GTPBP3 Gene (Protein Coding)

GTP Binding Protein 3, Mitochondrial

GC19P020721
GIFtS:
42
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... See more...

Aliases for GTPBP3 Gene

Aliases for GTPBP3 Gene

  • GTP Binding Protein 3, Mitochondrial 2 3 5
  • TRNA Modification GTPase GTPBP3, Mitochondrial 3 4
  • Mitochondrial GTP-Binding Protein 1 3 4
  • MTGP1 3 4
  • GTP-Binding Protein 3 4
  • COXPD23 3
  • GTPBG3 3
  • THDF1 3
  • MSS1 3

External Ids for GTPBP3 Gene

Previous GeneCards Identifiers for GTPBP3 Gene

  • GC19P017309
  • GC19P017448
  • GC19P017014
  • GC19P017529
  • GC19P017903
  • GC19P017503
  • GC19P017697
  • GC19P020470
  • GC19P020610
  • GC19P017720
  • GC19P018289
  • GC19P018689
  • GC19P018999
  • GC19P019317
  • GC19P019654
  • GC19P020009
  • GC19P020325

Summaries for GTPBP3 Gene

Entrez Gene Summary for GTPBP3 Gene

  • 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]

GeneCards Summary for GTPBP3 Gene

GTPBP3 (GTP Binding Protein 3, Mitochondrial) is a Protein Coding gene. Diseases associated with GTPBP3 include Combined Oxidative Phosphorylation Deficiency 23 and Lactic Acidosis. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include GTP binding and GTPase activity. An important paralog of this gene is ERAL1.

UniProtKB/Swiss-Prot Summary for GTPBP3 Gene

  • GTPase involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U34) of the wobble uridine base in mitochondrial tRNAs.

Gene Wiki entry for GTPBP3 Gene

Additional gene information for GTPBP3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GTPBP3 Gene

Genomics for GTPBP3 Gene

GeneHancer (GH) Regulatory Elements for GTPBP3 Gene

Promoters and enhancers for GTPBP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GTPBP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GTPBP3 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • FOXO1
  • FOXO1a
  • Nkx2-5
  • Olf-1

Genomic Locations for GTPBP3 Gene

Genomic Locations for GTPBP3 Gene
chr19:17,334,920-17,342,731
(GRCh38/hg38)
Size:
7,812 bases
Orientation:
Plus strand
chr19:17,445,729-17,453,544
(GRCh37/hg19)
Size:
7,816 bases
Orientation:
Plus strand

Genomic View for GTPBP3 Gene

Genes around GTPBP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GTPBP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GTPBP3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GTPBP3 Gene

Proteins for GTPBP3 Gene

Products:

  1. Antibody
  2. Protein
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  • Protein details for GTPBP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q969Y2-GTPB3_HUMAN
    Recommended name:
    tRNA modification GTPase GTPBP3, mitochondrial
    Protein Accession:
    Q969Y2
    Secondary Accessions:
    • A6NFH1
    • A6NIG5
    • A6NKR4
    • A8K7B4
    • B7Z4V8
    • Q8TCY6
    • Q8WUW9
    • Q969G4
    • Q9BX61

    Protein attributes for GTPBP3 Gene

    Size:
    492 amino acids
    Molecular mass:
    52058 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for GTPBP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GTPBP3 Gene

Protein Expression for GTPBP3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for GTPBP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for GTPBP3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GTPBP3 Gene

Domains & Families for GTPBP3 Gene

Gene Families for GTPBP3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for GTPBP3 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GTPBP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ53015, highly similar to Homo sapiens GTP binding protein 3 (GTPBP3), transcript variant IV, mRNA (B7Z563_HUMAN)
  • Mitochondrial GTP-binding protein 1 (GTPB3_HUMAN)
  • GTPBP3 protein (Q96H44_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q969Y2

UniProtKB/Swiss-Prot:

GTPB3_HUMAN :
  • Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family.
Family:
  • Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family.
genes like me logo Genes that share domains with GTPBP3: view

Function for GTPBP3 Gene

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  2. CRISPR
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Molecular function for GTPBP3 Gene

UniProtKB/Swiss-Prot Function:
GTPase involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U34) of the wobble uridine base in mitochondrial tRNAs.

