GTPBP10

gene
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Also known as DKFZP686A10121FLJ38242OBGH2

Summary

GTPBP10 (GTP binding protein 10, HGNC:25106) is a protein-coding gene on chromosome 7q21.13, encoding GTP-binding protein 10 (A4D1E9). May be involved in the ribosome maturation process. It is a selective cancer dependency (DepMap: 15.7% of cell lines).

Small G proteins, such as GTPBP10, act as molecular switches that play crucial roles in the regulation of fundamental cellular processes such as protein synthesis, nuclear transport, membrane trafficking, and signal transduction (Hirano et al., 2006 [PubMed 17054726]).

Source: NCBI Gene 85865 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 69 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 15.7% of screened cell lines
  • MANE Select transcript: NM_033107

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25106
Approved symbolGTPBP10
NameGTP binding protein 10
Location7q21.13
Locus typegene with protein product
StatusApproved
AliasesDKFZP686A10121, FLJ38242, OBGH2
Ensembl geneENSG00000105793
Ensembl biotypeprotein_coding
OMIM610920
Entrez85865

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 10 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000222511, ENST00000257659, ENST00000380058, ENST00000417207, ENST00000421719, ENST00000426366, ENST00000439832, ENST00000450619, ENST00000453512, ENST00000469675, ENST00000474503, ENST00000477972, ENST00000861578, ENST00000861579, ENST00000927587, ENST00000959248, ENST00000959249

RefSeq mRNA: 2 — MANE Select: NM_033107 NM_001042717, NM_033107

CCDS: CCDS43614, CCDS5617

Canonical transcript exons

ENST00000222511 — 10 exons

ExonStartEnd
ENSE000012722019034671690346774
ENSE000019014079038489290391453
ENSE000032514059035281690353009
ENSE000033166189035445890354549
ENSE000034735439035508690355230
ENSE000034977789037750790377614
ENSE000035209659037215590372228
ENSE000036031619037813490378211
ENSE000036740679038295690383079
ENSE000036937879037430290374354

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 89.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.6748 / max 344.4867, expressed in 1795 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
7944823.67481795

Top tissues by expression

297 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
corpus epididymisUBERON:000435989.86gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.89gold quality
calcaneal tendonUBERON:000370188.56gold quality
cauda epididymisUBERON:000436087.94gold quality
secondary oocyteCL:000065587.77gold quality
caput epididymisUBERON:000435887.71gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450286.57gold quality
islet of LangerhansUBERON:000000686.46gold quality
adrenal tissueUBERON:001830386.42gold quality
right lobe of liverUBERON:000111486.24gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.85gold quality
gastrocnemiusUBERON:000138885.32gold quality
biceps brachiiUBERON:000150785.30gold quality
rectumUBERON:000105285.22gold quality
hindlimb stylopod muscleUBERON:000425285.11gold quality
muscle of legUBERON:000138384.95gold quality
monocyteCL:000057684.55gold quality
granulocyteCL:000009484.51gold quality
leukocyteCL:000073884.31gold quality
mononuclear cellCL:000084284.24gold quality
colonic epitheliumUBERON:000039783.59gold quality
tendonUBERON:000004383.51gold quality
body of pancreasUBERON:000115083.48gold quality
corpus callosumUBERON:000233683.43gold quality
pancreasUBERON:000126483.32gold quality
heart right ventricleUBERON:000208083.23gold quality
olfactory segment of nasal mucosaUBERON:000538683.01gold quality
skin of abdomenUBERON:000141682.99gold quality
heart left ventricleUBERON:000208482.99gold quality
cardiac ventricleUBERON:000208282.93gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.73
E-MTAB-7303no112.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

225 targeting GTPBP10, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-5692A100.0074.406850
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4262100.0073.263931
HSA-MIR-3646100.0073.565283
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-186-5P99.9970.833707
HSA-MIR-480399.9871.993117
HSA-MIR-477599.9875.006394
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-302C-5P99.9772.563642

