PFDN1
gene geneOn this page
Also known as PFD1
Summary
PFDN1 (prefoldin subunit 1, HGNC:8866) is a protein-coding gene on chromosome 5q31.3, encoding Prefoldin subunit 1 (O60925). Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. It is a selective cancer dependency (DepMap: 72.2% of 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 5201 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 18 total
- Druggable target: yes
- Cancer dependency (DepMap): dependent in 72.2% of screened cell lines
- MANE Select transcript:
NM_002622
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:8866 |
| Approved symbol | PFDN1 |
| Name | prefoldin subunit 1 |
| Location | 5q31.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | PFD1 |
| Ensembl gene | ENSG00000113068 |
| Ensembl biotype | protein_coding |
| OMIM | 604897 |
| Entrez | 5201 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined
ENST00000261813, ENST00000507185, ENST00000510217, ENST00000512707, ENST00000512925, ENST00000514611, ENST00000524074, ENST00000893784, ENST00000934220
RefSeq mRNA: 1 — MANE Select: NM_002622
NM_002622
CCDS: CCDS4222
Canonical transcript exons
ENST00000261813 — 4 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001254110 | 140245035 | 140246057 |
| ENSE00002021425 | 140303041 | 140303101 |
| ENSE00003586707 | 140281449 | 140281533 |
| ENSE00003685183 | 140300416 | 140300582 |
Expression profiles
Bgee: expression breadth ubiquitous, 294 present calls, max score 97.88.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 71.9297 / max 1373.9073, expressed in 1815 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 63785 | 71.9297 | 1815 |
Top tissues by expression
302 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| calcaneal tendon | UBERON:0003701 | 97.88 | gold quality |
| ganglionic eminence | UBERON:0004023 | 96.89 | gold quality |
| ventricular zone | UBERON:0003053 | 96.70 | gold quality |
| hindlimb stylopod muscle | UBERON:0004252 | 96.68 | gold quality |
| islet of Langerhans | UBERON:0000006 | 96.63 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 96.47 | gold quality |
| prefrontal cortex | UBERON:0000451 | 96.35 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 96.33 | gold quality |
| apex of heart | UBERON:0002098 | 96.31 | gold quality |
| right frontal lobe | UBERON:0002810 | 96.27 | gold quality |
| cortical plate | UBERON:0005343 | 96.15 | gold quality |
| cingulate cortex | UBERON:0003027 | 95.97 | gold quality |
| heart left ventricle | UBERON:0002084 | 95.92 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 95.89 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 95.83 | gold quality |
| cardiac ventricle | UBERON:0002082 | 95.82 | gold quality |
| right atrium auricular region | UBERON:0006631 | 95.63 | gold quality |
| amygdala | UBERON:0001876 | 95.53 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 95.52 | gold quality |
| nucleus accumbens | UBERON:0001882 | 95.47 | gold quality |
| spinal cord | UBERON:0002240 | 95.46 | gold quality |
| muscle of leg | UBERON:0001383 | 95.45 | gold quality |
| caudate nucleus | UBERON:0001873 | 95.37 | gold quality |
| putamen | UBERON:0001874 | 95.36 | gold quality |
| heart | UBERON:0000948 | 95.25 | gold quality |
| gastrocnemius | UBERON:0001388 | 95.14 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 95.10 | gold quality |
| cardiac atrium | UBERON:0002081 | 94.94 | gold quality |
| neocortex | UBERON:0001950 | 94.91 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 94.91 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 12.90 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
43 targeting PFDN1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-4283 | 100.00 | 66.42 | 2097 |
| HSA-MIR-4803 | 99.98 | 71.99 | 3117 |
| HSA-MIR-302C-5P | 99.97 | 72.56 | 3642 |
| HSA-MIR-6888-3P | 99.97 | 65.95 | 1170 |
| HSA-MIR-1-3P | 99.93 | 72.35 | 1914 |
| HSA-MIR-206 | 99.93 | 72.50 | 1893 |
| HSA-MIR-450B-5P | 99.92 | 71.48 | 3175 |
| HSA-MIR-613 | 99.91 | 71.50 | 1710 |
| HSA-MIR-4492 | 99.87 | 68.25 | 3611 |
| HSA-MIR-4728-5P | 99.85 | 69.39 | 4718 |
| HSA-MIR-6785-5P | 99.82 | 68.68 | 4428 |
| HSA-MIR-149-3P | 99.72 | 68.22 | 3963 |
| HSA-MIR-6883-5P | 99.69 | 68.05 | 3785 |
| HSA-MIR-6892-3P | 99.68 | 66.40 | 1178 |
| HSA-MIR-3202 | 99.66 | 67.70 | 2737 |
| HSA-MIR-6134 | 99.63 | 65.68 | 1537 |
| HSA-MIR-4663 | 99.62 | 65.33 | 957 |
| HSA-MIR-4516 | 99.61 | 67.78 | 3390 |
| HSA-MIR-1207-5P | 99.49 | 69.11 | 2983 |
| HSA-MIR-5584-5P | 99.49 | 68.22 | 2814 |
| HSA-MIR-4498 | 99.47 | 67.42 | 2360 |
| HSA-MIR-3182 | 99.40 | 68.15 | 2454 |
| HSA-MIR-7515 | 99.31 | 68.22 | 1795 |
| HSA-MIR-4505 | 99.27 | 67.81 | 2678 |
| HSA-MIR-4685-5P | 99.25 | 65.99 | 1563 |
| HSA-MIR-6837-5P | 99.25 | 65.47 | 1632 |
| HSA-MIR-7974 | 99.24 | 65.48 | 1137 |
| HSA-MIR-5787 | 99.22 | 67.86 | 2628 |
| HSA-MIR-4763-3P | 99.10 | 67.83 | 2649 |
| HSA-MIR-939-3P | 98.97 | 65.07 | 2347 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 72.2% of screened cell lines.