Phenotypes From GWAS Catalog for GTPBP3 Gene

Gene Ontology (GO) - Molecular Function for GTPBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0005525 GTP binding IEA --
genes like me logo Genes that share ontologies with GTPBP3: view
genes like me logo Genes that share phenotypes with GTPBP3: view

Human Phenotype Ontology for GTPBP3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GTPBP3 Gene

MGI Knock Outs for GTPBP3:
  • Gtpbp3 Gtpbp3<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for GTPBP3 Gene

Localization for GTPBP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GTPBP3 Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GTPBP3 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GTPBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IBA 21873635
GO:0005739 mitochondrion IBA,IDA --
genes like me logo Genes that share ontologies with GTPBP3: view

Pathways & Interactions for GTPBP3 Gene

PathCards logo

SuperPathways for GTPBP3 Gene

genes like me logo Genes that share pathways with GTPBP3: view

Pathways by source for GTPBP3 Gene

Gene Ontology (GO) - Biological Process for GTPBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002098 tRNA wobble uridine modification IBA 21873635
GO:0006400 tRNA modification IEA --
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IBA 21873635
GO:0048568 embryonic organ development IBA 21873635
genes like me logo Genes that share ontologies with GTPBP3: view

No data available for SIGNOR curated interactions for GTPBP3 Gene

Drugs & Compounds for GTPBP3 Gene

Products:

  1. Drug

(1) Drugs for GTPBP3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0

(1) Additional Compounds for GTPBP3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with GTPBP3: view

Transcripts for GTPBP3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for GTPBP3 Gene

(4) REFSEQ mRNAs :
(21) Additional mRNA sequences :
(131) Selected AceView cDNA sequences:
(28) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GTPBP3 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b · 3c · 3d ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ·
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: -
SP6: - - - - - - - - - -
SP7: - - - - - - -
SP8: - - - - - -
SP9: - -
SP10:
SP11: -
SP12: - -
SP13:
SP14: -
SP15:

ExUns: 10c · 10d ^ 11a · 11b · 11c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for GTPBP3 Gene

GeneLoc Exon Structure for
GTPBP3
ECgene alternative splicing isoforms for
GTPBP3

Expression for GTPBP3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GTPBP3 Gene

mRNA expression in normal human tissues for GTPBP3 Gene
mRNA expression by BioGPS for GTPBP3 GenemRNA expression by GTEx for GTPBP3 Gene

Protein differential expression in normal tissues from HIPED for GTPBP3 Gene

This gene is overexpressed in Adrenal (34.8) and Peripheral blood mononuclear cells (12.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GTPBP3 Gene



Protein tissue co-expression partners for GTPBP3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GTPBP3 Gene:

GTPBP3

SOURCE GeneReport for Unigene cluster for GTPBP3 Gene:

Hs.334885

mRNA Expression by UniProt/SwissProt for GTPBP3 Gene:

Q969Y2-GTPB3_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for GTPBP3 Gene

  • Nervous system(4.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GTPBP3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
  • respiratory
  • skeletal muscle
Regions:
Head and neck:
  • ear
Thorax:
  • heart
  • heart valve
  • lung
General:
  • blood vessel
genes like me logo Genes that share expression patterns with GTPBP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for GTPBP3 Gene

Orthologs for GTPBP3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GTPBP3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia GTPBP3 33
  • 100 (a)
 OneToOne
LOC748414 32
  • 98.55 (n)
dog
(Canis familiaris)
 Mammalia GTPBP3 33 32
  • 86.04 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia GTPBP3 33 32
  • 83.49 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Gtpbp3 32
  • 79.07 (n)
mouse
(Mus musculus)
 Mammalia Gtpbp3 17 33 32
  • 78.73 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia GTPBP3 33
  • 62 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia mdo-mir-7295 33
  • 58 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LOC100857447 32
  • 62.79 (n)
tropical clawed frog
(Silurana tropicalis)
 Amphibia gtpbp3 32
  • 56.89 (n)
zebrafish
(Danio rerio)
 Actinopterygii gtpbp3 33 32
  • 59.87 (n)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG18528 33 32
  • 53.07 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP002133 32
  • 52.27 (n)
worm
(Caenorhabditis elegans)
 Secernentea F39B2.7 33 32
  • 42.71 (n)
 OneToOne
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ABR063C 32
  • 50.25 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes MSS1 35 33 32
  • 42.78 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0E07657g 32
  • 41.08 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT1G78010 32
  • 39.71 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU04149 32
  • 50.28 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes mss1 32
  • 42.97 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea Cin.7936 32
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.7936 32
Species where no ortholog for GTPBP3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GTPBP3 Gene

