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    GTPBP3 GTP binding protein 3, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 84705, updated on 3-Nov-2024

    Summary

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    Official Symbol
    GTPBP3provided by HGNC
    Official Full Name
    GTP binding protein 3, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:14880
    See related
    Ensembl:ENSG00000130299 MIM:608536; AllianceGenome:HGNC:14880
    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
    MSS1; MTGP1; THDF1; GTPBG3; COXPD23
    Summary
    This locus encodes a GTP-binding protein. The encoded protein is localized to the mitochondria and may play a role in mitochondrial tRNA modification. Polymorphisms at this locus may be associated with severity of aminoglycoside-induced deafness, a disease associated with a mutation in the 12S rRNA. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Sep 2010]
    Expression
    Ubiquitous expression in spleen (RPKM 3.4), skin (RPKM 3.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GTPBP3 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (17334982..17342731)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (17469817..17477573)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (17445791..17453540)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17404714-17405262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17405263-17405811 Neighboring gene mitochondrial ribosomal protein L34 Neighboring gene abhydrolase domain containing 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17411770-17412270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17412271-17412771 Neighboring gene Sharpr-MPRA regulatory region 8409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17419675-17420236 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17420237-17420800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17423026-17423526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17423527-17424027 Neighboring gene DET1 and DDB1 associated 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17432165-17432781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17435160-17435660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17437105-17437632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17438162-17438689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17438690-17439218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17439219-17439746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17439747-17440274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17440275-17440802 Neighboring gene anoctamin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:17447331-17448002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17448003-17448674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17448675-17449346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17456900-17457861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17459643-17460147 Neighboring gene plasmalemma vesicle associated protein Neighboring gene uncharacterized LOC105372298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17489969-17490857

    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. Pathogenicity Analysis of a Novel Variant in GTPBP3 Causing Mitochondrial Disease and Systematic Literature Review. Zhang Q, et al. Genes (Basel), 2023 Feb 22. PMID 36980825, Free PMC Article
    2. Chordoma-natural history, treatment and prognosis. The Florence Radiotherapy Department experience (1956-1990) and a critical review of the literature. Magrini SM, et al. Acta Oncol, 1992. PMID 1290633
    3. Characterization of human GTPBP3, a GTP-binding protein involved in mitochondrial tRNA modification. Villarroya M, et al. Mol Cell Biol, 2008 Dec. PMID 18852288, Free PMC Article
    4. Mutations in GTPBP3 cause a mitochondrial translation defect associated with hypertrophic cardiomyopathy, lactic acidosis, and encephalopathy. Kopajtich R, et al. Am J Hum Genet, 2014 Dec 4. PMID 25434004, Free PMC Article
    5. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. Asano K, et al. Nucleic Acids Res, 2018 Feb 28. PMID 29390138, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pathogenicity Analysis of a Novel Variant in GTPBP3 Causing Mitochondrial Disease and Systematic Literature Review.
      Title: Pathogenicity Analysis of a Novel Variant in GTPBP3 Causing Mitochondrial Disease and Systematic Literature Review.
    2. The human tRNA taurine modification enzyme GTPBP3 is an active GTPase linked to mitochondrial diseases.
      Title: The human tRNA taurine modification enzyme GTPBP3 is an active GTPase linked to mitochondrial diseases.
    3. Coding Variants in HOOK2 and GTPBP3 May Contribute to Risk of Primary Angle Closure Glaucoma
      Title: Coding Variants in HOOK2 and GTPBP3 May Contribute to Risk of Primary Angle Closure Glaucoma.
    4. Low GTPBP3 expression is associated with Mitochondrial diseases in neoplasms.
      Title: microRNA-mediated differential expression of TRMU, GTPBP3 and MTO1 in cell models of mitochondrial-DNA diseases.
    5. Defects in the mitochondrial tRNA modification enzymes MTO1 and GTPBP3 promote different metabolic reprogramming through a HIF-PPARgamma-UCP2-AMPK axis.
      Title: Defects in the mitochondrial-tRNA modification enzymes MTO1 and GTPBP3 promote different metabolic reprogramming through a HIF-PPARγ-UCP2-AMPK axis.
    6. GTPBP3 defective expression is associated with an mitochondrial-tRNA hypomodification status.GTPBP3 plays a role in the regulation of UCP2 and MCP1 proteins through AMPK signaling.
      Title: Defective Expression of the Mitochondrial-tRNA Modifying Enzyme GTPBP3 Triggers AMPK-Mediated Adaptive Responses Involving Complex I Assembly Factors, Uncoupling Protein 2, and the Mitochondrial Pyruvate Carrier.
    7. Results show that post-transcriptional expression of GTPBP3, MTO1 and TRMU genes is down-regulated, leading to mt-tRNA hypomodification and contributing to mitochondrial dysfunction in MELAS cybrids.
      Title: The ROS-sensitive microRNA-9/9* controls the expression of mitochondrial tRNA-modifying enzymes and is involved in the molecular mechanism of MELAS syndrome.
    8. Most individuals with GTPBP3 mutations developed neurological symptoms and MRI involvement of thalamus, putamen, and brainstem resembling Leigh syndrome.
      Title: Mutations in GTPBP3 cause a mitochondrial translation defect associated with hypertrophic cardiomyopathy, lactic acidosis, and encephalopathy.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    10. Meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Genetic association analysis of 13 nuclear-encoded mitochondrial candidate genes with type II diabetes mellitus: the DAMAGE study.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    Combined oxidative phosphorylation defect type 23
    MedGen: C5567743 OMIM: 616198 GeneReviews: Not available
    		Compare labs