Literature-anchored findings (GeneRIF, showing 5)
- antagonistic actions of PhLP3 and prefoldin serve to modulate CCT activity and play a key role in establishing a functional cytoskeleton in vivo (PMID:16415341)
- Studied PFDN1 as prognosis indicator for colorectal cancer and investigated the functions of PFDN1 in colorectal cancer. (PMID:26553318)
- High PFDN1 expression is associated with lung cancer progression. (PMID:27694898)
- Genome-wide significant (GWS) associations in single-nucleotide polymorphism (SNP)-based tests (P < 5 x 10(-8)) were identified for SNPs in PFDN1/HBEGF, USP6NL/ECHDC3, and BZRAP1-AS1. (PMID:28183528)
- Prefoldin and prefoldin-like complex subunits as predictive biomarkers for hepatocellular carcinoma immunotherapy. (PMID:35217267)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | pfdn1 | ENSDARG00000014536 |
| mus_musculus | Pfdn1 | ENSMUSG00000024346 |
| rattus_norvegicus | Pfdn1 | ENSRNOG00000018653 |
| drosophila_melanogaster | Pfdn1 | FBGN0031776 |
| caenorhabditis_elegans | WBGENE00007443 |
Protein
Protein identifiers
Prefoldin subunit 1 — O60925 (reviewed: O60925)
All UniProt accessions (3): D6RGG5, E5RGS4, O60925
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.
Similarity. Belongs to the prefoldin subunit beta family.
RefSeq proteins (1): NP_002613* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002777 | PFD_beta-like | Family |
| IPR009053 | Prefoldin | Homologous_superfamily |
Pfam: PF01920
UniProt features (5 total): sequence conflict 2, initiator methionine 1, chain 1, modified residue 1
Structure
Experimental structures (PDB)
6 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 7WU7 | ELECTRON MICROSCOPY | 3.85 |
| 6NR8 | ELECTRON MICROSCOPY | 7.8 |
| 6NRD | ELECTRON MICROSCOPY | 8.2 |
| 6NRC | ELECTRON MICROSCOPY | 8.3 |
| 6NR9 | ELECTRON MICROSCOPY | 8.5 |
| 6NRB | ELECTRON MICROSCOPY | 8.7 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O60925-F1 | 93.33 | 0.86 |
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 (1): 2
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-389957 | Prefoldin mediated transfer of substrate to CCT/TriC |
MSigDB gene sets: 121 (showing top):
TGCGCANK_UNKNOWN, GGGTGGRR_PAX4_03, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_PROTEIN_MATURATION, GOBP_PROTEIN_STABILIZATION, GOBP_PROTEIN_FOLDING, GARY_CD5_TARGETS_DN, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, PEART_HDAC_PROLIFERATION_CLUSTER_DN, MORF_PML, MORF_IKBKG, TGGAAA_NFAT_Q4_01, chr5q31, BLALOCK_ALZHEIMERS_DISEASE_DN
GO Biological Process (2): protein folding (GO:0006457), 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 (3): cytoplasm (GO:0005737), prefoldin complex (GO:0016272), protein-containing complex (GO:0032991)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular process | 1 |
| protein maturation | 1 |
| negative regulation of protein metabolic process | 1 |
| negative regulation of supramolecular fiber organization | 1 |
| regulation of amyloid fibril formation | 1 |
| amyloid fibril formation | 1 |
| peptide binding | 1 |
| molecular_function | 1 |
| protein folding | 1 |
| binding | 1 |
| intracellular anatomical structure | 1 |
| cellular anatomical structure | 1 |
| protein-containing complex | 1 |
| cellular_component | 1 |
Protein interactions and networks
STRING
1834 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| PFDN1 | VBP1 | P61758 | 993 |
| PFDN1 | PFDN4 | Q9NQP4 | 986 |
| PFDN1 | PFDN2 | Q9UHV9 | 986 |
