Human Gene GATM (uc001zvc.3)
  Description: Homo sapiens glycine amidinotransferase (L-arginine:glycine amidinotransferase) (GATM), nuclear gene encoding mitochondrial protein, mRNA.
RefSeq Summary (NM_001482): This gene encodes a mitochondrial enzyme that belongs to the amidinotransferase family. This enzyme is involved in creatine biosynthesis, whereby it catalyzes the transfer of a guanido group from L-arginine to glycine, resulting in guanidinoacetic acid, the immediate precursor of creatine. Mutations in this gene cause arginine:glycine amidinotransferase deficiency, an inborn error of creatine synthesis characterized by cognitive disability, language impairment, and behavioral disorders. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr15:45,653,322-45,670,980 Size: 17,659 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr15:45,654,307-45,670,651 Size: 16,345 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr15:45,653,322-45,670,980)mRNA (may differ from genome)Protein (423 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Glycine amidinotransferase, mitochondrial; EC=; AltName: Full=L-arginine:glycine amidinotransferase; AltName: Full=Transamidinase; Flags: Precursor;
FUNCTION: Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.
CATALYTIC ACTIVITY: L-arginine + glycine = L-ornithine + guanidinoacetate.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=2.0 uM for arginine; KM=3.0 uM for glycine; Vmax=0.44 umol/min/mg enzyme;
PATHWAY: Amine and polyamine biosynthesis; creatine biosynthesis; creatine from L-arginine and glycine: step 1/2.
SUBUNIT: Homodimer. There is an equilibrium between the monomeric and dimeric forms, shifted towards the side of the monomer.
INTERACTION: Q9D964:Gatm (xeno); NbExp=1; IntAct=EBI-2552594, EBI-2552599;
SUBCELLULAR LOCATION: Isoform 1: Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side. Note=Probably attached to the outer side of the inner membrane.
SUBCELLULAR LOCATION: Isoform 2: Cytoplasm.
TISSUE SPECIFICITY: Expressed in brain, heart, kidney, liver, lung, salivary gland and skeletal muscle tissue, with the highest expression in kidney. Biallelically expressed in placenta and fetal tissues.
INDUCTION: Expression is elevated in the myocardium during heart failure, and decreased in inter-uterine growth restriction (IUGR)- associated placenta.
DOMAIN: One chain folds into a compact single domain composed of repeating units, five beta-beta-alpha-beta modules, which surround the central active site.
DISEASE: Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:612718]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.
SIMILARITY: Belongs to the amidinotransferase family.
SEQUENCE CAUTION: Sequence=BAG60595.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=GeneReviews; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GATM
CDC HuGE Published Literature: GATM
Positive Disease Associations: renal function and chronic kidney disease
Related Studies:
  1. renal function and chronic kidney disease
    Kottgen ,et al. 2009, Multiple loci associated with indices of renal function and chronic kidney disease, Nature genetics 2009 . [PubMed 19430482]

-  MalaCards Disease Associations
  MalaCards Gene Search: GATM
Diseases sorted by gene-association score: cerebral creatine deficiency syndrome 3* (1590), l-arginine:glycine amidinotransferase deficiency* (519), cerebral creatine deficiency syndrome (23), cerebral creatine deficiency syndrome 2 (13), creatine deficiency syndromes (12), radiation cystitis (11), cerebral creatine deficiency syndrome 1 (10), uterine corpus cancer (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D003401 Creatine
  • C523799 MRK 003
  • D014635 Valproic Acid
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C023514 2,6-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C472791 3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid
  • C009505 4,4'-diaminodiphenylmethane
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 355.35 RPKM in Pancreas
Total median expression: 1458.72 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -179.60329-0.546 Picture PostScript Text
3' UTR -197.73985-0.201 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
IPR003198 - Amidino_trans

SCOP Domains:
55909 - Pentein

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1JDW - X-ray MuPIT 1JDX - X-ray MuPIT 2JDW - X-ray MuPIT 2JDX - X-ray MuPIT 3JDW - X-ray MuPIT 4JDW - X-ray MuPIT 5JDW - X-ray MuPIT 6JDW - X-ray MuPIT 7JDW - X-ray MuPIT 8JDW - X-ray MuPIT 9JDW - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P50440
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
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0015067 amidinotransferase activity
GO:0015068 glycine amidinotransferase activity
GO:0016740 transferase activity

