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GATM glycine amidinotransferase [ Homo sapiens (human) ]

Gene ID: 2628, updated on 2-Nov-2024

Summary

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Official Symbol
GATMprovided by HGNC
Official Full Name
glycine amidinotransferaseprovided by HGNC
Primary source
HGNC:HGNC:4175
See related
Ensembl:ENSG00000171766 MIM:602360; AllianceGenome:HGNC:4175
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AT; RFS; AGAT; FRTS; CCDS3; FRTS1
Summary
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]
Expression
Biased expression in kidney (RPKM 706.9), liver (RPKM 467.2) and 8 other tissues See more
Orthologs
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Genomic context

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See GATM in Genome Data Viewer
Location:
15q21.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (45361124..45402227, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (43169297..43210402, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (45653322..45694425, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene THAP domain containing 12 pseudogene Neighboring gene uncharacterized LOC124903482 Neighboring gene RNA, U6 small nuclear 953, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6408 Neighboring gene AFG2 AAA ATPase homolog B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:45716799-45717298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6409 Neighboring gene chromosome 15 open reading frame 48 Neighboring gene microRNA 147b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Creatine depletion in a new case with AGAT deficiency: clinical and genetic study in a large pedigree. Battini R, et al. Mol Genet Metab, 2002 Dec. PMID 12468279
  2. GATM polymorphism associated with the risk for statin-induced myopathy does not replicate in case-control analysis of 715 dyslipidemic individuals. Luzum JA, et al. Cell Metab, 2015 Apr 7. PMID 25863251, Free PMC Article
  3. Genome-wide association study identifies 3 genomic loci significantly associated with serum levels of homoarginine: the AtheroRemo Consortium. Kleber ME, et al. Circ Cardiovasc Genet, 2013 Oct. PMID 24047826
  4. Promiscuous activity of arginine:glycine amidinotransferase is responsible for the synthesis of the novel cardiovascular risk factor homoarginine. Davids M, et al. FEBS Lett, 2012 Oct 19. PMID 23010440
  5. l-arginine:glycine amidinotransferase (AGAT) deficiency: clinical presentation and response to treatment in two patients with a novel mutation. Edvardson S, et al. Mol Genet Metab, 2010 Oct-Nov. PMID 20682460

See all (63) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ClinGen variant curation expert panel recommendations for classification of variants in GAMT, GATM and SLC6A8 for cerebral creatine deficiency syndromes.
    Title: ClinGen variant curation expert panel recommendations for classification of variants in GAMT, GATM and SLC6A8 for cerebral creatine deficiency syndromes.
  2. Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells.
    Title: Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells.
  3. Association of Familial Fanconi Syndrome with a Novel GATM Variant.
    Title: Association of Familial Fanconi Syndrome with a Novel GATM Variant.
  4. A novel variant in GATM causes idiopathic renal Fanconi syndrome and predicts progression to end-stage kidney disease.
    Title: A novel variant in GATM causes idiopathic renal Fanconi syndrome and predicts progression to end-stage kidney disease.
  5. Polymorphism in the GATM Locus Associated with Dialysis-Independent Chronic Kidney Disease but Not Dialysis-Dependent Kidney Failure.
    Title: Polymorphism in the GATM Locus Associated with Dialysis-Independent Chronic Kidney Disease but Not Dialysis-Dependent Kidney Failure.
  6. Correlation between single-nucleotide polymorphisms and statin-induced myopathy: a mixed-effects model meta-analysis.
    Title: Correlation between single-nucleotide polymorphisms and statin-induced myopathy: a mixed-effects model meta-analysis.
  7. The association of GATM polymorphism with statin-induced myopathy: a systematic review and meta-analysis.
    Title: The association of GATM polymorphism with statin-induced myopathy: a systematic review and meta-analysis.
  8. Here, we provide genetic, histologic, cell biologic, and structural evidence for the association between monoallelic GATM mutations and a genetic disorder characterized by renal Fanconi syndrome and progressive kidney failure.
    Title: Glycine Amidinotransferase (GATM), Renal Fanconi Syndrome, and Kidney Failure.
  9. Measurements of creatine and guanidinoacetate in plasma are recommended for the diagnosis of AGAT and GAMT deficiency.Definitive confirmation of the diagnosis requires DNA sequencing of the appropriate gene and (if molecular analysis is ambiguous) measurement of AGAT or GAMT enzyme activity or of CRTR-mediated transport .
    Title: Laboratory diagnosis of creatine deficiency syndromes: a technical standard and guideline of the American College of Medical Genetics and Genomics.
  10. Results show the functional characterization of rare missense variants in GATM which cause GATM deficiency. Seven of them report 0% of wild-type GATM activity indicating a putative pathogenicity.
    Title: Arginine-Glycine Amidinotransferase Deficiency and Functional Characterization of Missense Variants in GATM.
Submit: New GeneRIF Correction See all GeneRIFs (19)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Arginine:glycine amidinotransferase deficiency
MedGen: C2675179 OMIM: 612718 GeneReviews: Creatine Deficiency Disorders
Compare labs
Fanconi renotubular syndrome 1
MedGen: C4551503 OMIM: 134600 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genetic determinants influencing human serum metabolome among African Americans.
EBI GWAS Catalog
Genome-wide association study identifies 3 genomic loci significantly associated with serum levels of homoarginine: the AtheroRemo Consortium.
EBI GWAS Catalog
Multiple loci associated with indices of renal function and chronic kidney disease.
EBI GWAS Catalog
New loci associated with kidney function and chronic kidney disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables amidinotransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycine amidinotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine amidinotransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in creatine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within creatine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in creatine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in creatine metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in learning or memory IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in muscle atrophy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in mitochondrial intermembrane space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrial intermembrane space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial intermembrane space TAS
Traceable Author Statement
more info
  