| PFDN1 | PFDN5 | Q99471 | 980 |
| PFDN1 | PFDN6 | O15212 | 962 |
| PFDN1 | ACTBL2 | Q562R1 | 786 |
| PFDN1 | TCP1 | P17987 | 716 |
| PFDN1 | PFN1 | P07737 | 635 |
| PFDN1 | CCT3 | P49368 | 607 |
| PFDN1 | UXT | Q9UBK9 | 572 |
| PFDN1 | YEATS4 | O95619 | 538 |
| PFDN1 | URI1 | O94763 | 536 |
| PFDN1 | TBCA | O75347 | 517 |
| PFDN1 | HBEGF | Q99075 | 477 |
| PFDN1 | ACTB | P02570 | 473 |
IntAct
136 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| PRKAG3 | PRKAB2 | psi-mi:“MI:0914”(association) | 0.800 |
| GIT1 | PFDN1 | psi-mi:“MI:0915”(physical association) | 0.750 |
| PFDN2 | PFDN1 | psi-mi:“MI:0915”(physical association) | 0.740 |
| PFDN1 | PFDN2 | psi-mi:“MI:0915”(physical association) | 0.740 |
| PFDN4 | PFDN6 | psi-mi:“MI:0914”(association) | 0.730 |
| VBP1 | PFDN6 | psi-mi:“MI:0914”(association) | 0.640 |
| MAPK7 | PFDN6 | psi-mi:“MI:0914”(association) | 0.640 |
| CCT2 | PPP6C | psi-mi:“MI:0914”(association) | 0.640 |
| PFDN1 | PFDN6 | psi-mi:“MI:0914”(association) | 0.640 |
| GNB1 | GNG7 | psi-mi:“MI:0914”(association) | 0.640 |
| DCAF12L2 | CETN3 | psi-mi:“MI:0914”(association) | 0.640 |
| DCAF7 | PFDN6 | psi-mi:“MI:0914”(association) | 0.570 |
| PFDN1 | DMAP1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| IMMT | PFDN1 | psi-mi:“MI:0915”(physical association) | 0.550 |
| GNB2 | PFDN6 | psi-mi:“MI:0914”(association) | 0.530 |
| DCAF5 | PFDN6 | psi-mi:“MI:0914”(association) | 0.530 |
| KLHDC2 | PFDN1 | psi-mi:“MI:0914”(association) | 0.530 |
| HDAC1 | PFDN6 | psi-mi:“MI:0914”(association) | 0.530 |
| SKIC8 | PFDN6 | psi-mi:“MI:0914”(association) | 0.530 |
| CCT6A | TXNDC9 | psi-mi:“MI:0914”(association) | 0.530 |
| ELSPBP1 | PFDN1 | psi-mi:“MI:0914”(association) | 0.530 |
| PFDN1 | ARHGAP32 | psi-mi:“MI:0914”(association) | 0.530 |
BioGRID (273): PFDN1 (Co-fractionation), PFDN2 (Co-fractionation), PFDN5 (Co-fractionation), PFDN6 (Co-fractionation), VBP1 (Co-fractionation), PFDN1 (Proximity Label-MS), PFDN1 (Proximity Label-MS), PFDN1 (Proximity Label-MS), PFDN1 (Affinity Capture-MS), PFDN1 (Affinity Capture-MS), PFDN1 (Affinity Capture-MS), PFDN1 (Affinity Capture-MS), PFDN1 (Affinity Capture-MS), PFDN1 (Affinity Capture-MS), PFDN1 (Affinity Capture-MS)
ESM2 similar proteins: A1A4P5, A7Y521, B0BN18, D3ZKU7, E2R766, F1LMZ8, F1LSG8, O00231, O08522, O55102, O60925, O70591, O75347, O88544, O94826, P48427, P48428, P80585, P97834, Q13098, Q2KI42, Q2NKW0, Q2TBU3, Q32L19, Q3SZ60, Q3SZA0, Q3SZE2, Q3T075, Q4R5E6, Q4SPU8, Q5D016, Q5RAM7, Q5RBL6, Q5ZKV9, Q5ZL19, Q61187, Q6I9Y2, Q6IRE4, Q6NRT5, Q6PEC1
Diamond homologs: O60925, Q17827, Q3SZE2, Q4SPU8, Q5D016, Q5RAM7, Q61SU8, Q94AF7, Q9CWM4, O14334, P46988, Q54JS0
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| PFDN1 | “form complex” | “Prefoldin co-chaperone” | binding |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 136 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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Prefoldin mediated transfer of substrate to CCT/TriC | 11 | 45.6× | 1e-13 |
| Formation of tubulin folding intermediates by CCT/TriC | 9 | 40.1× | 2e-10 |
| Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding | 9 | 38.6× | 2e-10 |
| Chaperonin-mediated protein folding | 9 | 28.5× | 3e-09 |
| Activation of AMPK downstream of NMDARs | 7 | 28.1× | 3e-07 |
| Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding | 8 | 25.3× | 7e-08 |
| Protein folding | 9 | 24.6× | 9e-09 |
