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PCNP

gene
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Summary

PCNP (PEST proteolytic signal containing nuclear protein, HGNC:30023) is a protein-coding gene on chromosome 3q12.3, encoding PEST proteolytic signal-containing nuclear protein (Q8WW12). May be involved in cell cycle regulation. It is a selective cancer dependency (DepMap: 10.8% of cell lines).

Involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Located in nuclear body.

Source: NCBI Gene 57092 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 26 total
  • Regional missense constraint (gnomAD): 1 of 4 regions constrained (≈10% of expected missense variation)
  • GTEx eGene: eQTL in 11 tissues, sQTL in 24 (q < 0.05)
  • Cancer dependency (DepMap): dependent in 10.8% of screened cell lines
  • Constraint (gnomAD): pLI 0.43 (intermediate), LOEUF 0.85 (unconstrained)
  • MANE Select transcript: NM_020357

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30023
Approved symbolPCNP
NamePEST proteolytic signal containing nuclear protein
Location3q12.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000081154
Ensembl biotypeprotein_coding
OMIM615210
Entrez57092

Gene structure

Transcript identifiers

Ensembl transcripts: 49 — 23 protein_coding, 23 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000265260

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 2: 4, TSL 5: 1

ENST00000265260, ENST00000460231, ENST00000465366, ENST00000469941, ENST00000470490, ENST00000486406, ENST00000498274, ENST00000627393, ENST00001004334, ENST00001004335, ENST00001004336, ENST00001004337, ENST00001004338, ENST00001049372, ENST00001049374, ENST00001049375, ENST00001049377, ENST00001049378, ENST00001049379, ENST00001049380, ENST00001049383, ENST00001069231, ENST00001069232, ENST00001069233, ENST00001069234, ENST00001069235, ENST00001069237, ENST00001069238, ENST00001069240, ENST00001069241, ENST00001069242, ENST00001069243, ENST00001069244, ENST00001069246, ENST00001102601, ENST00001102602, ENST00001102603, ENST00001102604, ENST00001102605, ENST00001102606, ENST00001102607, ENST00001102608, ENST00001102609, ENST00001102610, ENST00001129449, ENST00001129450, ENST00001129451, ENST00001129452, ENST00001140041

RefSeq mRNA: 7 — MANE Select: NM_020357 NM_001320395, NM_001320397, NM_001320398, NM_001320399, NM_001320400, NM_001320401, NM_020357

CCDS: CCDS2942

Canonical transcript exons

ENST00000265260 — 5 exons

ExonStartEnd
ENSE00001837860101574180101574279
ENSE00003515634101585437101585511
ENSE00003588145101590215101590270
ENSE00003620981101579790101580004
ENSE00003892584101592627101594465

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 98.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.1000 / max 709.1135, expressed in 1807 samples.

Highest expression (Bgee): calcaneal tendon, endothelial cell, cerebellar vermis, upper leg skin, endometrium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PCNP is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 11 tissues and its splicing (sQTL) in 24 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 35 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Artery Tibialsqtl1.8e-19+0.563:101582031:C:T
Esophagus Muscularissqtl1.4e-10-0.453:101598786:TAATC:T
Muscle Skeletalsqtl2.7e-10+0.393:101556067:G:C
Nerve Tibialsqtl2.0e-09-0.363:101595529:C:T
Thyroidsqtl4.3e-08+0.383:101586234:G:A
Adipose Subcutaneoussqtl7.9e-08+0.393:101427518:A:C
Breast Mammary Tissuesqtl1.4e-06-0.393:101613885:T:A
Brain Anterior cingulate cortex BA24sqtl3.4e-06+0.623:101401186:G:T
Heart Atrial Appendagesqtl1.7e-05+0.423:101536880:A:C
Brain Hypothalamussqtl6.6e-04+0.573:101575728:C:T
Skin Sun Exposed Lower legsqtl2.5e-03+0.293:101586326:T:G
Whole Bloodeqtl2.7e-03-0.063:101251218:A:G
Brain Frontal Cortex BA9sqtl3.9e-03-0.463:101607971:C:T
Cells Cultured fibroblastssqtl4.5e-03+0.183:101575728:C:T
Adipose Visceral Omentumsqtl5.2e-03-0.293:101595529:C:T
Brain Nucleus accumbens basal gangliasqtl5.5e-03+0.453:101562865:A:G
Brain Amygdalaeqtl6.0e-03-0.193:101193560:G:GGC
Lungsqtl7.8e-03+0.293:101555163:C:T
Testissqtl9.5e-03-0.303:101607971:C:T
Artery Tibialeqtl1.1e-02-0.073:101634904:A:AGAG