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • Knock-down of ObgH1 by RNAi induced mitochondria elongation, whereas knock-down of ObgH2 resulted in the disorganization of the nucleolar architecture. (PMID:17054726)
  • Our results suggest that GTPBP10 is a ribosome biogenesis factor of the mtLSU required for late stages of maturation. (PMID:30085210)
  • GTPBP10 primarily ensures proper mtLSU maturation and ultimately serves to coordinate mtSSU and mtLSU accumulation (PMID:30321378)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogtpbp10ENSDARG00000040300
mus_musculusGtpbp10ENSMUSG00000040464
rattus_norvegicusGtpbp10ENSRNOG00000007098
drosophila_melanogasterCG10628FBGN0032818
caenorhabditis_elegansWBGENE00016145

Paralogs (4): MTG2 (ENSG00000101181), GTPBP4 (ENSG00000107937), DRG2 (ENSG00000108591), DRG1 (ENSG00000185721)

Protein

Protein identifiers

GTP-binding protein 10A4D1E9 (reviewed: A4D1E9)

Alternative names: Protein obg homolog 2

All UniProt accessions (7): A4D1E9, C9J8R7, C9JEQ8, C9JNI1, F8WBB5, F8WBY0, F8WCN4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the ribosome maturation process. Complements an ObgE(CgtA) function in E.coli ribosome maturation. Plays a role of GTPase in vitro. When missing, disorganization of the nucleolar architecture is observed.

Subcellular location. Nucleus. Nucleolus. Chromosome.

Similarity. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family.

Isoforms (3)

UniProt IDNamesCanonical?
A4D1E9-11yes
A4D1E9-22
A4D1E9-33

RefSeq proteins (2): NP_001036182, NP_149098* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006073GTP-bdDomain
IPR006169GTP1_OBG_domDomain
IPR014100GTP-bd_Obg/CgtAFamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR031167G_OBGDomain
IPR036726GTP1_OBG_dom_sfHomologous_superfamily
IPR045086OBG_GTPaseFamily

Pfam: PF01018, PF01926

UniProt features (14 total): sequence variant 4, binding site 3, splice variant 3, domain 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8PK0ELECTRON MICROSCOPY3.03
7OI6ELECTRON MICROSCOPY5.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A4D1E9-F179.970.40

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 155–162; 202–206; 278–281

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_RIBOSOME_ASSEMBLY, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, DODD_NASOPHARYNGEAL_CARCINOMA_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GRADE_COLON_AND_RECTAL_CANCER_UP

GO Biological Process (2): mitochondrial large ribosomal subunit assembly (GO:1902775), ribosome biogenesis (GO:0042254)

GO Molecular Function (8): magnesium ion binding (GO:0000287), RNA binding (GO:0003723), GTPase activity (GO:0003924), GTP binding (GO:0005525), rRNA binding (GO:0019843), mitochondrial large ribosomal subunit binding (GO:0140978), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (5): chromosome (GO:0005694), nucleolus (GO:0005730), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle2
intracellular membrane-bounded organelle2
ribosomal large subunit assembly1
mitochondrial ribosome assembly1
ribonucleoprotein complex biogenesis1
metal ion binding1
nucleic acid binding1
ribonucleoside triphosphate phosphatase activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
RNA binding1
ribosomal large subunit binding1
mitochondrial ribosome binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
nuclear lumen1
cytoplasm1
mitochondrion1
intracellular organelle lumen1

Protein interactions and networks

STRING

1830 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GTPBP10MKI67P46013840
GTPBP10MALSU1Q96EH3835
GTPBP10MTG1Q9BT17832
GTPBP10GTPBP6O43824763
GTPBP10DDX28Q9NUL7754
GTPBP10ERAL1O75616728
GTPBP10MTERF4Q7Z6M4720
GTPBP10MRM2Q9UI43710
GTPBP10GTPBP8Q8N3Z3709
GTPBP10NSUN4Q96CB9681
GTPBP10NGRNQ9NPE2676
GTPBP10MRM3Q9HC36661
GTPBP10TRUB2O95900647
GTPBP10NOA1Q8NC60646
GTPBP10RPUSD4Q96CM3635

