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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RPAP3
RNA polymerase II associated protein 3
Chromosome 12 · 12q13.11
NCBI Gene: 79657Ensembl: ENSG00000005175.11HGNC: HGNC:26151UniProt: Q9H6T3
120PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingcytosolR2TP complexprotein stabilizationneurodegenerative diseasespermatocelecardiovascular diseaselysosomal storage disease
✦AI Summary

RPAP3 (RNA polymerase II associated protein 3) functions as a central adapter protein within the R2TP/PAQosome co-chaperone complex, which works with HSP90 to facilitate assembly and stabilization of diverse macromolecular complexes 1. RPAP3 contains a conserved C-terminal domain that directly binds RUVBL1/RUVBL2 AAA+ ATPases, which is essential for R2TP complex formation and is found in all R2TP and R2TP-like complexes 2. The protein spans both faces of a single RUVBL ring, providing an extended flexible scaffold that recruits client proteins and tethers HSP90 to facilitate their assembly 3. RPAP3 recruits specific clients through its TPR domains and collaborates with PIH1D1 to direct substrate recognition and positioning 4. Beyond its canonical role in RNA polymerase II assembly, RPAP3 participates in assembly of phosphatidylinositol-3-kinase-like kinase (PIKK) complexes including mTORC1 and ATR/ATRIP 2, and directly interacts with TSC2 to support TSC complex assembly, a key regulator of mTORC1 5. Emerging evidence implicates RPAP3 in ciliogenesis, RNA silencing, DNA damage response, and metabolic regulation 1. The RPAP3 C-terminal domain is conserved across species and serves as an identifying feature of R2TP-like complexes with specialized functions 6, highlighting its fundamental importance in quaternary protein assembly mechanisms.

Sources cited
1
RPAP3 C-terminal domain directly interacts with RUVBL2 and is essential for R2TP assembly; conserved across all R2TP and R2TP-like complexes
PMID: 32384603
2
RPAP3 and PIH1D1 are central adaptors in the PAQosome complex involved in diverse biological processes including ciliogenesis, RNA silencing, DNA damage response, metabolic regulation, and oncogenesis
PMID: 41424038
3
RPAP3 spans both faces of a RUVBL ring, providing a flexible scaffold that recruits clients and tethers HSP90; C-terminal domain interacts with RUVBL2 ATPase domain
PMID: 29662061
4
RPAP3 contains two TPR domains essential for HSP90 recruitment; forms tight RPAP3:PIH1D1 sub-complex; human R2TP shows differential client binding compared to yeast
PMID: 30033218
5
RPAP3 makes independent interactions with TSC2 and HSP90 to support TSC complex assembly
PMID: 39490680
6
RPAP3 C-terminal domain identifies R2TP-like quaternary chaperones; homologous domains in other proteins enable formation of specialized R2TP-like complexes
PMID: 29844425
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.42Moderate
spermatoceleOpen Targets
0.28Weak
cardiovascular diseaseOpen Targets
0.25Weak
lysosomal storage diseaseOpen Targets
0.12Weak
kidney diseaseOpen Targets
0.07Suggestive
lung cancerOpen Targets
0.06Suggestive
alcohol drinkingOpen Targets
0.05Suggestive
pseudohypoparathyroidism type 2Open Targets
0.05Suggestive
diabetes mellitusOpen Targets
0.05Suggestive
cardiomyopathyOpen Targets
0.05Suggestive
acute myeloid leukemiaOpen Targets
0.04Suggestive
familial isolated hypoparathyroidism due to agenesis of parathyroid glandOpen Targets
0.04Suggestive
liver diseaseOpen Targets
0.04Suggestive
hypoparathyroidism, familial isolated, 2Open Targets
0.04Suggestive
congenital adrenal hyperplasia due to 3-beta-hydroxysteroid dehydrogenase deficiencyOpen Targets
0.03Suggestive
Familial isolated hypoparathyroidismOpen Targets
0.03Suggestive
hypoparathyroidism, familial isolated 1Open Targets
0.03Suggestive
Kennedy diseaseOpen Targets
0.03Suggestive
Parathyroid Gland CarcinomaOpen Targets
0.03Suggestive
pseudohypoparathyroidism type 1BOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
CPN2Shared pathway100%TSPAN1Shared pathway100%PYURFShared pathway100%HAPSTR2Shared pathway100%PAQR4Shared pathway100%NAA30Shared pathway100%
Tissue Expression6 tissues
Heart
100%
Ovary
92%
Brain
83%
Bone Marrow
67%
Liver
48%
Lung
46%
Gene Interaction Network
Click a node to explore
RPAP3CPN2TSPAN1PYURFHAPSTR2PAQR4NAA30
PROTEIN STRUCTURE
Preparing viewer…
PDB6ZBK · 1.49 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.14LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.80 [0.57–1.14]
RankingsWhere RPAP3 stands among ~20K protein-coding genes
  • #3,938of 20,598
    Most Researched120 · top quartile
  • #11,882of 17,882
    Most Constrained (LOEUF)1.14
Genes detectedRPAP3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
RPAP3 C-Terminal Domain: A Conserved Domain for the Assembly of R2TP Co-Chaperone Complexes.
PMID: 32384603
Cells · 2020
1.00
2
The HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex.
PMID: 39490680
J Mol Biol · 2024
0.90
3
PIH1D1 and RPAP3, Components of the PAQosome: Emerging Roles in Cellular Physiology.
PMID: 41424038
Mol Cell Biol · 2026
0.80
4
Structure of the Human TELO2-TTI1-TTI2 Complex.
PMID: 34838521
J Mol Biol · 2022
0.70
5
The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones.
PMID: 29844425
Nat Commun · 2018
0.60