PFDN5

gene
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Also known as PFD5MM-1

Summary

PFDN5 (prefoldin subunit 5, HGNC:8869) is a protein-coding gene on chromosome 12q13.13, encoding Prefoldin subunit 5 (Q99471). Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. It is a selective cancer dependency (DepMap: 78.1% of cell lines).

This gene encodes a member of the prefoldin alpha 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. The encoded protein may also repress the transcriptional activity of the proto-oncogene c-Myc. Alternatively spliced transcript variants encoding different isoforms have been described.

Source: NCBI Gene 5204 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 9 total
  • Cancer dependency (DepMap): dependent in 78.1% of screened cell lines
  • MANE Select transcript: NM_002624

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8869
Approved symbolPFDN5
Nameprefoldin subunit 5
Location12q13.13
Locus typegene with protein product
StatusApproved
AliasesPFD5, MM-1
Ensembl geneENSG00000123349
Ensembl biotypeprotein_coding
OMIM604899
Entrez5204

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 16 retained_intron, 9 protein_coding, 3 nonsense_mediated_decay

ENST00000243040, ENST00000334478, ENST00000351500, ENST00000547130, ENST00000547228, ENST00000548984, ENST00000549759, ENST00000549995, ENST00000550069, ENST00000550513, ENST00000550846, ENST00000550880, ENST00000550964, ENST00000551018, ENST00000551223, ENST00000552341, ENST00000552548, ENST00000552742, ENST00000553171, ENST00000628881, ENST00000676468, ENST00000677184, ENST00000677199, ENST00000677326, ENST00000677712, ENST00000678256, ENST00000678284, ENST00000935332

RefSeq mRNA: 2 — MANE Select: NM_002624 NM_002624, NM_145897

CCDS: CCDS8853, CCDS8854

Canonical transcript exons

ENST00000334478 — 6 exons

ExonStartEnd
ENSE000008382495329624453296275
ENSE000034811215329926953299450
ENSE000035268005329554253295639
ENSE000035612235329804553298150
ENSE000035700765329583953295941
ENSE000036096805329785053297924

Expression profiles

Bgee: expression breadth ubiquitous, 147 present calls, max score 99.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 291.8818 / max 2953.2634, expressed in 1827 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
125736291.16181827
1257370.7200445

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pituitary glandUBERON:000000799.71gold quality
adenohypophysisUBERON:000219699.71gold quality
granulocyteCL:000009499.69gold quality
left testisUBERON:000453399.69gold quality
endocervixUBERON:000045899.68gold quality
amygdalaUBERON:000187699.68gold quality
nucleus accumbensUBERON:000188299.68gold quality
hypothalamusUBERON:000189899.68gold quality
right testisUBERON:000453499.68gold quality
monocyteCL:000057699.67gold quality
leukocyteCL:000073899.67gold quality
right uterine tubeUBERON:000130299.67gold quality
substantia nigraUBERON:000203899.67gold quality
left ovaryUBERON:000211999.67gold quality
calcaneal tendonUBERON:000370199.67gold quality
ovaryUBERON:000099299.66gold quality
left lobe of thyroid glandUBERON:000112099.66gold quality
temporal lobeUBERON:000187199.66gold quality
putamenUBERON:000187499.66gold quality
thyroid glandUBERON:000204699.66gold quality
C1 segment of cervical spinal cordUBERON:000646999.66gold quality
right lobe of thyroid glandUBERON:000111999.65gold quality
caudate nucleusUBERON:000187399.64gold quality
Ammon’s hornUBERON:000195499.64gold quality
olfactory segment of nasal mucosaUBERON:000538699.64gold quality
right ovaryUBERON:000211899.63gold quality
corpus callosumUBERON:000233699.63gold quality
prostate glandUBERON:000236799.62gold quality
fallopian tubeUBERON:000388999.62gold quality
body of uterusUBERON:000985399.62gold quality

Single-cell (SCXA)

Detected in 16 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-CURD-88yes52.69
E-HCAD-9yes29.55
E-MTAB-10042yes12.14
E-CURD-89no1229.67
E-MTAB-8205no1199.89
E-MTAB-7381no797.47
E-CURD-53no666.89
E-HCAD-4no215.36
E-HCAD-1no78.12
E-HCAD-8no50.67
E-MTAB-6701no35.30
E-MTAB-9467no30.21
E-CURD-46no26.71
E-MTAB-8410no12.15
E-GEOD-125970no6.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting PFDN5, 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-472999.6972.184233
HSA-MIR-3189-5P97.5566.71655
HSA-MIR-191397.0766.201417

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 78.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 9)