IntAct

124 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
PNMA1GTPBP10psi-mi:“MI:0915”(physical association)0.600
GTPBP10PNMA1psi-mi:“MI:0915”(physical association)0.600
GOLGA2GTPBP10psi-mi:“MI:0915”(physical association)0.560
GTPBP10MTUS2psi-mi:“MI:0915”(physical association)0.560
MTUS2GTPBP10psi-mi:“MI:0915”(physical association)0.560
PLEKHO1UBA6psi-mi:“MI:0914”(association)0.530
BPNT1GTPBP10psi-mi:“MI:0914”(association)0.530
FGF3GTPBP10psi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
MAGEB10GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530

BioGRID (161): GTPBP10 (Two-hybrid), GTPBP10 (Two-hybrid), GTPBP10 (Two-hybrid), PCBP4 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), GTPBP10 (Two-hybrid), GTPBP10 (Two-hybrid), GTPBP10 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), GTPBP10 (Affinity Capture-MS), PCBP4 (Affinity Capture-MS)

ESM2 similar proteins: A4D1E9, A4IHT9, A6QLJ3, A6QPU5, A9JTX2, B1H116, B3RXR7, E1BMP7, E3TDS3, I0IUP3, O23617, O80738, P06801, P13697, P31754, P32296, P51530, Q0E671, Q16798, Q1LZ83, Q29K06, Q2KI15, Q2TAA5, Q3MHG6, Q4V7N2, Q503J2, Q5M8V6, Q5R7Z6, Q5RDW1, Q5U528, Q5VV42, Q6DHF7, Q6NS23, Q6NS26, Q6P4Y0, Q6PI48, Q7SYM0, Q8BIP0, Q8BMF3, Q8C3X4

Diamond homologs: A0AIY6, A0M5C6, A0Q1T4, A0RJ47, A4D1E9, A4IRC7, A4J7I9, A4XJS8, A5D410, A5GD29, A5I666, A5ITG8, A5VJ99, A6QHI6, A6TQJ6, A6U2B2, A7FXU6, A7GHK2, A7X361, A7Z781, A8FFS8, A8MHK8, A8Z2H2, A9AXD9, A9VIR5, B0K414, B0KAB8, B0TBW1, B1ILY5, B1KZR3, B2G6R9, B2KAW2, B2V968, B3E609, B5E958, B5YEQ1, B5YJ65, B7GIR2, B7HE73, B7HQJ8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 95 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Peptide chain elongation1323.9×5e-13
Viral mRNA Translation1323.9×5e-13
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1323.6×5e-13
Mitochondrial ribosome-associated quality control1323.1×5e-13
Selenocysteine synthesis1322.6×5e-13
Eukaryotic Translation Termination1322.6×5e-13
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1322.2×5e-13
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1322.2×5e-13

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation1428.0×1e-14
cytoplasmic translation1327.7×1e-13
translation2023.6×1e-19
negative regulation of translation715.8×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

69 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance47
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1350 predictions. Top by Δscore:

VariantEffectΔscore
7:90353006:GCAA:Gdonor_gain1.0000
7:90353010:G:GGdonor_gain1.0000
7:90372225:GCAT:Gdonor_gain1.0000
7:90372229:G:GGdonor_gain1.0000
7:90374300:A:AGacceptor_gain1.0000
7:90374301:G:GAacceptor_gain1.0000
7:90377612:GTT:Gdonor_gain1.0000
7:90377615:G:GGdonor_gain1.0000
7:90378212:G:GGdonor_gain1.0000
7:90382946:T:TAacceptor_gain1.0000
7:90382952:A:AGacceptor_gain1.0000
7:90382952:AAAG:Aacceptor_gain1.0000
7:90382953:A:AGacceptor_gain1.0000
7:90382953:AAG:Aacceptor_gain1.0000
7:90382954:A:AGacceptor_gain1.0000
7:90382954:AG:Aacceptor_gain1.0000
7:90382955:G:GAacceptor_gain1.0000
7:90382955:GG:Gacceptor_gain1.0000
7:90382955:GGA:Gacceptor_gain1.0000
7:90382955:GGAGT:Gacceptor_gain1.0000
7:90383077:AAGGT:Adonor_loss1.0000
7:90383078:AGGTA:Adonor_loss1.0000
7:90383080:G:GAdonor_loss1.0000
7:90383080:G:GGdonor_gain1.0000
7:90383081:T:Gdonor_loss1.0000
7:90385038:G:GTdonor_gain1.0000
7:90385039:A:Tdonor_gain1.0000
7:90346756:T:Gdonor_gain0.9900
7:90352813:A:AGacceptor_gain0.9900
7:90352814:A:Gacceptor_gain0.9900

