant
rs1553638266	C>-,CC	Pathogenic-likely-pathogenic, likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553638405	A>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553638408	->A	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553638457	CTTCTTGACACACCTCCACACCA>-	Likely-pathogenic	Splice donor variant, non coding transcript variant, intron variant, coding sequence variant
rs1553638460	C>T	Likely-pathogenic	Splice donor variant
rs1553638649	CA>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, intron variant, coding sequence variant
rs1575303218	G>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1575305901	C>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1575308129	C>T	Likely-pathogenic	Splice donor variant

Show/Hide all(19)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018253	hsa-miR-335-5p	Microarray	18185580
MIRT780659	hsa-miR-1	CLIP-seq
MIRT780660	hsa-miR-185	CLIP-seq
MIRT780661	hsa-miR-206	CLIP-seq
MIRT780662	hsa-miR-3065-3p	CLIP-seq
MIRT780663	hsa-miR-3190	CLIP-seq
MIRT780664	hsa-miR-4306	CLIP-seq
MIRT780665	hsa-miR-4481	CLIP-seq
MIRT780666	hsa-miR-4491	CLIP-seq
MIRT780667	hsa-miR-4644	CLIP-seq
MIRT780668	hsa-miR-4657	CLIP-seq
MIRT780669	hsa-miR-4745-5p	CLIP-seq
MIRT780670	hsa-miR-613	CLIP-seq
MIRT780671	hsa-miR-7	CLIP-seq
MIRT780672	hsa-miR-759	CLIP-seq
MIRT780662	hsa-miR-3065-3p	CLIP-seq
MIRT1930447	hsa-miR-3121-5p	CLIP-seq
MIRT2384146	hsa-miR-4710	CLIP-seq
MIRT2384147	hsa-miR-4792	CLIP-seq

Show/Hide all(12)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004047	Function	Aminomethyltransferase activity	IBA	21873635
GO:0004047	Function	Aminomethyltransferase activity	IMP	16051266
GO:0004047	Function	Aminomethyltransferase activity	TAS
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	IBA	21873635
GO:0005739	Component	Mitochondrion	IC	16051266
GO:0005739	Component	Mitochondrion	IDA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006546	Process	Glycine catabolic process	TAS	9600239
GO:0008483	Function	Transaminase activity	IEA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IBA	21873635
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IMP	16051266

MIM	HGNC	e!Ensembl
238310	473	ENSG00000145020

Protein

UniProt ID

P48728

Protein name

Aminomethyltransferase, mitochondrial (EC 2.1.2.10) (Glycine cleavage system T protein) (GCVT)

Protein function

The glycine cleavage system catalyzes the degradation of glycine.

PDB

1WSR , 1WSV

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01571	GCV_T	38 → 291	Aminomethyltransferase folate-binding domain	Domain
PF08669	GCV_T_C	318 → 396	Glycine cleavage T-protein C-terminal barrel domain	Domain

Sequence

MQRAVSVVARLGFRLQAFPPALCRPLSCAQEVLRRTPLYDFHLAHGGKMVAFAGWSLPVQ
YRDSHTDSHLHTRQHCSLFDVSHMLQTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFT
NEAGGILDDLIVTNTSEGHLYVVSNAGCWEKDLALMQDKVRELQNQGRDVGLEVLDNALL
ALQGPTAAQVLQAGVADDLRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGA
VHLATAILKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRAAM
DFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCPSPSLKKNV
AMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYTLK

Sequence length

403

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 Causal Diseases (4)

Disease term	Disease name	dbSNP ID
Causal
Agenesis of corpus callosum	Agenesis of corpus callosum	rs754914260, rs1057519053, rs1057519056, rs1057519054, rs1057519055, rs1057519057, rs1384496494, rs1599017933
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, rs866625610, rs201437896, rs773988915 View all (3 more)
Mental retardation	Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)

Show/Hide Unknown Diseases (3)

Disease term	Disease name	References	Source
Unknown
Crohn disease	Crohn Disease	17804789	ClinVar
Hyperglycinuria	HYPERGLYCINURIA (disorder)		ClinVar
Glycine Encephalopathy	glycine encephalopathy, glycine encephalopathy 2		GenCC

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text Mining
Adenomyosis	Associate	40527793
Hyperglycinemia Nonketotic	Associate	19299230, 27164344, 27362913
Lymphatic Metastasis	Associate	33819484
Meningomyelocele	Associate	27620832
Neural Tube Defects	Associate	27620832
Schizophrenia	Associate	29232014
Smooth Muscle Tumor	Associate	37387208
Spasms Infantile	Associate	19299230

AMT (aminomethyltransferase)