Human Gene AMT (ENST00000273588.9) from GENCODE V44
  Description: Homo sapiens aminomethyltransferase (AMT), transcript variant 5, non-coding RNA. (from RefSeq NR_028435)
RefSeq Summary (NM_000481): 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 RefSeq, Sep 2011].
Gencode Transcript: ENST00000273588.9
Gencode Gene: ENSG00000145020.16
Transcript (Including UTRs)
   Position: hg38 chr3:49,416,778-49,422,473 Size: 5,696 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr3:49,417,540-49,422,450 Size: 4,911 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:49,416,778-49,422,473)mRNA (may differ from genome)Protein (403 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GCST_HUMAN
DESCRIPTION: RecName: Full=Aminomethyltransferase, mitochondrial; EC=2.1.2.10; AltName: Full=Glycine cleavage system T protein; Short=GCVT; Flags: Precursor;
FUNCTION: The glycine cleavage system catalyzes the degradation of glycine.
CATALYTIC ACTIVITY: [Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10- methylenetetrahydrofolate + NH(3).
SUBUNIT: The glycine cleavage system is composed of four proteins: P, T, L and H.
SUBCELLULAR LOCATION: Mitochondrion.
DISEASE: Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:605899]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.
SIMILARITY: Belongs to the GcvT family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/AMT";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: AMT
Diseases sorted by gene-association score: glycine encephalopathy* (1247), d-glycericacidemia* (231), glycine encephalopathy with normal serum glycine* (202), neonatal glycine encephalopathy* (202), infantile glycine encephalopathy* (175), amt-related glycine encephalopathy* (100), early myoclonic encephalopathy (7), autosomal recessive disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.45 RPKM in Brain - Cerebellum
Total median expression: 703.71 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -9.9023-0.430 Picture PostScript Text
3' UTR -274.50762-0.360 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013977 - GCV_T_C
IPR006222 - GCV_T_N
IPR006223 - GcvT

Pfam Domains:
PF01571 - Aminomethyltransferase folate-binding domain
PF08669 - Glycine cleavage T-protein C-terminal barrel domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WSR - X-ray MuPIT 1WSV - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P48728
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsemblEnsembl SGD
Protein SequenceProtein SequenceProtein SequenceProtein Sequence Protein Sequence
AlignmentAlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004047 aminomethyltransferase activity
GO:0008483 transaminase activity
GO:0016740 transferase activity

Biological Process:
GO:0006546 glycine catabolic process
GO:0019464 glycine decarboxylation via glycine cleavage system
GO:0032259 methylation

Cellular Component:
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  BC044792 - Homo sapiens aminomethyltransferase, mRNA (cDNA clone MGC:42387 IMAGE:4821331), complete cds.
BC007546 - Homo sapiens aminomethyltransferase, mRNA (cDNA clone IMAGE:2959737), partial cds.
AK091738 - Homo sapiens cDNA FLJ34419 fis, clone HEART2008257, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AX747153 - Sequence 678 from Patent EP1308459.
AK296177 - Homo sapiens cDNA FLJ55081 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK096062 - Homo sapiens cDNA FLJ38743 fis, clone KIDNE2012025, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
D13811 - Homo sapiens mRNA for glycine cleavage system T-protein, complete cds.
BC094771 - Homo sapiens cDNA clone IMAGE:5310714, containing frame-shift errors.
JD239886 - Sequence 220910 from Patent EP1572962.
JD200933 - Sequence 181957 from Patent EP1572962.
JD232113 - Sequence 213137 from Patent EP1572962.
JD538786 - Sequence 519810 from Patent EP1572962.
JD537497 - Sequence 518521 from Patent EP1572962.
JD079187 - Sequence 60211 from Patent EP1572962.
JD240025 - Sequence 221049 from Patent EP1572962.
JD073268 - Sequence 54292 from Patent EP1572962.
JD238747 - Sequence 219771 from Patent EP1572962.
JD267453 - Sequence 248477 from Patent EP1572962.
JD470609 - Sequence 451633 from Patent EP1572962.
JD117878 - Sequence 98902 from Patent EP1572962.
KJ901282 - Synthetic construct Homo sapiens clone ccsbBroadEn_10676 AMT gene, encodes complete protein.
KR710103 - Synthetic construct Homo sapiens clone CCSBHm_00009645 AMT (AMT) mRNA, encodes complete protein.
KR710104 - Synthetic construct Homo sapiens clone CCSBHm_00009648 AMT (AMT) mRNA, encodes complete protein.
KR710105 - Synthetic construct Homo sapiens clone CCSBHm_00009650 AMT (AMT) mRNA, encodes complete protein.
KR710106 - Synthetic construct Homo sapiens clone CCSBHm_00009653 AMT (AMT) mRNA, encodes complete protein.
JD289522 - Sequence 270546 from Patent EP1572962.
JD199422 - Sequence 180446 from Patent EP1572962.
LF208627 - JP 2014500723-A/16130: Polycomb-Associated Non-Coding RNAs.
MA444204 - JP 2018138019-A/16130: Polycomb-Associated Non-Coding RNAs.
JD078079 - Sequence 59103 from Patent EP1572962.
JD131344 - Sequence 112368 from Patent EP1572962.
AK293481 - Homo sapiens cDNA FLJ59845 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK293594 - Homo sapiens cDNA FLJ59850 complete cds, moderately similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK294592 - Homo sapiens cDNA FLJ59878 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK290600 - Homo sapiens cDNA FLJ76259 complete cds, highly similar to Homo sapiens aminomethyltransferase (glycine cleavage system protein T) (AMT), mRNA.
CU675697 - Synthetic construct Homo sapiens gateway clone IMAGE:100023336 5' read AMT mRNA.
AK301072 - Homo sapiens cDNA FLJ60001 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK311636 - Homo sapiens cDNA, FLJ18678.
JD325503 - Sequence 306527 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00260 - Glycine, serine and threonine metabolism
hsa00670 - One carbon pool by folate
hsa00910 - Nitrogen metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
GLYCLEAV-PWY - glycine cleavage

Reactome (by CSHL, EBI, and GO)

Protein P48728 (Reactome details) participates in the following event(s):

R-HSA-5693977 AMT transfers NH2CH2 from GCSH:SAMDLL to THF
R-HSA-6783984 Glycine degradation
R-HSA-389661 Glyoxylate metabolism and glycine degradation
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8K3I5, B4DE61, B4DJQ0, ENST00000273588.1, ENST00000273588.2, ENST00000273588.3, ENST00000273588.4, ENST00000273588.5, ENST00000273588.6, ENST00000273588.7, ENST00000273588.8, GCST, GCST_HUMAN, NR_028435, P48728, uc003cww.1, uc003cww.2, uc003cww.3, uc003cww.4, uc003cww.5, uc003cww.6
UCSC ID: ENST00000273588.9
RefSeq Accession: NM_000481
Protein: P48728 (aka GCST_HUMAN)
CCDS: CCDS2797.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene AMT:
nkh (Nonketotic Hyperglycinemia)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.