PWP1

gene
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Also known as IEF-SSP-9502

Summary

PWP1 (PWP1 homolog, endonuclein, HGNC:17015) is a protein-coding gene on chromosome 12q23.3, encoding Periodic tryptophan protein 1 homolog (Q13610). Chromatin-associated factor that regulates transcription. It is a selective cancer dependency (DepMap: 83.5% of cell lines).

The protein encoded by this gene contains several WD-40 repeats and is found mostly in the nucleus. The expression and localization of this protein are cell cycle dependent. Expression of this gene is upregulated in pancreatic adenocarcinoma. Three transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 11137 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 70 total
  • Cancer dependency (DepMap): dependent in 83.5% of screened cell lines
  • MANE Select transcript: NM_007062

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17015
Approved symbolPWP1
NamePWP1 homolog, endonuclein
Location12q23.3
Locus typegene with protein product
StatusApproved
AliasesIEF-SSP-9502
Ensembl geneENSG00000136045
Ensembl biotypeprotein_coding
OMIM620055
Entrez11137

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000412830, ENST00000541166, ENST00000547120, ENST00000547995, ENST00000552760, ENST00000867450, ENST00000920793, ENST00000920794, ENST00000920795, ENST00000920796, ENST00000945394, ENST00000945395

RefSeq mRNA: 3 — MANE Select: NM_007062 NM_001317962, NM_001317963, NM_007062

CCDS: CCDS81735, CCDS9114

Canonical transcript exons

ENST00000412830 — 15 exons

ExonStartEnd
ENSE00000923100107692814107692899
ENSE00000923103107697467107697597
ENSE00000923104107699373107699434
ENSE00000923105107702935107703031
ENSE00000923106107703685107703746
ENSE00000923107107704636107704747
ENSE00000923108107708926107709016
ENSE00000923109107709111107709232
ENSE00000923110107710405107710510
ENSE00002270920107712111107713162
ENSE00002420342107685799107685971
ENSE00003471987107693000107693096
ENSE00003479325107688448107688506
ENSE00003499155107688615107688802
ENSE00003564677107696474107696584

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.9339 / max 553.9949, expressed in 1829 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
12785955.13301829
1278601.83961127
1278620.8354464
1278610.125931

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.86gold quality
oocyteCL:000002398.74gold quality
nippleUBERON:000203098.24gold quality
pylorusUBERON:000116696.85gold quality
cardia of stomachUBERON:000116296.29gold quality
tongue squamous epitheliumUBERON:000691996.00gold quality
renal medullaUBERON:000036295.74gold quality
pericardiumUBERON:000240795.25gold quality
calcaneal tendonUBERON:000370195.14gold quality
cortical plateUBERON:000534395.06gold quality
mammalian vulvaUBERON:000099795.05gold quality
ponsUBERON:000098895.01gold quality
parietal pleuraUBERON:000240095.01gold quality
urethraUBERON:000005794.99gold quality
pharyngeal mucosaUBERON:000035594.95gold quality
tibiaUBERON:000097994.92gold quality
mammary ductUBERON:000176594.89gold quality
epithelium of mammary glandUBERON:000324494.86gold quality
pleuraUBERON:000097794.82gold quality
saphenous veinUBERON:000731894.82gold quality
cauda epididymisUBERON:000436094.78gold quality
visceral pleuraUBERON:000240194.76gold quality
ventral tegmental areaUBERON:000269194.64gold quality
adult organismUBERON:000702394.47gold quality
penisUBERON:000098994.39gold quality
entorhinal cortexUBERON:000272894.37gold quality
cranial nerve IIUBERON:000094194.32gold quality
lateral nuclear group of thalamusUBERON:000273694.31gold quality
substantia nigra pars reticulataUBERON:000196694.30gold quality
superior surface of tongueUBERON:000737194.25gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.11