    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

    Clone Names

    • FLJ14700, FLJ17836

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA wobble uridine modification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    tRNA modification GTPase GTPBP3, mitochondrial
    Names
    mitochondrial GTP-binding protein 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_027824.1 RefSeqGene

      Range
      7572..12750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001128855.3 → NP_001122327.1  tRNA modification GTPase GTPBP3, mitochondrial isoform III

      Status: REVIEWED

      Description
      Transcript Variant: This variant (III) lacks an in-frame segment and uses an alternate, in-frame splice site in the CDS, compared to variant IV. The resulting protein (isoform III) is shorter than isoform IV.
      Source sequence(s)
      AF360743, AK298485, BC019261, DA044241
      Consensus CDS
      CCDS59364.1
      UniProtKB/Swiss-Prot
      Q969Y2
      UniProtKB/TrEMBL
      B7Z563
      Related
      ENSP00000473150.1, ENST00000600625.5
      Conserved Domains (3) summary
      cd04164
      Location:247 → 395
      trmE; trmE is a tRNA modification GTPase
      PRK05291
      Location:35 → 471
      trmE; tRNA modification GTPase TrmE; Reviewed
      pfam10396
      Location:35 → 152
      TrmE_N; GTP-binding protein TrmE N-terminus

    2. NM_001195422.1 → NP_001182351.1  tRNA modification GTPase GTPBP3, mitochondrial isoform VII

      Status: REVIEWED

      Description
      Transcript Variant: This variant (VII) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant IV. The encoded isoform (VII) has a distinct N-terminus and is shorter than isoform IV.
      Source sequence(s)
      AK297953, AK298485, BC019261, DC339966
      Consensus CDS
      CCDS56088.1
      UniProtKB/Swiss-Prot
      Q969Y2
      UniProtKB/TrEMBL
      B7Z563
      Related
      ENSP00000354598.4, ENST00000361619.9
      Conserved Domains (3) summary
      cd04164
      Location:269 → 438
      trmE; trmE is a tRNA modification GTPase
      PRK05291
      Location:57 → 514
      trmE; tRNA modification GTPase TrmE; Reviewed
      pfam10396
      Location:57 → 174
      TrmE_N; GTP-binding protein TrmE N-terminus

    3. NM_032620.4 → NP_116009.2  tRNA modification GTPase GTPBP3, mitochondrial isoform V

      See identical proteins and their annotated locations for NP_116009.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (V) lacks an in-frame segment in the CDS, compared to variant IV. The resulting protein (isoform V) is shorter than isoform IV. This variant is also referred to as isoform I in PubMed IDs 12370316 and 18852288.
      Source sequence(s)
      AY078988, BC019261, DA044241
      Consensus CDS
      CCDS32951.1
      UniProtKB/Swiss-Prot
      A6NFH1, A6NIG5, A6NKR4, A8K7B4, B7Z4V8, Q8TCY6, Q8WUW9, Q969G4, Q969Y2, Q9BX61
      Related
      ENSP00000313818.7, ENST00000324894.13
      Conserved Domains (3) summary
      cd04164
      Location:247 → 416
      trmE; trmE is a tRNA modification GTPase
      PRK05291
      Location:35 → 492
      trmE; tRNA modification GTPase TrmE; Reviewed
      pfam10396
      Location:35 → 152
      TrmE_N; GTP-binding protein TrmE N-terminus

    4. NM_133644.4 → NP_598399.2  tRNA modification GTPase GTPBP3, mitochondrial isoform IV

      Status: REVIEWED

      Description
      Transcript Variant: This variant (IV) represents the longest transcript and it encodes the longest protein (isoform IV). This variant is also referred to as isoform V in PubMed IDs 12370316 and 18852288.
      Source sequence(s)
      AK298485, AY078987, BC019261, DA044241
      Consensus CDS
      CCDS32950.1
      UniProtKB/Swiss-Prot
      Q969Y2
      UniProtKB/TrEMBL
      B7Z563
      Related
      ENSP00000351644.6, ENST00000358792.11
      Conserved Domains (3) summary
      cd04164
      Location:279 → 448
      trmE; trmE is a tRNA modification GTPase
      PRK05291
      Location:35 → 524
      trmE; tRNA modification GTPase TrmE; Reviewed
      pfam10396
      Location:35 → 152
      TrmE_N; GTP-binding protein TrmE N-terminus

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      17334982..17342731
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      17469817..17477573
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969Y2.2 GenPept UniProtKB/Swiss-Prot:Q969Y2

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