  • Physical interaction of p73 with c-Myc and MM1, a c-Myc-binding protein, and modulation of the p73 function. (PMID:11844794)
  • MM-1alpha, MM-1gamma, and MM-1gamma, but not MM-1beta, were found to repress transcription activity of c-Myc (PMID:16173081)
  • Wnt4 gene, a member of the Wnt-beta-catenin pathway, was identified as a target gene of MM-1. (PMID:18281035)
  • MM-1, a c-Myc interacting protein, interacts with HCV ARFP/F protein, which can result in the enhancement of the c-Myc activity. (PMID:18398700)
  • Rabring7 stimulates c-Myc degradation via mono-ubiquitination of MM-1 (PMID:22844532)
  • 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)
  • Results from a study on gene expression variability markers in early-stage human embryos shows that PFDN5 is a putative expression variability marker for the 3-day, 8-cell embryo stage. (PMID:26288249)
  • Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression. (PMID:38216914)
  • PFDN5 plays a dual role in breast cancer and regulates tumor immune microenvironment: Insights from integrated bioinformatics analysis and experimental validation. (PMID:39396557)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopfdn5ENSDARG00000035043
mus_musculusPfdn5ENSMUSG00000001289
rattus_norvegicusPfdn5ENSRNOG00000012985
drosophila_melanogasterPfdn5FBGN0038976
caenorhabditis_elegansWBGENE00020112

Protein

Protein identifiers

Prefoldin subunit 5Q99471 (reviewed: Q99471)

Alternative names: Myc modulator 1, c-Myc-binding protein Mm-1

All UniProt accessions (7): A0A0D9SFR8, A0A7I2V5H9, Q99471, F8VNW6, F8VQZ2, H3BMQ1, H3BPF6

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. Represses the transcriptional activity of MYC.

Subunit / interactions. Heterohexamer of two PFD-alpha type and four PFD-beta type subunits. Binds to MYC; interacts with its N-terminal domain.

Subcellular location. Nucleus Cytoplasm Nucleus.

Tissue specificity. Highly expressed in pancreas and skeletal muscle and moderately in other tissues.

Miscellaneous. Does not repress transcription activity of MYC.

Similarity. Belongs to the prefoldin subunit alpha family.

Isoforms (3)

UniProt IDNamesCanonical?
Q99471-11, MM1-alphayes
Q99471-22, MM1-beta
Q99471-33, MM1-gamma

RefSeq proteins (2): NP_002615, NP_665904 (=MANE)

Domains & families (InterPro)

IDNameType
IPR004127Prefoldin_subunit_alphaFamily
IPR009053PrefoldinHomologous_superfamily
IPR011599PFD_alpha_archaeaFamily

Pfam: PF02996

UniProt features (7 total): modified residue 3, splice variant 2, initiator methionine 1, chain 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-Q99471-F192.450.85

Functional residue map

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

Post-translational modifications (3): 2, 42, 56

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 187 (showing top): ENK_UV_RESPONSE_KERATINOCYTE_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, HSIAO_HOUSEKEEPING_GENES, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_PROTEIN_MATURATION, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_PROTEIN_STABILIZATION, GOBP_PROTEIN_FOLDING, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, AFFAR_YY1_TARGETS_DN, GOBP_SENSORY_ORGAN_DEVELOPMENT

GO Biological Process (9): regulation of DNA-templated transcription (GO:0006355), protein folding (GO:0006457), negative regulation of DNA-templated transcription (GO:0045892), retina development in camera-type eye (GO:0060041), negative regulation of canonical Wnt signaling pathway (GO:0090090), negative regulation of amyloid fibril formation (GO:1905907), RNA polymerase I assembly (GO:1990113), RNA polymerase II core complex assembly (GO:1990114), RNA polymerase III assembly (GO:1990115)

GO Molecular Function (4): amyloid-beta binding (GO:0001540), transcription corepressor activity (GO:0003714), obsolete unfolded protein binding (GO:0051082), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), prefoldin complex (GO:0016272), intermediate filament cytoskeleton (GO:0045111), 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
protein-containing complex assembly3
DNA-templated transcription2
cellular anatomical structure2
regulation of gene expression1
regulation of RNA biosynthetic process1
cellular process1
protein maturation1
regulation of DNA-templated transcription1
negative regulation of RNA biosynthetic process1
camera-type eye development1
anatomical structure development1
negative regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
negative regulation of protein metabolic process1
negative regulation of supramolecular fiber organization1
regulation of amyloid fibril formation1
amyloid fibril formation1
peptide binding1
transcription coregulator activity1
negative regulation of DNA-templated transcription1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
protein-containing complex1
cytoskeleton1
cellular_component1