| Selective autophagy | 7 | 20.5× | 3e-06 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| positive regulation of telomere maintenance via telomerase | 5 | 31.1× | 1e-04 |
| mitotic spindle organization | 5 | 11.5× | 7e-03 |
| mitotic cell cycle | 8 | 9.1× | 4e-04 |
| protein folding | 10 | 8.8× | 7e-05 |
| microtubule cytoskeleton organization | 8 | 8.2× | 7e-04 |
| protein stabilization | 11 | 6.2× | 3e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
18 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 9 |
| Likely benign | 1 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
655 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 5:140246053:TTCTG:T | acceptor_gain | 1.0000 |
| 5:140246055:CTG:C | acceptor_gain | 1.0000 |
| 5:140246058:C:CC | acceptor_gain | 1.0000 |
| 5:140281442:AACTT:A | donor_loss | 1.0000 |
| 5:140281443:ACTT:A | donor_loss | 1.0000 |
| 5:140281444:CTTAC:C | donor_loss | 1.0000 |
| 5:140281445:TTACT:T | donor_loss | 1.0000 |
| 5:140281446:TA:T | donor_loss | 1.0000 |
| 5:140281447:A:AC | donor_gain | 1.0000 |
| 5:140281447:ACT:A | donor_loss | 1.0000 |
| 5:140281447:ACTT:A | donor_gain | 1.0000 |
| 5:140281448:C:A | donor_loss | 1.0000 |
| 5:140281448:C:CA | donor_gain | 1.0000 |
| 5:140281448:CT:C | donor_gain | 1.0000 |
| 5:140281448:CTT:C | donor_gain | 1.0000 |
| 5:140281448:CTTC:C | donor_gain | 1.0000 |
| 5:140281448:CTTCT:C | donor_gain | 1.0000 |
| 5:140281450:T:TA | donor_gain | 1.0000 |
| 5:140281529:TAAAC:T | acceptor_gain | 1.0000 |
| 5:140281530:AAAC:A | acceptor_gain | 1.0000 |
| 5:140281531:AAC:A | acceptor_gain | 1.0000 |
| 5:140281533:CC:C | acceptor_loss | 1.0000 |
| 5:140281533:CCTA:C | acceptor_gain | 1.0000 |
| 5:140281534:C:CA | acceptor_loss | 1.0000 |
| 5:140281534:C:CC | acceptor_gain | 1.0000 |
| 5:140281536:A:C | acceptor_gain | 1.0000 |
| 5:140300410:ACTT:A | donor_loss | 1.0000 |
| 5:140300412:TTAC:T | donor_loss | 1.0000 |
| 5:140300413:TACAT:T | donor_loss | 1.0000 |
| 5:140300414:A:AC | donor_gain | 1.0000 |
AlphaMissense
810 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 5:140246021:C:G | A108P | 1.000 |
| 5:140281530:A:C | F68L | 1.000 |
| 5:140281530:A:T | F68L | 1.000 |
| 5:140281532:A:G | F68L | 1.000 |
| 5:140246005:C:G | R113P | 0.999 |
| 5:140281531:A:G | F68S | 0.999 |
| 5:140300422:C:T | G65E | 0.999 |
| 5:140300506:A:G | L37P | 0.999 |
| 5:140300569:A:G | L16P | 0.999 |
| 5:140300577:G:C | F13L | 0.999 |
| 5:140300577:G:T | F13L | 0.999 |
| 5:140300578:A:G | F13S | 0.999 |
| 5:140300579:A:G | F13L | 0.999 |
| 5:140303048:A:G | L9P | 0.999 |
| 5:140245996:A:G | L116P | 0.998 |
| 5:140245999:A:G | M115T | 0.998 |
| 5:140246008:A:C | I112S | 0.998 |
| 5:140246008:A:T | I112N | 0.998 |
| 5:140246041:A:G | L101P | 0.998 |
| 5:140281453:A:G | L94P | 0.998 |
| 5:140281495:A:G | L80P | 0.998 |
| 5:140300418:T:A | R66S | 0.998 |
| 5:140300418:T:G | R66S | 0.998 |
| 5:140300419:C:G | R66T | 0.998 |
| 5:140300422:C:A | G65V | 0.998 |
| 5:140300423:C:G | G65R | 0.998 |
| 5:140300423:C:T | G65R | 0.998 |
| 5:140300435:A:C | Y61D | 0.998 |
| 5:140300479:A:G | L46P | 0.998 |
| 5:140300486:C:G | A44P | 0.998 |
dbSNP variants (sampled 300 via entrez): RS1000058291 (5:140278453 C>G), RS1000184013 (5:140272324 T>A,C), RS1000299545 (5:140278760 G>C), RS1000323924 (5:140265286 G>A), RS1000360692 (5:140254152 A>C), RS1000376549 (5:140264960 A>C), RS1000449686 (5:140268674 TACTC>T), RS1000450364 (5:140302551 C>A), RS1000572815 (5:140273381 G>A), RS1000639290 (5:140272147 G>A), RS1000692913 (5:140266981 A>C), RS1000790080 (5:140281353 T>A,C), RS1000846859 (5:140274308 CAT>C), RS1000869100 (5:140251603 C>T), RS1000935433 (5:140259695 A>C)
