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    GATM glycine amidinotransferase [ Homo sapiens (human) ]

    Gene ID: 2628, updated on 28-Oct-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
    mouse all
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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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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