GPN3

gene
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Also known as MGC14560

Summary

GPN3 (GPN-loop GTPase 3, HGNC:30186) is a protein-coding gene on chromosome 12q24.11, encoding GPN-loop GTPase 3 (Q9UHW5). Small GTPase involved in the correct assembly of RNA polymerase II (RNAPII) complex, ensuring proper nuclear import of RNAPII. It is a common-essential gene (DepMap: required in 98.6% of cancer cell lines).

Predicted to enable GTPase activity. Part of protein-containing complex.

Source: NCBI Gene 51184 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 29 total
  • Cancer dependency (DepMap): dependent in 98.6% of screened cell lines (common-essential)
  • MANE Select transcript: NM_016301

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30186
Approved symbolGPN3
NameGPN-loop GTPase 3
Location12q24.11
Locus typegene with protein product
StatusApproved
AliasesMGC14560
Ensembl geneENSG00000111231
Ensembl biotypeprotein_coding
Entrez51184

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000228827, ENST00000537466, ENST00000543199, ENST00000546592, ENST00000547323, ENST00000549963, ENST00000550228, ENST00000550974, ENST00000551079, ENST00000552180, ENST00000912297

RefSeq mRNA: 3 — MANE Select: NM_016301 NM_001164372, NM_001164373, NM_016301

CCDS: CCDS53830, CCDS53831, CCDS9147

Canonical transcript exons

ENST00000228827 — 8 exons

ExonStartEnd
ENSE00000755100110453743110453871
ENSE00000834802110455586110455682
ENSE00000834803110455815110455930
ENSE00000834804110457510110457634
ENSE00000834805110459695110459862
ENSE00001133231110468156110468257
ENSE00002351545110452486110453096
ENSE00003681158110465106110465214

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 96.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.4492 / max 146.3959, expressed in 1797 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
13323416.69671791
1332331.0913594
1332370.6320166
1332360.01724
1332350.01195

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skeletal muscle tissue of biceps brachiiUBERON:000450296.05gold quality
biceps brachiiUBERON:000150795.88gold quality
vastus lateralisUBERON:000137993.28gold quality
heart right ventricleUBERON:000208092.86gold quality
gastrocnemiusUBERON:000138892.65gold quality
quadriceps femorisUBERON:000137792.63gold quality
muscle organUBERON:000163092.60gold quality
skeletal muscle organUBERON:001489292.60gold quality
muscle of legUBERON:000138392.59gold quality
skeletal muscle tissueUBERON:000113492.23gold quality
nephron tubuleUBERON:000123192.07gold quality
hindlimb stylopod muscleUBERON:000425291.78gold quality
deltoidUBERON:000147691.62gold quality
renal glomerulusUBERON:000007491.30gold quality
right testisUBERON:000453491.30gold quality
left testisUBERON:000453391.23gold quality
metanephric glomerulusUBERON:000473691.23gold quality
testisUBERON:000047390.97gold quality
spermCL:000001990.86gold quality
parotid glandUBERON:000183190.74gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451190.73gold quality
popliteal arteryUBERON:000225090.65gold quality
tibial arteryUBERON:000761090.64gold quality
calcaneal tendonUBERON:000370190.58gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.52gold quality
muscle tissueUBERON:000238590.40gold quality
arteryUBERON:000163790.35gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.10gold quality
heart left ventricleUBERON:000208490.08gold quality
cardiac ventricleUBERON:000208290.05gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.54
E-CURD-112yes9.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting GPN3, 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-190A-3P100.0080.355520
HSA-MIR-5692A100.0074.406850
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-335-3P99.9373.364958
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-369-3P99.8570.522264
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-548AZ-5P99.8369.943230
HSA-MIR-548T-5P99.8369.913220
HSA-MIR-313399.8170.923506
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-808499.7369.571760
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-46699.6770.852863
HSA-MIR-360999.5269.892587
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-608399.4768.732393

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 6)

