PFDN2

gene
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Summary

PFDN2 (prefoldin subunit 2, HGNC:8867) is a protein-coding gene on chromosome 1q23.3, encoding Prefoldin subunit 2 (Q9UHV9). Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. It is a common-essential gene (DepMap: required in 99.6% of cancer cell lines).

This gene encodes a member of the prefoldin beta subunit family. The encoded protein is one of six subunits of prefoldin, a molecular chaperone complex that binds and stabilizes newly synthesized polypeptides, thereby allowing them to fold correctly. The complex, consisting of two alpha and four beta subunits, forms a double beta barrel assembly with six protruding coiled-coils.

Source: NCBI Gene 5202 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 26 total
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 99.6% of screened cell lines (common-essential)
  • MANE Select transcript: NM_012394

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8867
Approved symbolPFDN2
Nameprefoldin subunit 2
Location1q23.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000143256
Ensembl biotypeprotein_coding
OMIM613466
Entrez5202

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000368010, ENST00000468311, ENST00000851379, ENST00000918210, ENST00000918211, ENST00000918212

RefSeq mRNA: 1 — MANE Select: NM_012394 NM_012394

CCDS: CCDS1217

Canonical transcript exons

ENST00000368010 — 4 exons

ExonStartEnd
ENSE00000958900161102287161102375
ENSE00000958901161102048161102171
ENSE00001957682161117952161118037
ENSE00003674485161100561161100859

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 66.9223 / max 673.2269, expressed in 1824 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1559066.92231824

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646998.84gold quality
cortical plateUBERON:000534398.57gold quality
anterior cingulate cortexUBERON:000983598.48gold quality
cingulate cortexUBERON:000302798.44gold quality
spinal cordUBERON:000224098.23gold quality
adenohypophysisUBERON:000219698.21gold quality
ganglionic eminenceUBERON:000402398.18gold quality
amygdalaUBERON:000187698.01gold quality
gastrocnemiusUBERON:000138898.00gold quality
prefrontal cortexUBERON:000045197.99gold quality
Brodmann (1909) area 9UBERON:001354097.95gold quality
hypothalamusUBERON:000189897.87gold quality
putamenUBERON:000187497.77gold quality
nucleus accumbensUBERON:000188297.72gold quality
right frontal lobeUBERON:000281097.72gold quality
muscle of legUBERON:000138397.69gold quality
caudate nucleusUBERON:000187397.65gold quality
substantia nigraUBERON:000203897.65gold quality
hindlimb stylopod muscleUBERON:000425297.56gold quality
pituitary glandUBERON:000000797.52gold quality
dorsolateral prefrontal cortexUBERON:000983497.25gold quality
midbrainUBERON:000189197.23gold quality
omental fat padUBERON:001041497.23gold quality
monocyteCL:000057697.22gold quality
peritoneumUBERON:000235897.22gold quality
neocortexUBERON:000195097.18gold quality
adipose tissue of abdominal regionUBERON:000780897.02gold quality
frontal cortexUBERON:000187096.95gold quality
mononuclear cellCL:000084296.89gold quality
forebrainUBERON:000189096.81gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-ANND-3yes13.80
E-MTAB-10042yes4.06
E-MTAB-9689no835.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting PFDN2, 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-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-6755-5P99.9565.59464
HSA-MIR-539-5P99.9370.302855
HSA-MIR-338-5P99.9272.342951
HSA-MIR-95-5P99.8972.173973
HSA-MIR-391999.8769.452489
HSA-MIR-127699.3668.181642
HSA-MIR-431199.3170.473041
HSA-MIR-4650-3P99.0168.391062
HSA-MIR-1233-5P98.1966.711201
HSA-MIR-6778-5P98.1966.591239
HSA-MIR-313297.9667.91711
HSA-MIR-197-5P97.2368.10596
HSA-MIR-6823-5P96.2665.69919
HSA-MIR-425696.2267.70669
HSA-MIR-11181-5P96.1267.46665

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

  • Is part of an RNA polymerase II-associated complex with possible chaperone activity. (PMID:19450687)
  • knockdown of PFD2 and PFD5 disrupted prefoldin formation in HTT-expressing cells, resulting in accumulation of aggregates of a pathogenic form of HTT and in induction of cell death. (PMID:23720755)
  • prefoldin is amplified at 1q23.3-q24.1 in bladder cancer (PMID:23914742)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopfdn2ENSDARG00000025391
mus_musculusPfdn2ENSMUSG00000006412
rattus_norvegicusENSRNOG00000083250
drosophila_melanogasterPfdn2FBGN0010741
caenorhabditis_elegansWBGENE00019220