Disease associations
OMIM: gene MIM:604897 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
5 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002817_7 | Alzheimer’s disease in APOE e4- carriers | 3.000000e-07 |
| GCST004246_1 | Alzheimer’s disease | 7.000000e-09 |
| GCST006268_511 | Reaction time | 2.000000e-09 |
| GCST008103_180 | Bipolar disorder | 9.000000e-06 |
| GCST008115_56 | Bipolar I disorder | 8.000000e-07 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0008393 | reaction time measurement |
| EFO:0009963 | bipolar I disorder |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: yes
ChEMBL targets (1): CHEMBL6067021 (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).
| pChembl | Type | Value | Unit | Molecule |
|---|---|---|---|---|
| 6.78 | Kd | 165.4 | nM | CHEMBL5653589 |
| 6.49 | ED50 | 326.7 | nM | CHEMBL5653589 |
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.
| Compound | Assay | Type | Value | Unit |
|---|---|---|---|---|
| 4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide | 2148979: Binding affinity to human PFDN1 incubated for 45 mins by Kinobead based pull down assay | kd | 0.1654 | uM |
CTD chemical–gene interactions
25 total (human), top 25 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Aflatoxin B1 | decreases methylation, increases methylation | 2 |
| aristolochic acid I | increases expression | 1 |
| alpha-pinene | affects cotreatment, increases oxidation, increases abundance | 1 |
| bisphenol A | increases expression | 1 |
| sodium arsenite | affects cotreatment, decreases expression, increases abundance | 1 |
| manganese chloride | increases abundance, affects cotreatment, decreases expression | 1 |
| methacrylaldehyde | affects cotreatment, increases oxidation, increases abundance | 1 |
| cylindrospermopsin | increases expression | 1 |
| CGP 52608 | increases reaction, affects binding | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | increases expression, affects cotreatment | 1 |
| ICG 001 | decreases expression | 1 |
| quinocetone | decreases expression | 1 |
| LDN 193189 | affects cotreatment, increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Acetaminophen | affects response to substance | 1 |
| Acrolein | affects cotreatment, increases oxidation, increases abundance | 1 |
| Air Pollutants | affects cotreatment, increases abundance, increases oxidation | 1 |
| Arsenic | increases abundance, affects cotreatment, decreases expression | 1 |
| Diuron | decreases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Manganese | decreases expression, increases abundance, affects cotreatment | 1 |
| Ozone | affects cotreatment, increases oxidation, increases abundance | 1 |
| Cadmium Chloride | increases expression | 1 |
| Volatile Organic Compounds | affects cotreatment, increases oxidation | 1 |
ChEMBL screening assays
1 unique, capped per target: 1 binding
Representative assays (with source publication via chembl_document):
| Assay ID | Type | Description | Source paper |
|---|---|---|---|
| CHEMBL5652021 | Binding | Binding affinity to human PFDN1 incubated for 45 mins by Kinobead based pull down assay | NVP-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.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.