AlphaMissense

2552 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:90372228:T:CF180L0.990
7:90374303:T:AF180L0.990
7:90374303:T:GF180L0.990
7:90377573:T:CF220L0.989
7:90377575:C:AF220L0.989
7:90377575:C:GF220L0.989
7:90372172:A:TK161I0.987
7:90383014:A:TK279I0.979
7:90352916:T:AV45D0.977
7:90353005:A:CS75R0.974
7:90353007:C:AS75R0.974
7:90353007:C:GS75R0.974
7:90377516:G:CA201P0.973
7:90377517:C:AA201D0.970
7:90378149:T:CF239L0.969
7:90378151:T:AF239L0.969
7:90378151:T:GF239L0.969
7:90372171:A:GK161E0.967
7:90355157:T:CF131L0.966
7:90355159:C:AF131L0.966
7:90355159:C:GF131L0.966
7:90377523:T:CL203P0.966
7:90377532:T:CL206S0.966
7:90372172:A:CK161T0.965
7:90372173:A:CK161N0.963
7:90372173:A:TK161N0.963
7:90383015:A:CK279N0.963
7:90383015:A:TK279N0.963
7:90352874:G:AG31D0.962
7:90372171:A:CK161Q0.962

dbSNP variants (sampled 300 via entrez): RS1000003266 (7:90370153 C>T), RS1000111796 (7:90376533 C>T), RS1000235077 (7:90348850 A>G), RS1000253799 (7:90355136 G>A,C), RS1000264669 (7:90379824 A>G), RS1000320132 (7:90347505 A>G), RS1000352131 (7:90385652 T>G), RS1000368718 (7:90354775 T>C), RS1000496000 (7:90368051 G>C,T), RS1000556802 (7:90374854 G>A), RS1000581220 (7:90364507 G>A), RS1000655657 (7:90391523 G>A), RS1000710672 (7:90387834 C>A), RS1000732390 (7:90347803 G>A), RS1000737493 (7:90381061 C>A)

Disease associations

OMIM: gene MIM:610920 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066355 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.23Kd58.31nMCHEMBL5653589
7.19ED5063.95nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148477: Binding affinity to human GTPBP10 incubated for 45 mins by Kinobead based pull down assaykd0.0583uM

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsdecreases expression, affects cotreatment, increases abundance, increases oxidation2
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
pirinixic acidaffects binding, increases activity, increases expression1
deoxynivalenolincreases expression1
beta-lapachoneincreases expression1
sodium arseniteaffects cotreatment, decreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
di-n-butylphosphoric acidaffects expression1
MT19c compoundincreases expression1
Acroleinincreases abundance, affects cotreatment, increases oxidation1
Benzo(a)pyrenedecreases methylation1
Coaldecreases expression, increases abundance1
Gallic Aciddecreases expression1
Methyl Methanesulfonateincreases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Phenobarbitalaffects expression1
Ribonucleotidesaffects binding1
Smokedecreases expression, increases abundance1
Tretinoinaffects cotreatment, decreases expression1
Urethanedecreases expression1
Cyclosporineincreases expression1
Aflatoxin M1decreases expression1
Antirheumatic Agentsdecreases expression1
Cadmium Chloridedecreases expression1
Volatile Organic Compoundsaffects cotreatment, increases oxidation1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651519BindingBinding affinity to human GTPBP10 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.