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	275
Gene name	Aminomethyltransferase
Gene symbol	AMT
Synonyms (NCBI Gene)	GCEGCE2GCSTGCVTNKH
Chromosome	3
Chromosome location	3p21.31
Summary	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 (18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004047	Function	Aminomethyltransferase activity	IEA
GO:0004047	Function	Aminomethyltransferase activity	IMP	16051266
GO:0004047	Function	Aminomethyltransferase activity	TAS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IC	16051266
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	TAS	8188235
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005960	Component	Glycine cleavage complex	IEA
GO:0006546	Process	Glycine catabolic process	IEA
GO:0006546	Process	Glycine catabolic process	TAS	9600239
GO:0008483	Function	Transaminase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IMP	16051266

MIM	HGNC	e!Ensembl
238310	473	ENSG00000145020

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

840

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Glycine encephalopathy	Pathogenic; Likely pathogenic	rs1279743247, rs1352631535, rs562695274, rs1266259634, rs2107932226, rs2107933839, rs1249645541, rs748522054, rs2107937267, rs2107937536, rs2107937574, rs2049058298, rs2107933731, rs2107933735, rs386833680 View all (98 more)	RCV001312233 RCV001329302 RCV001329301 RCV001972587 RCV001384518 RCV001390880 RCV001383889 RCV001381284 RCV001388721 RCV001382319 RCV001385076 RCV001383790 RCV003470848 RCV001806813 RCV001825146 RCV001844504 RCV001870436 RCV001968995 RCV002037709 RCV002001336 RCV002002454 RCV001915076 RCV001961638 RCV001935293 RCV002011866 RCV002471300 RCV003087006 RCV002624512 RCV002664312 RCV002651706 RCV002750240 RCV002756630 RCV000190566 RCV002814674 RCV002829439 RCV002830118 RCV002913231 RCV002944167 RCV002972569 RCV003019611 RCV003023656 RCV003063840 RCV003036415 RCV003142289 RCV003147203 RCV000012756 RCV000012758 RCV000012759 RCV000012760 RCV000012761 RCV003331830 RCV003461882 RCV003461884 RCV003470219 RCV003461890 RCV003512917 RCV003513590 RCV003513592 RCV003511688 RCV003512653 RCV003512607 RCV003625227 RCV003625255 RCV003625368 RCV003625464 RCV003625426 RCV003625468 RCV003625915 RCV003625984 RCV003624969 RCV003830821 RCV003856526 RCV000495928 RCV002525127 RCV000533799 RCV000638279 RCV000670825 RCV000666301 RCV000673332 RCV000668200 RCV000673783 RCV000674000 RCV000667775 RCV000671316 RCV000669862 RCV000665764 RCV000672693 RCV000666875 RCV000672268 RCV000668737 RCV000666927 RCV000685122 RCV001868952 RCV000761472 RCV000813481 RCV000817660 RCV000806703 RCV000049638 RCV000049639 RCV000049641 RCV000049642 RCV000049643 RCV000049644 RCV000049645 RCV000049646 RCV000049647 RCV000049648 RCV000049649 RCV000049650 RCV000049651 RCV000049653 RCV000987270 RCV000987271 RCV002505520 RCV001056489 RCV001236819 RCV001226600 RCV001244920 RCV001239628 RCV001257431 RCV001305807
Glycine encephalopathy 1	Pathogenic; Likely pathogenic	rs2049124862, rs121964983, rs121964984, rs121964985, rs121964986, rs181134220, rs748522054, rs2471158260, rs2049119534, rs769468125, rs1553638405, rs1553638457, rs1553638460, rs1053797603, rs1238918084 View all (23 more)	RCV004571689 RCV004566726 RCV005430459 RCV004566727 RCV004566728 RCV004566729 RCV004574038 RCV004574273 RCV004576230 RCV005430541 RCV005430585 RCV005430683 RCV005430392 RCV004568499 RCV005430564 RCV005430764 RCV005430798 RCV004568513 RCV005430777 RCV004568563 RCV005430576 RCV005430699 RCV005430637 RCV005430421 RCV004568549 RCV005430446 RCV005430450 RCV005430726 RCV005430802 RCV004568518 RCV005430454 RCV004576965 RCV004569693 RCV004566904 RCV004566905 RCV004566906 RCV005430478 RCV005430479 RCV004570598
Glycine encephalopathy 2	Pathogenic; Likely pathogenic	rs1279743247, rs1352631535, rs2107937574, rs2107932966, rs2107938475, rs2107937352, rs2471150599, rs2471158020, rs121964983, rs121964984, rs121964985, rs121964986, rs181134220, rs2471160420, rs769468125 View all (13 more)	RCV003888014 RCV005911078 RCV005038192 RCV003492272 RCV003492273 RCV005023306 RCV005034800 RCV003492842 RCV003230355 RCV003230356 RCV003230357 RCV003230358 RCV003230359 RCV005230588 RCV003230522 RCV005027783 RCV005004333 RCV005860124 RCV003492125 RCV005027817 RCV003492126 RCV005231306 RCV005025098 RCV003492394 RCV005025099 RCV003230387 RCV005036515 RCV004570624
Neurodevelopmental delay	Likely pathogenic; Pathogenic	rs386833683	RCV002273950

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
AMT-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	rs772179698, rs368129012, rs745689345, rs375440699, rs781474146, rs141246107, rs2471158208, rs367726589, rs555045517, rs138259479, rs779002947, rs144790394, rs367604855, rs140380954	RCV003956119 RCV003898569 RCV004756436 RCV004731305 RCV003403973 RCV004755817 RCV003954282 RCV003910368 RCV003972464 RCV003937920 RCV003918108 RCV003892519 RCV003938323 RCV004756128
Malignant tumor of esophagus	Uncertain significance	rs201189946	RCV005913886
Malignant tumor of urinary bladder	Likely benign	rs143731179	RCV005897710
See cases	Conflicting classifications of pathogenicity	rs386833679	RCV002251953

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
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)