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

44 targeting PWP1, 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-548C-3P99.9974.017587
HSA-MIR-223-3P99.9970.141140
HSA-MIR-56899.9869.862084
HSA-MIR-433-3P99.9869.371203
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-365899.9673.874379
HSA-MIR-568099.9169.833421
HSA-MIR-4697-3P99.8967.091123
HSA-MIR-548AG99.7769.251492
HSA-MIR-62399.7668.161170
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-548AI99.6969.241494
HSA-MIR-548BA99.6969.141514
HSA-MIR-570-5P99.6969.241494
HSA-MIR-1212499.6869.172700
HSA-MIR-580-3P99.6769.231841
HSA-MIR-4762-5P99.5768.541424
HSA-MIR-312899.5067.851258
HSA-MIR-616599.4467.121389
HSA-MIR-377-3P99.3770.181905
HSA-MIR-542-3P99.3467.581270
HSA-MIR-431299.3467.30511
HSA-MIR-130A-5P99.3370.262623
HSA-MIR-4777-5P99.3367.531148
HSA-MIR-4477B99.2370.491733
HSA-MIR-6780B-3P99.1367.18622
HSA-MIR-1-5P98.7068.661017
HSA-MIR-797798.6566.182590

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 83.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Endonuclein interacts with several proteins indicating a broad function including signal transduction and chaperone activity (PMID:20028516)
  • High PWP1 expression is associated with head and neck squamous cell carcinoma. (PMID:29065309)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopwp1ENSDARG00000015921
mus_musculusPwp1ENSMUSG00000001785
rattus_norvegicusPwp1ENSRNOG00000005350
drosophila_melanogasternclbFBGN0263510
caenorhabditis_elegansWBGENE00021316

Protein

Protein identifiers

Periodic tryptophan protein 1 homologQ13610 (reviewed: Q13610)

Alternative names: Keratinocyte protein IEF SSP 9502

All UniProt accessions (3): B4DJV5, Q13610, F8VZ56

UniProt curated annotations — full annotation on UniProt →

Function. Chromatin-associated factor that regulates transcription. Regulates Pol I-mediated rRNA biogenesis and, probably, Pol III-mediated transcription. Regulates the epigenetic status of rDNA.

Subunit / interactions. Associates with the RNA polymerase (Pol I) complex. Interacts with POLR1E.

Subcellular location. Nucleus. Nucleolus. Chromosome.

Tissue specificity. High levels seen in the placenta, skeletal muscle, kidney and pancreas while lower levels were seen in the heart, brain and lung.

Similarity. Belongs to the WD repeat PWP1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13610-11yes
Q13610-22

RefSeq proteins (3): NP_001304891, NP_001304892, NP_008993* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR020472WD40_PAC1Repeat
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR044285PWP1Family

Pfam: PF00400

UniProt features (21 total): modified residue 8, repeat 7, splice variant 2, chain 1, sequence variant 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13610-F181.450.62

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 (8): 21, 50, 55, 57, 59, 86, 485, 494

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 228 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, MORF_MTA1, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GOBP_RIBOSOME_BIOGENESIS, GRUETZMANN_PANCREATIC_CANCER_DN, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GCM_NPM1, MORF_CDK2, MORF_HDAC2, GOBP_RRNA_TRANSCRIPTION, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, GCM_PPP1CC, MORF_RAF1, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION

GO Biological Process (8): DNA-templated transcription (GO:0006351), rRNA processing (GO:0006364), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901838), positive regulation of stem cell differentiation (GO:2000738), chromatin organization (GO:0006325), regulation of DNA-templated transcription (GO:0006355), ribosome biogenesis (GO:0042254)

GO Molecular Function (3): histone chaperone activity (GO:0140713), histone H4K20me3 reader activity (GO:1990889), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), chromosome (GO:0005694), nucleolus (GO:0005730), Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA-templated transcription2
intracellular membrane-bounded organelle2
intracellular membraneless organelle2
gene expression1
RNA biosynthetic process1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
regulation of DNA-templated transcription1
negative regulation of RNA biosynthetic process1
nucleolar large rRNA transcription by RNA polymerase I1
positive regulation of transcription by RNA polymerase I1
regulation of transcription of nucleolar large rRNA by RNA polymerase I1
positive regulation of cell differentiation1
stem cell differentiation1
regulation of stem cell differentiation1
cellular component organization1
regulation of gene expression1
regulation of RNA biosynthetic process1
ribonucleoprotein complex biogenesis1
histone binding1
protein carrier activity1
histone H4 reader activity1
binding1
nuclear lumen1
cytoplasm1
endomembrane system1