Protein interactions and networks

STRING

2251 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PFDN5VBP1P61758988
PFDN5PFDN4Q9NQP4987
PFDN5PFDN6O15212984
PFDN5PFDN1O60925980
PFDN5PFDN2Q9UHV9912
PFDN5MYCP01106781
PFDN5UXTQ9UBK9753
PFDN5TCP1P17987657
PFDN5PDRG1Q9NUG6601
PFDN5MYG1Q9HB07590
PFDN5SLC61A1Q6N075560
PFDN5URI1O94763540
PFDN5CCT7Q99832536
PFDN5CSTPP1Q9H6J7524
PFDN5LCA5LO95447497

IntAct

485 interactions, top by confidence:

ABTypeScore
IKZF3PFDN5psi-mi:“MI:0915”(physical association)0.780
PFDN5IKZF3psi-mi:“MI:0915”(physical association)0.780
PFDN4PFDN6psi-mi:“MI:0914”(association)0.730
DDB2CCT2psi-mi:“MI:0914”(association)0.730
PSME3PFDN5psi-mi:“MI:0915”(physical association)0.720
PFDN5PSME3psi-mi:“MI:0915”(physical association)0.720
PFDN5vIRF-3psi-mi:“MI:0915”(physical association)0.680
vIRF-3PFDN5psi-mi:“MI:0915”(physical association)0.680
vIRF-3PFDN5psi-mi:“MI:0407”(direct interaction)0.680
PFDN5vIRF-3psi-mi:“MI:0407”(direct interaction)0.680
PFDN5CALCOCO2psi-mi:“MI:0915”(physical association)0.670
VBP1PFDN6psi-mi:“MI:0914”(association)0.640
GLRX3PFDN5psi-mi:“MI:0915”(physical association)0.560
PFDN5GLRX3psi-mi:“MI:0915”(physical association)0.560
BHLHE40PFDN5psi-mi:“MI:0915”(physical association)0.560
PFDN5psi-mi:“MI:0915”(physical association)0.560
PFDN5FAM110Apsi-mi:“MI:0915”(physical association)0.560
NTAQ1PFDN5psi-mi:“MI:0915”(physical association)0.560
PFDN5SCNM1psi-mi:“MI:0915”(physical association)0.560
GNB2PFDN6psi-mi:“MI:0914”(association)0.530

BioGRID (432): PFDN5 (Affinity Capture-MS), PSME3 (Two-hybrid), CALCOCO2 (Two-hybrid), GLRX3 (Two-hybrid), IKZF3 (Two-hybrid), PFDN5 (Affinity Capture-MS), PFDN5 (Affinity Capture-MS), PFDN5 (Affinity Capture-MS), PFDN5 (Affinity Capture-MS), PFDN5 (Affinity Capture-MS), FLNA (Co-fractionation), GFPT1 (Co-fractionation), PFDN5 (Co-fractionation), PFDN5 (Co-fractionation), PFDN5 (Co-fractionation)

ESM2 similar proteins: A7T0W1, A8WVJ9, A8X0Z1, A8XPL7, A8Y197, O14334, O14450, O15212, O18054, O94307, P40005, P48363, P52553, P52554, P57741, P57742, P61758, P61759, Q03958, Q04493, Q10143, Q12ZJ7, Q17435, Q17827, Q17Q89, Q21993, Q2HIK4, Q2TBR6, Q2TBX2, Q54JS0, Q54LS2, Q54V55, Q55GN3, Q5RAY0, Q5RCG9, Q5TJE6, Q61SU8, Q8HYI9, Q8I3Y6, Q99471

Diamond homologs: A8XPL7, O94307, P57742, Q04493, Q21993, Q54V55, Q5RAY0, Q8HYI9, Q99471, Q9VCZ8, Q9WU28, A0B9G1, A1RXA9, Q0W5H4, O58263, Q5JIE3, Q8U3T0, Q8PYQ1, A5UL29, B0R7X6, B6YWD9, B9LUU4, O66961, Q12ZJ7, Q18EV0, Q2NGQ5, Q3IUJ7, Q46F99, Q58362, Q5JE63, Q5UY26, Q8TIN6, Q8TUY7, Q9HMN2, Q54ND3, A0RUF1, A2STI6, A3CWZ2, A6UQB4, A6UWR8

SIGNOR signaling

1 interactions.