Protein

Protein identifiers

Prefoldin subunit 2Q9UHV9 (reviewed: Q9UHV9)

All UniProt accessions (2): Q9UHV9, B1AQP2

UniProt curated annotations — full annotation on UniProt →

Function. Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Subunit / interactions. Heterohexamer of two PFD-alpha type and four PFD-beta type subunits. Component of the PAQosome complex which is responsible for the biogenesis of several protein complexes and which consists of R2TP complex members RUVBL1, RUVBL2, RPAP3 and PIH1D1, URI complex members PFDN2, PFDN6, PDRG1, UXT and URI1 as well as ASDURF, POLR2E and DNAAF10/WDR92. Interacts with URI1; the interaction is phosphorylation-dependent and occurs in a growth-dependent manner.

Subcellular location. Nucleus. Cytoplasm. Mitochondrion.

Similarity. Belongs to the prefoldin subunit beta family.

RefSeq proteins (1): NP_036526* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002777PFD_beta-likeFamily
IPR009053PrefoldinHomologous_superfamily
IPR027235PFD2Family

Pfam: PF01920

UniProt features (7 total): sequence conflict 3, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
7WU7ELECTRON MICROSCOPY3.85
6NR8ELECTRON MICROSCOPY7.8
6NRDELECTRON MICROSCOPY8.2
6NRCELECTRON MICROSCOPY8.3
6NR9ELECTRON MICROSCOPY8.5
6NRBELECTRON MICROSCOPY8.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UHV9-F181.220.64

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-389957Prefoldin mediated transfer of substrate to CCT/TriC

MSigDB gene sets: 138 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, USF_C, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_PROTEIN_MATURATION, GOBP_PROTEIN_STABILIZATION, USF_01, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOBP_PROTEIN_FOLDING, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, USF_02, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_REGULATION_OF_CYTOSKELETON_ORGANIZATION

GO Biological Process (4): protein folding (GO:0006457), protein stabilization (GO:0050821), positive regulation of cytoskeleton organization (GO:0051495), negative regulation of amyloid fibril formation (GO:1905907)

GO Molecular Function (4): amyloid-beta binding (GO:0001540), protein folding chaperone (GO:0044183), obsolete unfolded protein binding (GO:0051082), protein binding (GO:0005515)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829), prefoldin complex (GO:0016272), protein folding chaperone complex (GO:0101031), RPAP3/R2TP/prefoldin-like complex (GO:1990062), protein-containing complex (GO:0032991)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
intracellular membrane-bounded organelle2
cytoplasm2
protein-containing complex2
cellular process1
protein maturation1
regulation of protein stability1
cytoskeleton organization1
positive regulation of organelle organization1
regulation of cytoskeleton organization1
negative regulation of protein metabolic process1
negative regulation of supramolecular fiber organization1
regulation of amyloid fibril formation1
amyloid fibril formation1
peptide binding1
molecular_function1
protein folding1
binding1
nuclear lumen1
intracellular anatomical structure1
intracellular protein-containing complex1
cellular_component1

Protein interactions and networks

STRING

2042 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PFDN2PFDN6O15212997
PFDN2PDRG1Q9NUG6996
PFDN2UXTQ9UBK9995
PFDN2POLR2EP19388993
PFDN2PFDN1O60925986
PFDN2PFDN4Q9NQP4986
PFDN2DNAAF10Q96MX6982
PFDN2URI1O94763966
PFDN2VBP1P61758928
PFDN2PFDN5Q99471912
PFDN2RUVBL1P82276903
PFDN2ACTBL2Q562R1888
PFDN2RUVBL2Q9Y230884
PFDN2RPAP3Q9H6T3833
PFDN2TENT4AQ5XG87776

IntAct

206 interactions, top by confidence:

