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    GATM glycine amidinotransferase [ Homo sapiens (human) ]

    Gene ID: 2628, updated on 28-Oct-2024

    Summary

    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

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 

    General protein information

    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_001321015.2NP_001307944.1  glycine amidinotransferase, mitochondrial isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC025580, AI253042, BC039389
      Conserved Domains (1) summary
      cl19186
      Location:4280
      Amidinotransf; Amidinotransferase
    2. NM_001482.3NP_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:86409
      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_047432387.1XP_047288343.1  glycine amidinotransferase, mitochondrial isoform X2

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

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

    4. XM_047432388.1XP_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_054377725.1XP_054233700.1  glycine amidinotransferase, mitochondrial isoform X1

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

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

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

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