ENSEMBL:
Gene Tree for GTPBP3 (if available)
TreeFam:
Gene Tree for GTPBP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GTPBP3: view image

Paralogs for GTPBP3 Gene

Paralogs for GTPBP3 Gene

genes like me logo Genes that share paralogs with GTPBP3: view

Variants for GTPBP3 Gene

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Polymorphic Variants from UniProtKB/Swiss-Prot for GTPBP3 Gene

GTPB3_HUMAN-Q969Y2
Val-250 variation may influence aminoglycoside-induced deafness (AID) [MIM:580000]. AID is characterized by deafness, varying from profond congenital hearing loss to normal hearing, and is caused by homoplasmic A1555G mutation in the mitochondrial 12S rRNA. Val-250 may affect the accuracy of codon-anticodon interaction, leading to modulate the translational efficiency and thereby affecting the severity of deafness in patients homozygous for 12S rRNA A1555G mutation.

Sequence variations from dbSNP and Humsavar for GTPBP3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1057518138 uncertain-significance, not specified, Combined oxidative phosphorylation deficiency 23 (COXPD23) [MIM:616198] 17,337,619(+) G/C/T coding_sequence_variant, intron_variant, missense_variant
rs1274363168 likely-pathogenic, Combined oxidative phosphorylation deficiency 23 17,338,667(+) C/T coding_sequence_variant, missense_variant
rs1555726849 pathogenic, Combined oxidative phosphorylation deficiency 23 17,339,005(+) G/T coding_sequence_variant, stop_gained
rs372174278 pathogenic, Combined oxidative phosphorylation deficiency 23, - 17,339,589(+) G/C/T coding_sequence_variant, missense_variant
rs373370177 Combined oxidative phosphorylation deficiency 23 (COXPD23) [MIM:616198] 17,339,123(+) C/A/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for GTPBP3 Gene

Variant ID Type Subtype PubMed ID
esv21604 CNV gain 19812545
esv3643817 CNV loss 21293372
esv3643818 CNV gain 21293372
nsv470129 CNV loss 18288195
nsv578741 CNV gain 21841781
nsv833768 CNV loss 17160897

Variation tolerance for GTPBP3 Gene

Residual Variation Intolerance Score: 48.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.18; 69.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GTPBP3 Gene

Human Gene Mutation Database (HGMD)
GTPBP3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GTPBP3

Disorders for GTPBP3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for GTPBP3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

GTPB3_HUMAN
  • Combined oxidative phosphorylation deficiency 23 (COXPD23) [MIM:616198]: An autosomal recessive mitochondrial disorder characterized by hypertrophic cardiomyopathy and/or neurologic symptoms with onset in early childhood. Disease features include hypertrophic cardiomyopathy, hypotonia, delayed psychomotor development, lactic acidosis, impaired activities of respiratory complexes I and IV, and defective translation of mitochondrial proteins. Disease severity is variable, ranging from death in early infancy to survival into the second decade of life. {ECO:0000269 PubMed:25434004, ECO:0000269 PubMed:26741492}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GTPBP3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GTPBP3: view

No data available for Genatlas for GTPBP3 Gene

Publications for GTPBP3 Gene

  1. Phenotype of non-syndromic deafness associated with the mitochondrial A1555G mutation is modulated by mitochondrial RNA modifying enzymes MTO1 and GTPBP3. (PMID: 15542390) Bykhovskaya Y … Fischel-Ghodsian N (Molecular genetics and metabolism 2004) 3 4 23 56
  2. A human mitochondrial GTP binding protein related to tRNA modification may modulate phenotypic expression of the deafness-associated mitochondrial 12S rRNA mutation. (PMID: 12370316) Li X … Guan MX (Molecular and cellular biology 2002) 3 4 23 56
  3. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. (PMID: 29390138) Asano K … Suzuki T (Nucleic acids research 2018) 2 3 56
  4. Mutations in GTPBP3 cause a mitochondrial translation defect associated with hypertrophic cardiomyopathy, lactic acidosis, and encephalopathy. (PMID: 25434004) Kopajtich R … Prokisch H (American journal of human genetics 2014) 3 4 56
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 43 56

ExternalLinks

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