Biological Process:
GO:0006600 creatine metabolic process
GO:0006601 creatine biosynthetic process
GO:0007275 multicellular organism development
GO:0007611 learning or memory
GO:0014889 muscle atrophy

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005758 mitochondrial intermembrane space
GO:0016020 membrane
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  S68805 - L-arginine:glycine amidinotransferase [human, kidney carcinoma cells, mRNA, 2330 nt].
HM005559 - Homo sapiens clone HTL-S-19 testicular secretory protein Li 19 mRNA, complete cds.
AK098055 - Homo sapiens cDNA FLJ40736 fis, clone TKIDN2003597, highly similar to GLYCINE AMIDINOTRANSFERASE PRECURSOR (EC
AK098393 - Homo sapiens cDNA FLJ25527 fis, clone CBR07379, highly similar to GLYCINE AMIDINOTRANSFERASE PRECURSOR (EC
FW340076 - Screening.
BC004141 - Homo sapiens glycine amidinotransferase (L-arginine:glycine amidinotransferase), mRNA (cDNA clone MGC:1744 IMAGE:3010128), complete cds.
JD083471 - Sequence 64495 from Patent EP1572962.
JD037142 - Sequence 18166 from Patent EP1572962.
JD246177 - Sequence 227201 from Patent EP1572962.
X86401 - H.sapiens mRNA for L-arginine:glycine amidinotransferase.
JD410803 - Sequence 391827 from Patent EP1572962.
JD044364 - Sequence 25388 from Patent EP1572962.
JD061532 - Sequence 42556 from Patent EP1572962.
AK298350 - Homo sapiens cDNA FLJ56372 complete cds, highly similar to Glycine amidinotransferase, mitochondrial precursor (EC
AK223585 - Homo sapiens mRNA for glycine amidinotransferase (L-arginine:glycine amidinotransferase) variant, clone: FCC130D06.
JD262704 - Sequence 243728 from Patent EP1572962.
JD305792 - Sequence 286816 from Patent EP1572962.
JD325633 - Sequence 306657 from Patent EP1572962.
JD486115 - Sequence 467139 from Patent EP1572962.
JD076063 - Sequence 57087 from Patent EP1572962.
JD059200 - Sequence 40224 from Patent EP1572962.
KJ891222 - Synthetic construct Homo sapiens clone ccsbBroadEn_00616 GATM gene, encodes complete protein.
AK294995 - Homo sapiens cDNA FLJ58313 complete cds, highly similar to Glycine amidinotransferase, mitochondrial precursor (EC
CU678590 - Synthetic construct Homo sapiens gateway clone IMAGE:100018254 5' read GATM mRNA.
KM576744 - Homo sapiens clone BC039389-GATM_B3-G3 mRNA sequence.
KM576745 - Homo sapiens clone BC039389-GATM_B3-G2 mRNA sequence.
JD196509 - Sequence 177533 from Patent EP1572962.
JD460635 - Sequence 441659 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00260 - Glycine, serine and threonine metabolism
hsa00330 - Arginine and proline metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
GLYCGREAT-PWY - glycine degradation (creatine biosynthesis)
PWY3DJ-35588 - creatine biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein P50440 (Reactome details) participates in the following event(s):

R-HSA-71275 arginine + glycine => ornithine + guanidoacetate
R-HSA-71288 Creatine metabolism
R-HSA-351202 Metabolism of polyamines
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: AGAT, B4DH99, B4DPI3, GATM_HUMAN, NM_001482, NP_001473, P50440, Q53EQ4
UCSC ID: uc001zvc.3
RefSeq Accession: NM_001482
Protein: P50440 (aka GATM_HUMAN)
CCDS: CCDS10122.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GATM:
creatine (Creatine Deficiency Disorders)
dystonia-ov (Hereditary Dystonia Overview)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001482.2
exon count: 9CDS single in 3' UTR: no RNA size: 2602
ORF size: 1272CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3060.00frame shift in genome: no % Coverage: 99.39
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.