ABTypeScore
VBP1PFDN2psi-mi:“MI:0915”(physical association)0.870
PFDN5PFDN2psi-mi:“MI:0915”(physical association)0.850
URI1POLR2Epsi-mi:“MI:0914”(association)0.850
CHAF1BCBX5psi-mi:“MI:0914”(association)0.790
POLR2EPOLR1Cpsi-mi:“MI:0914”(association)0.770
PFDN2PFDN1psi-mi:“MI:0915”(physical association)0.740
PFDN1PFDN2psi-mi:“MI:0915”(physical association)0.740
PPP1CCCCDC85Cpsi-mi:“MI:0914”(association)0.740
PPP1CCCCDC85Cpsi-mi:“MI:2364”(proximity)0.740
PFDN2URI1psi-mi:“MI:0915”(physical association)0.740
PFDN2PDRG1psi-mi:“MI:0915”(physical association)0.740
PFDN4PFDN6psi-mi:“MI:0914”(association)0.730
POLR2EMED19psi-mi:“MI:0914”(association)0.730
L3MBTL2E2F6psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
PFDN2RPAP3psi-mi:“MI:0915”(physical association)0.710
PPP1CACCDC85Cpsi-mi:“MI:0914”(association)0.670
PPP1CACCDC85Cpsi-mi:“MI:2364”(proximity)0.670
PFDN2POLR3Apsi-mi:“MI:0914”(association)0.670
POLR3APFDN2psi-mi:“MI:0915”(physical association)0.670
MAPK7PFDN6psi-mi:“MI:0914”(association)0.640

BioGRID (430): PFDN2 (Affinity Capture-MS), PFDN2 (Affinity Capture-MS), CD2AP (Co-fractionation), FLNA (Co-fractionation), HINT1 (Co-fractionation), NUP50 (Co-fractionation), PFDN2 (Co-fractionation), PFDN2 (Co-fractionation), PFDN2 (Co-fractionation), PFDN2 (Co-fractionation), PFDN2 (Co-fractionation), PFDN2 (Co-fractionation), PFDN2 (Co-fractionation), PFDN5 (Co-fractionation), PRKAB1 (Co-fractionation)

ESM2 similar proteins: A1A4P5, A1DGS2, A2R7Z2, B0BN18, O04350, O35685, O70591, O75347, O76031, P48427, P48428, P50502, P50503, P80584, Q07866, Q08851, Q08DB5, Q0VCY1, Q13190, Q15691, Q17QG2, Q3ZBD9, Q4SPU8, Q5D016, Q5R581, Q5R601, Q5R7N3, Q5R7Z5, Q5RF31, Q5U2U0, Q5ZLC7, Q5ZLF0, Q61166, Q63525, Q66HR2, Q66T82, Q68FJ8, Q6P848, Q6V291, Q8K1E0

Diamond homologs: A1A4P5, A8WVJ9, B0BN18, O70591, P40005, Q55GN3, Q9LJ98, Q9N5M2, Q9UHV9, Q9UTC9, Q9VTE5

SIGNOR signaling

2 interactions.

AEffectBMechanism
PFDN2“form complex”“URI1 prefoldin co-chaperone”binding
PFDN2“form complex”“Prefoldin co-chaperone”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 181 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 Elongation739.0×4e-08
FGFR2 mutant receptor activation533.4×7e-06
RNA Polymerase III Transcription Termination730.5×2e-07
RNA Polymerase III Transcription Initiation From Type 2 Promoter829.7×4e-08
RNA Polymerase III Transcription Initiation From Type 1 Promoter828.6×4e-08
RNA Polymerase III Transcription Initiation From Type 3 Promoter828.6×4e-08
Activation of AMPK downstream of NMDARs826.7×6e-08
Signaling by FGFR2 IIIa TM526.4×2e-05

GO biological processes:

GO termPartnersFoldFDR
microtubule cytoskeleton organization118.7×2e-05
protein stabilization167.0×1e-06
mitotic cell cycle87.0×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

26 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

329 predictions. Top by Δscore:

VariantEffectΔscore
1:161100857:TAT:Tacceptor_gain1.0000
1:161100858:AT:Aacceptor_gain1.0000
1:161100860:C:CCacceptor_gain1.0000
1:161100860:C:CGacceptor_loss1.0000
1:161102043:CTCA:Cdonor_loss1.0000
1:161102046:A:ACdonor_gain1.0000
1:161102047:C:CCdonor_gain1.0000
1:161102047:CCTG:Cdonor_gain1.0000
1:161102167:CTAGG:Cacceptor_gain1.0000
1:161102168:TAGG:Tacceptor_gain1.0000
1:161102169:AGG:Aacceptor_gain1.0000
1:161102170:GG:Gacceptor_gain1.0000
1:161102172:C:CCacceptor_gain1.0000
1:161102177:A:ACacceptor_gain1.0000
1:161102177:A:Cacceptor_gain1.0000
1:161102282:CTCA:Cdonor_loss1.0000
1:161102283:TCA:Tdonor_loss1.0000
1:161102284:CA:Cdonor_loss1.0000
1:161102317:G:Cdonor_gain1.0000
1:161102371:ATCAC:Aacceptor_gain1.0000
1:161102372:TCAC:Tacceptor_gain1.0000
1:161102373:CAC:Cacceptor_gain1.0000
1:161102373:CACC:Cacceptor_gain1.0000
1:161102375:CCTA:Cacceptor_loss1.0000
1:161102376:CTAA:Cacceptor_loss1.0000
1:161102380:C:CTacceptor_gain1.0000
1:161102384:G:Cacceptor_gain1.0000
1:161102384:G:GCacceptor_gain1.0000
1:161117949:CA:Cdonor_loss1.0000
1:161117950:A:ATdonor_loss1.0000

AlphaMissense

997 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:161100804:A:GL115P1.000
1:161100825:A:GL108P1.000
1:161102067:A:CL90W1.000
1:161102088:A:TV83D1.000
1:161102094:C:GR81P1.000
1:161102103:A:GL78P1.000
1:161102103:A:TL78Q1.000
1:161102121:C:GR72P1.000
1:161102122:G:TR72S1.000
1:161102126:G:CC70W1.000
1:161102127:C:TC70Y1.000
1:161102128:A:GC70R1.000
1:161102133:C:GR68P1.000
1:161102134:G:TR68S1.000
1:161102154:A:GL61P1.000
1:161102167:C:TV57M1.000
1:161102169:A:GL56P1.000
1:161100693:A:GL152S0.999
1:161100777:A:CI124S0.999
1:161100777:A:TI124N0.999
1:161100792:C:GR119P0.999
1:161100837:A:GL104P0.999
1:161102066:C:AL90F0.999
1:161102066:C:GL90F0.999
1:161102067:A:GL90S0.999
1:161102076:A:GL87P0.999
1:161102103:A:CL78R0.999
1:161102112:C:AG75V0.999
1:161102112:C:TG75E0.999
1:161102113:C:GG75R0.999

dbSNP variants (sampled 300 via entrez): RS1000050394 (1:161119877 G>A), RS1000111474 (1:161109513 T>G), RS1000347712 (1:161102801 T>C), RS1000448521 (1:161108164 A>C), RS1000820564 (1:161104893 A>G,T), RS1000934890 (1:161104501 T>C), RS1001077302 (1:161115290 C>A,T), RS1001090256 (1:161107813 C>T), RS1001124523 (1:161111053 G>A), RS1001361497 (1:161114764 A>C), RS1001498301 (1:161110071 T>C), RS1001564603 (1:161111674 G>C), RS1001744696 (1:161104573 C>T), RS1001843079 (1:161116037 A>G), RS1001961229 (1:161116475 C>T)

Disease associations

OMIM: gene MIM:613466 | 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): CHEMBL4295976 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 3 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.00IC501e+04nMMOLIBRESIB

PubChem BioAssay actives

1 with measured affinity, of 9 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
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2178542: Inhibition of PFDN2 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysisic5010.0000uM

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, increases expression3
Cyclosporineincreases expression3
bisphenol Faffects cotreatment, increases expression2
sodium arseniteincreases expression2
sodium arsenatedecreases expression1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
methylparabenincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
dinophysistoxin 1increases expression1
perfluorooctane sulfonic acidincreases expression1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
LDN 193189increases expression, affects cotreatment1
Sunitinibincreases expression1
Leflunomideincreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicaffects methylation1
Atrazineincreases expression1
Benzo(a)pyreneincreases methylation1
Dexamethasoneaffects cotreatment, increases expression1
Hydrogen Peroxideincreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Phenobarbitalaffects expression1
Silicon Dioxideincreases expression1
Smokeincreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidincreases expression1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4118701BindingBinding affinity to PFDN2 in human NCI-H23 cells at 1 uM by mass spectrometry based pull down assayStudies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. — Bioorg Med Chem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E1MVHyCyte SK-HEP-1 KO-hPFDN2Cancer cell lineMale

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.