FANTOM5 promoters

3 alternative TSS:

Promoter IDTPM avgSamples expressed
3764231.63641807
376440.3197116
376430.144043

Top tissues by expression

showing 100 of 297 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370198.74gold quality
endothelial cellCL:000011598.62gold quality
cerebellar vermisUBERON:000472098.57gold quality
upper leg skinUBERON:000426298.54gold quality
endometriumUBERON:000129598.51gold quality
skin of hipUBERON:000155498.41gold quality
mucosa of stomachUBERON:000119998.29gold quality
ganglionic eminenceUBERON:000402398.28gold quality
monocyteCL:000057698.27gold quality
ventricular zoneUBERON:000305398.25gold quality
mononuclear cellCL:000084298.23gold quality
urethraUBERON:000005798.14gold quality
seminal vesicleUBERON:000099898.14gold quality
blood vessel layerUBERON:000479798.14gold quality
popliteal arteryUBERON:000225098.13gold quality
tibial arteryUBERON:000761098.13gold quality
leukocyteCL:000073898.10gold quality
left ovaryUBERON:000211998.08gold quality
ponsUBERON:000098897.98gold quality
endocervixUBERON:000045897.97gold quality
ovaryUBERON:000099297.97gold quality
mammary ductUBERON:000176597.97gold quality
gall bladderUBERON:000211097.97gold quality
descending thoracic aortaUBERON:000234597.96gold quality
body of uterusUBERON:000985397.95gold quality
uterusUBERON:000099597.94gold quality
smooth muscle tissueUBERON:000113597.94gold quality
aortaUBERON:000094797.92gold quality
right lungUBERON:000216797.88gold quality
right coronary arteryUBERON:000162597.83gold quality
synovial jointUBERON:000221797.83gold quality
C1 segment of cervical spinal cordUBERON:000646997.82gold quality
lower esophagus muscularis layerUBERON:003583397.82gold quality
peripheral nervous systemUBERON:000001097.81gold quality
nerveUBERON:000102197.81gold quality
tibial nerveUBERON:000132397.81gold quality
lower esophagusUBERON:001347397.81gold quality
substantia nigra pars compactaUBERON:000196597.80gold quality
esophagogastric junction muscularis propriaUBERON:003584197.80gold quality
lymph nodeUBERON:000002997.79gold quality
rectumUBERON:000105297.76gold quality
right ovaryUBERON:000211897.76gold quality
penisUBERON:000098997.72gold quality
hypothalamusUBERON:000189897.72gold quality
tendonUBERON:000004397.71gold quality
colonic epitheliumUBERON:000039797.71gold quality
spinal cordUBERON:000224097.71gold quality
cerebellar cortexUBERON:000212997.70gold quality
choroid plexus epitheliumUBERON:000391197.70gold quality
muscle layer of sigmoid colonUBERON:003580597.70gold quality
cerebellar hemisphereUBERON:000224597.68gold quality
amygdalaUBERON:000187697.66gold quality
nucleus accumbensUBERON:000188297.66gold quality
anterior cingulate cortexUBERON:000983597.65gold quality
thoracic aortaUBERON:000151597.64gold quality
cerebellumUBERON:000203797.63gold quality
cingulate cortexUBERON:000302797.63gold quality
ascending aortaUBERON:000149697.62gold quality
medial globus pallidusUBERON:000247797.61gold quality
embryoUBERON:000092297.60gold quality
left coronary arteryUBERON:000162697.59gold quality
dorsolateral prefrontal cortexUBERON:000983497.59gold quality
cauda epididymisUBERON:000436097.57gold quality
myometriumUBERON:000129697.56gold quality
islet of LangerhansUBERON:000000697.55gold quality
trigeminal ganglionUBERON:000167597.53gold quality
urinary bladderUBERON:000125597.52gold quality
subthalamic nucleusUBERON:000190697.52gold quality
thoracic mammary glandUBERON:000520097.52gold quality
mammary glandUBERON:000191197.50gold quality
globus pallidusUBERON:000187597.47gold quality