located_in mitochondrion HTP PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
glycine amidinotransferase, mitochondrial
Names
glycine amidinotransferase (L-arginine:glycine amidinotransferase)
testicular secretory protein Li 19
transamidinase
NP_001307944.1
NP_001473.1
XP_047288341.1
XP_047288342.1
XP_047288343.1
XP_047288344.1
XP_054233700.1
XP_054233701.1
XP_054233702.1
XP_054233703.1
XP_054233704.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011674.2 RefSeqGene

    Range
    28774..46194
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001321015.2 → NP_001307944.1  glycine amidinotransferase, mitochondrial isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC025580, AI253042, BC039389
    Conserved Domains (1) summary
    cl19186
    Location:4 → 280
    Amidinotransf; Amidinotransferase

  2. NM_001482.3 → NP_001473.1  glycine amidinotransferase, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_001473.1

    Status: REVIEWED

    Source sequence(s)
    BC004141, CD365153, DB457418
    Consensus CDS
    CCDS10122.1
    UniProtKB/Swiss-Prot
    B4DH99, B4DPI3, P50440, Q53EQ4
    UniProtKB/TrEMBL
    A0A140VK19, A0A6Q8PHC6
    Related
    ENSP00000379895.3, ENST00000396659.8
    Conserved Domains (1) summary
    cl19186
    Location:86 → 409
    Amidinotransf; Amidinotransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    45361124..45402227 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432387.1 → XP_047288343.1  glycine amidinotransferase, mitochondrial isoform X2

  2. XM_047432385.1 → XP_047288341.1  glycine amidinotransferase, mitochondrial isoform X1

  3. XM_047432386.1 → XP_047288342.1  glycine amidinotransferase, mitochondrial isoform X2

  4. XM_047432388.1 → XP_047288344.1  glycine amidinotransferase, mitochondrial isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    43169297..43210402 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377725.1 → XP_054233700.1  glycine amidinotransferase, mitochondrial isoform X1

  2. XM_054377727.1 → XP_054233702.1  glycine amidinotransferase, mitochondrial isoform X2

  3. XM_054377728.1 → XP_054233703.1  glycine amidinotransferase, mitochondrial isoform X2

  4. XM_054377726.1 → XP_054233701.1  glycine amidinotransferase, mitochondrial isoform X2

  5. XM_054377729.1 → XP_054233704.1  glycine amidinotransferase, mitochondrial isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P50440.1 GenPept UniProtKB/Swiss-Prot:P50440

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