Protein interactions and networks

STRING

2398 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PWP1EBNA1BP2Q99848860
PWP1TBL3Q12788720
PWP1PDCD11Q14690709
PWP1PWP2Q15269678
PWP1WDR12Q9GZL7673
PWP1NSA2O95478663
PWP1RPF2Q9H7B2601
PWP1WDR3Q9UNX4598
PWP1TYW1Q9NV66575
PWP1GNL2Q13823562
PWP1RRP15Q9Y3B9558
PWP1UTP6Q9NYH9550
PWP1RSL24D1Q9UHA3503
PWP1SDF2L1Q9HCN8491
PWP1BRIX1Q8TDN6491

IntAct

103 interactions, top by confidence:

ABTypeScore
FBLNOP56psi-mi:“MI:0914”(association)0.800
TUBG1TUBG1psi-mi:“MI:2364”(proximity)0.760
PWP1ANK3psi-mi:“MI:0914”(association)0.530
RPL7ANVLpsi-mi:“MI:0914”(association)0.530
EN1NFIBpsi-mi:“MI:2364”(proximity)0.470
ESR2FBLL1psi-mi:“MI:0914”(association)0.460
PWP1DAPK1psi-mi:“MI:0407”(direct interaction)0.440
H3C1SMCHD1psi-mi:“MI:2364”(proximity)0.410
PWP1TNS2psi-mi:“MI:0915”(physical association)0.370
PIK3R3PWP1psi-mi:“MI:0915”(physical association)0.370
HOXA3PWP1psi-mi:“MI:0915”(physical association)0.370
NFYAPWP1psi-mi:“MI:0915”(physical association)0.370
Srp72psi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
C9orf72CHD2psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
CUL1LGALS8psi-mi:“MI:0914”(association)0.350
CUL4AHAX1psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
NEDD8DDX3Xpsi-mi:“MI:0914”(association)0.350
COPS6DDX3Xpsi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
RPL15PRMT5psi-mi:“MI:0914”(association)0.350
PTPRRTCP1psi-mi:“MI:0914”(association)0.350
TSPYL5CBX4psi-mi:“MI:0914”(association)0.350
repNOP56psi-mi:“MI:0914”(association)0.350

BioGRID (500): PWP1 (Affinity Capture-MS), PWP1 (Affinity Capture-MS), PWP1 (Affinity Capture-MS), FBL (Co-fractionation), GTPBP4 (Co-fractionation), KIAA0020 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), PWP1 (Co-fractionation), TOP1 (Co-fractionation)

ESM2 similar proteins: A1L112, A4IHS2, A8NZM5, B2ZZS9, O00423, O80775, O95834, P93107, P97452, Q05BC3, Q0DYP5, Q13216, Q13610, Q13685, Q15269, Q1JQD2, Q2HJ56, Q32KQ2, Q32P44, Q3SZK1, Q4V8C3, Q562C2, Q58DT8, Q5BIM8, Q5F3K4, Q5R9T6, Q5RCG7, Q5RFQ3, Q5VU92, Q5XI13, Q5ZK69, Q6DRF9, Q6P6T4, Q6PFM9, Q7TNG5, Q7YR70, Q810D6, Q8BH57, Q8BHB4, Q8BU03

Diamond homologs: A1Z8D0, O17468, Q13610, Q2HJ56, Q54YD8, Q99LL5, Q9P775, P21304, Q5R1S9, A5GFN6, A7EZJ5, O13923, O13985, O14435, O35353, O93277, O94620, P29387, P54311, P62871, P62872, P62873, P62874, P78406, P79959, Q04199, Q13112, Q3MV14, Q3SWS8, Q4IBR4, Q4R6D2, Q5E9A4, Q5FVA9, Q5GIS3, Q5R5W8, Q5RF99, Q6PH57, Q6ZD63, Q7RZI0, Q7ZWF0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 138 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
Constitutive Signaling by Aberrant PI3K in Cancer78.8×6e-03
PIP3 activates AKT signaling96.0×6e-03

GO biological processes:

GO termPartnersFoldFDR
peptidyl-tyrosine phosphorylation516.6×1e-03
cell surface receptor protein tyrosine kinase signaling pathway1013.7×2e-06
regulation of autophagy59.5×9e-03
neuron differentiation107.9×1e-04
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction127.4×2e-05
gene expression95.7×3e-03
protein stabilization105.3×2e-03
positive regulation of MAPK cascade85.1×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1809 predictions. Top by Δscore:

VariantEffectΔscore
12:107685972:G:GCdonor_loss1.0000
12:107685973:T:Gdonor_loss1.0000
12:107688445:CA:Cacceptor_loss1.0000
12:107688446:A:AGacceptor_gain1.0000
12:107688447:G:GAacceptor_gain1.0000
12:107688447:GGT:Gacceptor_gain1.0000
12:107688447:GGTA:Gacceptor_gain1.0000
12:107688502:TTGCA:Tdonor_gain1.0000
12:107688503:TGCA:Tdonor_gain1.0000
12:107688504:GCA:Gdonor_gain1.0000
12:107688504:GCAG:Gdonor_gain1.0000
12:107688505:CA:Cdonor_gain1.0000
12:107688506:AG:Adonor_loss1.0000
12:107688507:G:Cdonor_loss1.0000
12:107688507:G:GGdonor_gain1.0000
12:107688508:TAA:Tdonor_loss1.0000
12:107688604:T:Aacceptor_gain1.0000
12:107688606:T:TAacceptor_gain1.0000
12:107688611:A:AGacceptor_gain1.0000
12:107688612:T:Gacceptor_gain1.0000
12:107688613:A:AGacceptor_gain1.0000
12:107688614:G:GCacceptor_gain1.0000
12:107688614:GA:Gacceptor_gain1.0000
12:107688614:GAGA:Gacceptor_gain1.0000
12:107688614:GAGAA:Gacceptor_gain1.0000
12:107688738:G:GTdonor_gain1.0000
12:107688759:GGC:Gdonor_gain1.0000
12:107688760:GC:Gdonor_gain1.0000
12:107688761:C:Gdonor_gain1.0000
12:107688765:G:GGdonor_gain1.0000

AlphaMissense

3322 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:107697479:C:AA209D1.000
12:107699404:T:AV259D1.000
12:107702948:A:CS274R1.000
12:107702950:T:AS274R1.000
12:107702950:T:GS274R1.000
12:107702978:T:AW284R1.000
12:107702978:T:CW284R1.000
12:107704718:T:AW350R1.000
12:107704718:T:CW350R1.000
12:107709122:A:CS394R1.000
12:107709124:C:AS394R1.000
12:107709124:C:GS394R1.000
12:107697511:T:AW220R0.999
12:107697511:T:CW220R0.999
12:107702946:C:AA273E0.999
12:107702954:T:CS276P0.999
12:107702960:G:CD278H0.999
12:107702980:G:CW284C0.999
12:107702980:G:TW284C0.999
12:107703686:T:AV302D0.999
12:107703700:T:CF307L0.999
12:107703702:T:AF307L0.999
12:107703702:T:GF307L0.999
12:107703725:T:CL315P0.999
12:107703734:G:AG318D0.999
12:107708929:A:CS361R0.999
12:107708931:T:AS361R0.999
12:107708931:T:GS361R0.999
12:107708942:G:AG365D0.999
12:107708942:G:TG365V0.999

dbSNP variants (sampled 300 via entrez): RS1000061216 (12:107689739 C>G), RS1000076371 (12:107693991 A>G), RS1000112495 (12:107711187 G>A), RS1000156109 (12:107701361 C>T), RS1000194906 (12:107710910 T>A,C), RS1000209346 (12:107701108 G>A), RS1000246255 (12:107695091 T>A), RS1000274163 (12:107695139 G>A), RS1000407001 (12:107695421 A>C), RS1000696119 (12:107684397 G>A,C,T), RS1000725161 (12:107684037 G>C), RS1000784263 (12:107687617 C>A,T), RS1000846879 (12:107691051 A>G), RS1000907280 (12:107706817 T>C), RS1001012369 (12:107697003 G>T)

Disease associations

OMIM: gene MIM:620055 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST002481_2Acne (severe)5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression2
sodium arsenitedecreases expression2
Cyclosporinedecreases expression, increases expression2
FR900359affects phosphorylation1
dicrotophosdecreases expression1
geranioldecreases expression1
ochratoxin Adecreases acetylation, decreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
chromium hexavalent ionaffects expression1
bisphenol Sincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Diethylstilbestroldecreases expression1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Potassium Dichromateincreases expression1
Quercetindecreases expression1
Seleniumaffects cotreatment, decreases expression1
Tretinoindecreases expression1
Valproic Acidaffects expression1
Vitamin Eaffects cotreatment, decreases expression1
Cadmium Chloridedecreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): acne