AEffectBMechanism
PFDN5“form complex”“Prefoldin co-chaperone”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 139 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
Prefoldin mediated transfer of substrate to CCT/TriC740.0×1e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance4
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

659 predictions. Top by Δscore:

VariantEffectΔscore
12:53295940:GG:Gdonor_gain1.0000
12:53295941:GG:Gdonor_gain1.0000
12:53297849:GAT:Gacceptor_gain1.0000
12:53297926:T:Adonor_loss1.0000
12:53298040:T:Aacceptor_gain1.0000
12:53298041:GTAG:Gacceptor_loss1.0000
12:53298043:A:AGacceptor_gain1.0000
12:53298044:G:GAacceptor_gain1.0000
12:53298044:GA:Gacceptor_gain1.0000
12:53298044:GAC:Gacceptor_gain1.0000
12:53298044:GACA:Gacceptor_gain1.0000
12:53298146:ACAGG:Adonor_gain1.0000
12:53298147:CAGG:Cdonor_gain1.0000
12:53298147:CAGGG:Cdonor_loss1.0000
12:53298148:AGG:Adonor_gain1.0000
12:53298149:GG:Gdonor_gain1.0000
12:53298149:GGG:Gdonor_gain1.0000
12:53298150:GG:Gdonor_gain1.0000
12:53298151:G:GGdonor_gain1.0000
12:53298151:G:Tdonor_gain1.0000
12:53298151:GTA:Gdonor_loss1.0000
12:53299267:A:AGacceptor_gain1.0000
12:53299268:G:GCacceptor_gain1.0000
12:53299268:GCC:Gacceptor_gain1.0000
12:53295635:ACCAG:Adonor_loss0.9900
12:53295636:CCAGG:Cdonor_loss0.9900
12:53295637:CAGGT:Cdonor_loss0.9900
12:53295638:AG:Adonor_loss0.9900
12:53295639:GG:Gdonor_loss0.9900
12:53295640:GTG:Gdonor_loss0.9900

AlphaMissense

1026 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:53296259:T:AV64D1.000
12:53297857:T:AV72D1.000
12:53297901:G:AG87R1.000
12:53297901:G:CG87R1.000
12:53297902:G:AG87E1.000
12:53297902:G:TG87V1.000
12:53295611:T:CL15P0.999
12:53295620:T:CL18P0.999
12:53295632:T:CL22P0.999
12:53295860:T:CS32P0.999
12:53295873:T:CL36P0.999
12:53295902:G:CA46P0.999
12:53296265:T:CL66P0.999
12:53297862:G:AG74R0.999
12:53297862:G:CG74R0.999
12:53297862:G:TG74W0.999
12:53297863:G:AG74E0.999
12:53298057:G:CA99P0.999
12:53298058:C:AA99D0.999
12:53298080:G:CK106N0.999
12:53298080:G:TK106N0.999
12:53298091:T:CL110P0.999
12:53298124:T:CL121P0.999
12:53299272:T:AV131D0.999
12:53295885:A:CQ40P0.998
12:53296262:C:AP65Q0.998
12:53297890:T:CL83P0.998
12:53297899:T:AV86E0.998
12:53297902:G:CG87A0.998
12:53297907:G:TG89W0.998

dbSNP variants (sampled 300 via entrez): RS1000658582 (12:53299549 T>C), RS1000872246 (12:53297837 T>C), RS1001310089 (12:53294360 C>T), RS1001886505 (12:53293652 A>T), RS1002146273 (12:53299013 G>C), RS1002159135 (12:53298887 G>A), RS1002540669 (12:53296417 T>C), RS1002591722 (12:53296191 T>A), RS1003212322 (12:53297895 G>A), RS1003286789 (12:53299148 A>G), RS1004252513 (12:53294684 G>A), RS1004415213 (12:53299884 G>A,T), RS1004668312 (12:53294435 A>C), RS1006339538 (12:53296121 A>C,G), RS1006609964 (12:53298433 C>A,T)

Disease associations

OMIM: gene MIM:604899 | 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: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression3
bisphenol Aaffects expression, increases expression2
Arsenicincreases expression, decreases expression, affects methylation, affects cotreatment, increases abundance2
Benzo(a)pyreneincreases methylation, decreases expression2
Valproic Acidaffects expression, decreases expression2
dicrotophosdecreases expression1
biochanin Adecreases expression1
triphenyl phosphateaffects expression1
methylselenic aciddecreases expression1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
chloropicrinaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
bisphenol Bincreases expression1
bisphenol Sdecreases methylation1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Ethanoldecreases expression1
Atrazinedecreases expression1
Calcitriolincreases expression1
Carbon Tetrachloridedecreases expression1
Cisplatinaffects expression, affects reaction1
Doxorubicinincreases expression1
Estradioldecreases expression1
Folic Acidaffects expression, affects reaction1
Hydrogen Peroxideincreases expression1
Ivermectindecreases expression1
Ouabainaffects expression1
Tobacco Smoke Pollutionaffects expression1
Vitamin Eincreases expression1

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.