  • Data show that GPN1/GPN3 define a new family of small GTPases that are specialized for the transport of RNA polymerase II into the nucleus. (PMID:21768307)
  • Parcs/Gpn3 plays a critical role in the nuclear accumulation of RNAP II, and this function explains the relative importance of Parcs/Gpn3 in cell proliferation. (PMID:21782856)
  • Gpn1-Gpn3 interaction was essential to maintain steady-state protein levels of both GTPases (PMID:25241168)
  • an acquired PDZ-binding motif in Gpn3 Q279* caused Gpn3 nuclear entry, and inhibited Gpn1 nuclear export and Gpn3-mediated RNAPII nuclear targeting. (PMID:28940195)
  • Results indicate that polyubiquitination on lysine 216 is a regulatory process for proteasomal degradation of Gpn3 that is not in a complex with Gpn1, a critical partner of Gpn3 in human cells. (PMID:29029378)
  • our analysis of public data revealed that Gpn3 overexpression was associated with a significant decrease in overall survival in patients with estrogen receptor-positive and Human epidermal growth factor receptor 2 (HER2+) breast cancer, supporting our proposal that targeting Gpn3 could potentially benefit patients with breast cancer. (PMID:31431135)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogpn3ENSDARG00000069525
mus_musculusGpn3ENSMUSG00000029464
rattus_norvegicusGpn3ENSRNOG00000001278
drosophila_melanogasterCG2656FBGN0037478
caenorhabditis_elegansWBGENE00013550

Paralogs (2): GPN2 (ENSG00000142751), GPN1 (ENSG00000198522)

Protein

Protein identifiers

GPN-loop GTPase 3Q9UHW5 (reviewed: Q9UHW5)

Alternative names: ATP-binding domain 1 family member C

All UniProt accessions (5): Q9UHW5, F8W1F4, H0YHZ5, H0YI19, S4R3M7

UniProt curated annotations — full annotation on UniProt →

Function. Small GTPase involved in the correct assembly of RNA polymerase II (RNAPII) complex, ensuring proper nuclear import of RNAPII.

Subunit / interactions. Heterodimer with GPN1. Binds to RNA polymerase II (RNAPII). Interacts directly with subunits RPB4 and RPB7 and the CTD of RPB1.

Subcellular location. Cytoplasm. Nucleus.

Post-translational modifications. Polyubiquitinated and degraded by the proteasome in the nucleus. Polyubiquitination is tightly controlled by GPN1 through interaction.

Similarity. Belongs to the GPN-loop GTPase family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UHW5-11yes
Q9UHW5-22
Q9UHW5-33

RefSeq proteins (3): NP_001157844, NP_001157845, NP_057385* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004130GpnFamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR030228Gpn3Family

Pfam: PF03029

Catalyzed reactions (Rhea), 1 shown:

  • GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (32 total): binding site 13, short sequence motif 6, sequence conflict 3, splice variant 2, sequence variant 2, mutagenesis site 2, chain 1, domain 1, site 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UHW5-F185.880.57

Functional residue map

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

Catalytic / active sites (1): 74 (stabilizes the phosphate intermediate; shared with dimeric partner)

Ligand- & substrate-binding residues (13): 15; 15; 16; 17; 17; 17; 18; 18; 40; 177; 177; 13

Post-translational modifications (1): 216

Mutagenesis-validated functional residues (2):

PositionPhenotype
210slightly decreased ubiquitination. further decreased ubiquitination; when associated with r-216.
216markedly decreased ubiquitination. does not affect the movement between the cytoplasm and the nucleus. slowly decreased

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 172 (showing top): E2F_Q4_01, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NUCLEAR_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, E2F_Q3, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, E2F1_Q3, DANG_BOUND_BY_MYC, GOBP_PROTEIN_LOCALIZATION_TO_NUCLEUS, E2F_Q3_01, MARSON_BOUND_BY_FOXP3_STIMULATED

GO Biological Process (1): protein import into nucleus (GO:0006606)

GO Molecular Function (5): GTPase activity (GO:0003924), GTP binding (GO:0005525), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), protein-containing complex (GO:0032991)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular protein transport1
protein localization to nucleus1
import into nucleus1
establishment of protein localization to organelle1
ribonucleoside triphosphate phosphatase activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
cellular_component1

Protein interactions and networks

STRING

1839 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPN3RPAP2Q8IXW5736
GPN3RPAP1Q9BWH6691
GPN3GPN1Q9HCN4679
GPN3POLR2KP53803663
GPN3SLC7A6OSQ96CW6662
GPN3GPN2Q9H9Y4652
GPN3POLR2LP52436616
GPN3POLR2CP19387615
GPN3POLR2BP30876603
GPN3FAM216AQ8WUB2596
GPN3POLR2JP52435555
GPN3POLR2FP41584555
GPN3POLR2DO15514524
GPN3POLR2AP24928516
GPN3POLR2EP19388484

IntAct

96 interactions, top by confidence:

ABTypeScore
POLR2EPOLR3Apsi-mi:“MI:0914”(association)0.870
POLR2JPOLR1Cpsi-mi:“MI:0914”(association)0.830
MED9MED19psi-mi:“MI:0914”(association)0.790
MED14MED19psi-mi:“MI:0914”(association)0.790
MED26MED19psi-mi:“MI:0914”(association)0.730
POLR2CPOLR2Dpsi-mi:“MI:0914”(association)0.730
RPRD1BRECQL5psi-mi:“MI:0914”(association)0.730
VAPBFAM83Gpsi-mi:“MI:0914”(association)0.730
POLR2JPOLR2Dpsi-mi:“MI:0914”(association)0.730
RPRD1BPOLR2Dpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
GPN3GPN1psi-mi:“MI:0915”(physical association)0.700
GPN1GPN3psi-mi:“MI:0915”(physical association)0.700
GPN3GPN1psi-mi:“MI:0403”(colocalization)0.700
POLR2LRCCD1psi-mi:“MI:0914”(association)0.640
SCN2BEXOC5psi-mi:“MI:0914”(association)0.640
POLR3KPOLR3Apsi-mi:“MI:0914”(association)0.640
POLR2DRECQL5psi-mi:“MI:0914”(association)0.640
POLR2FPOLR3Apsi-mi:“MI:0914”(association)0.640
GTPBP2GPN3psi-mi:“MI:0915”(physical association)0.560
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
POLR2ISUPT5Hpsi-mi:“MI:0914”(association)0.530

BioGRID (220): RPRD1A (Affinity Capture-MS), POLR3K (Affinity Capture-MS), PIH1D1 (Affinity Capture-MS), POLR2G (Affinity Capture-MS), POLR3H (Affinity Capture-MS), POLR1E (Affinity Capture-MS), POLR1B (Affinity Capture-MS), ASPM (Affinity Capture-MS), POLR1A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), RPAP2 (Affinity Capture-MS), POLR3E (Affinity Capture-MS), POLR2A (Affinity Capture-MS), POLR2D (Affinity Capture-MS), POLR3B (Affinity Capture-MS)

ESM2 similar proteins: A4FV08, A4IHW6, A5PJI5, G3V9T7, O43681, O54984, O94973, P16298, P17427, P18484, P20651, P48452, P48453, P63328, P63329, Q08209, Q08211, Q0IIZ2, Q0P5E2, Q0VCK5, Q17QL1, Q28141, Q2KJ61, Q2YDH6, Q2YDM2, Q3MHC2, Q503E1, Q5HZM6, Q5NVE6, Q5R5S4, Q5R874, Q5RIC0, Q5TA45, Q5ZHS1, Q5ZIH0, Q6GNQ1, Q6IQE5, Q6NVL5, Q6R518, Q7RTP6

Diamond homologs: A6H7F2, D4A7C0, O14443, P0CN94, P0CN95, Q06543, Q08726, Q0P5E2, Q28I42, Q4IQT8, Q4PF70, Q4R579, Q4V7Z0, Q4WT40, Q54NK8, Q54TE7, Q56XY2, Q58DD9, Q5A0W6, Q5BJ53, Q66KF6, Q6BI59, Q6CBB5, Q6CQA6, Q6FSS0, Q6PUR6, Q6R518, Q6ZM63, Q750Q9, Q8VEJ1, Q9D3W4, Q9H9Y4, Q9UHW5, Q9UTL7, Q54C25, Q8W586, A4FUD1, O42906, P46577, P47122

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 109 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
RNA Polymerase III Chain Elongation12101.5×1e-20
FGFR2 mutant receptor activation10101.5×8e-18
Signaling by FGFR2 IIIa TM1080.1×2e-16
RNA Polymerase III Transcription Termination1279.4×2e-19
RNA Polymerase III Transcription Initiation From Type 2 Promoter1373.3×4e-20
Abortive elongation of HIV-1 transcript in the absence of Tat1172.8×2e-17
RNA Polymerase III Transcription Initiation From Type 1 Promoter1370.7×4e-20
RNA Polymerase III Transcription Initiation From Type 3 Promoter1370.7×4e-20

GO biological processes:

GO termPartnersFoldFDR
positive regulation of transcription elongation by RNA polymerase II721.7×9e-06
RNA polymerase II preinitiation complex assembly616.8×2e-04
positive regulation of transcription initiation by RNA polymerase II616.8×2e-04
transcription by RNA polymerase II118.0×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1440 predictions. Top by Δscore:

VariantEffectΔscore
12:110453101:C:CTacceptor_gain1.0000
12:110453103:CAA:Cacceptor_gain1.0000
12:110453105:A:ACacceptor_gain1.0000
12:110453105:A:Cacceptor_gain1.0000
12:110453738:ATTAC:Adonor_loss1.0000
12:110453739:TTAC:Tdonor_loss1.0000
12:110453740:TACC:Tdonor_loss1.0000
12:110453741:A:Cdonor_loss1.0000
12:110453742:CCTT:Cdonor_loss1.0000
12:110453835:C:CTacceptor_gain1.0000
12:110453836:G:Cacceptor_gain1.0000
12:110453868:CAAT:Cacceptor_gain1.0000
12:110453875:CAAGT:Cacceptor_gain1.0000
12:110453879:T:TCacceptor_gain1.0000
12:110455813:A:ACdonor_gain1.0000
12:110455814:C:CCdonor_gain1.0000
12:110455814:CTT:Cdonor_gain1.0000
12:110455814:CTTCT:Cdonor_gain1.0000
12:110455820:AATTT:Adonor_gain1.0000
12:110455926:ATAAA:Aacceptor_gain1.0000
12:110455927:TAAA:Tacceptor_gain1.0000
12:110455928:AAAC:Aacceptor_loss1.0000
12:110455930:AC:Aacceptor_loss1.0000
12:110455931:C:CCacceptor_gain1.0000
12:110455932:T:Gacceptor_loss1.0000
12:110457501:G:Cdonor_gain1.0000
12:110459721:T:TAdonor_gain1.0000
12:110459776:C:CAdonor_gain1.0000
12:110459860:TGT:Tacceptor_gain1.0000
12:110465100:ACTT:Adonor_loss1.0000

AlphaMissense

1916 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:110455857:T:AK175I1.000
12:110459780:G:CC80W1.000
12:110459781:C:TC80Y1.000
12:110468160:C:TG15E1.000
12:110468161:C:AG15W1.000
12:110468176:C:GG10R1.000
12:110455856:T:AK175N0.999
12:110455856:T:GK175N0.999
12:110457630:C:AQ110H0.999
12:110457630:C:GQ110H0.999
12:110457634:C:TG109D0.999
12:110459695:C:AG109C0.999
12:110459695:C:GG109R0.999
12:110459701:A:GC107R0.999
12:110459703:T:CD106G0.999
12:110459703:T:GD106A0.999
12:110459798:G:CN74K0.999
12:110459798:G:TN74K0.999
12:110459805:C:TG72D0.999
12:110459856:C:GR55P0.999
12:110465141:G:TP41Q0.999
12:110465143:A:CD40E0.999
12:110465143:A:TD40E0.999
12:110465144:T:AD40V0.999
12:110465144:T:CD40G0.999
12:110465149:G:CN38K0.999
12:110465149:G:TN38K0.999
12:110465168:C:GR32P0.999
12:110465203:A:CC20W0.999
12:110465204:C:TC20Y0.999

dbSNP variants (sampled 300 via entrez): RS1000234468 (12:110467687 C>G,T), RS1000288999 (12:110453836 G>A,T), RS1000308884 (12:110461376 A>G), RS1000350321 (12:110467906 GGTT>G), RS1000458476 (12:110460920 C>T), RS1000462140 (12:110461120 G>A), RS1000757989 (12:110453459 A>G), RS1000795077 (12:110459578 G>A,T), RS1000867822 (12:110459326 C>A), RS1000974828 (12:110465993 C>T), RS1001604658 (12:110452489 T>G), RS1001684684 (12:110462246 A>G), RS1001685093 (12:110460018 A>G), RS1001755729 (12:110454148 G>A), RS1001929509 (12:110452868 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008103_92Bipolar disorder1.000000e-06
GCST010988_502Adult body size3.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects expression, increases abundance, decreases expression2
Cyclosporinedecreases expression, increases expression2
dicrotophosdecreases expression1
pirinixic acidincreases activity, affects binding, decreases expression1
bisphenol Adecreases expression1
sodium arseniteincreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
MT19c compoundincreases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenic Trioxidedecreases expression1
Air Pollutants, Occupationaldecreases expression1
Arsenicincreases abundance, increases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Hydrogen Peroxideaffects expression1
Nickeldecreases expression1
Ozoneincreases abundance, affects expression1
Plant Extractsaffects cotreatment, increases expression1
Tretinoindecreases expression1
Valproic Acidincreases expression1
Vitamin Edecreases expression1
Lactic Aciddecreases expression1
Particulate Matterdecreases expression, increases abundance1

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.