Brodmann (1909) area 9UBERON:001354097.47gold quality
epithelium of mammary glandUBERON:000324497.46gold quality
body of pancreasUBERON:000115097.45gold quality
coronary arteryUBERON:000162197.44gold quality
female reproductive systemUBERON:000047497.42gold quality
germinal epithelium of ovaryUBERON:000130497.41gold quality
ectocervixUBERON:001224997.41gold quality
right hemisphere of cerebellumUBERON:001489097.40gold quality
prefrontal cortexUBERON:000045197.39gold quality
left uterine tubeUBERON:000130397.38gold quality
trabecular bone tissueUBERON:000248397.38gold quality
superior vestibular nucleusUBERON:000722797.38gold quality
caudate nucleusUBERON:000187397.36gold quality
saphenous veinUBERON:000731897.35gold quality
corpus callosumUBERON:000233697.32gold quality
caecumUBERON:000115397.30gold quality
vermiform appendixUBERON:000115497.30gold quality
vena cavaUBERON:000408797.30gold quality
thyroid glandUBERON:000204697.29gold quality
lower lobe of lungUBERON:000894997.27gold quality
pigmented layer of retinaUBERON:000178297.23gold quality
subcutaneous adipose tissueUBERON:000219097.22gold quality
cortical plateUBERON:000534397.22gold quality
retinaUBERON:000096697.21gold quality
parietal pleuraUBERON:000240097.21gold quality
connective tissueUBERON:000238497.19gold quality
adipose tissueUBERON:000101397.18gold quality
substantia nigra pars reticulataUBERON:000196697.15gold quality
left lobe of thyroid glandUBERON:000112097.13gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-10yes3.93
E-MTAB-6386no363.63
E-ANND-3no0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Corpus callosumtissue119.2
Midbraintissue96.5
Thalamustissue96.5
Spinal cordtissue93.8
Cerebellumtissue91.9high
Ponstissue91.3
Putamentissue90.0
Cerebral cortextissue88.8medium
Somatosensory cortextissue88.8
Substantia nigratissue88.6
Occipital cortextissue86.5
Medulla oblongatatissue85.7
Superior colliculitissue84.9
Septumtissue81.2
Prefrontal cortextissue79.3
Motor cortextissue79.0
Hippocampal formationtissue78.4
Entorhinal cortextissue78.4
Ventral forebraintissue78.4
Hypothalamustissue78.2
Olfactory bulbtissue77.6
Temporal cortextissue77.1
Retrosplenial cortextissue77.0
Retrosplenial and cingulate cortextissue76.4
Periaqueductal graytissue76.1
Amygdalatissue70.4
Insular cortextissue67.0
Basal gangliatissue64.6medium
Ovarytissue62.9medium
Skeletal muscletissue62.3high
Tonguetissue62.0
Choroid plexustissue61.2
Bone marrowtissue55.4medium
Heart muscletissue54.0low
Thymustissue54.0
Retinatissue53.9
Tonsiltissue53.9high
Lymph nodetissue53.6high
Frontal cortextissue52.9
Endometrium 1tissue50.3medium
Breasttissue50.1medium
Smooth muscletissue49.9medium
Epididymistissue49.7high
Kidneytissue48.5high
Placentatissue47.5high
Urinary bladdertissue47.4high
Parathyroid glandtissue47.1medium
Thyroid glandtissue46.6medium
Livertissue46.4low
Seminal vesicletissue46.2high
Cervixtissue45.4high
Esophagustissue45.1high
Adrenal glandtissue44.9high
Prostatetissue44.6medium
Adipose tissuetissue44.1medium
Rectumtissue42.5high
Vaginatissue41.3high
Fallopian tubetissue41.2high
Appendixtissue41.1high
Postcentral gyrustissue40.4

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — White matter (119.2), Ventral spinal cord (93.8), Dorsal spinal cord (86.6), Subiculum (77.3), Dorsal hippocampus (73.1).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PCNP by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 149 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3646100.0073.565283
HSA-MIR-4262100.0073.263931
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-3163100.0077.238605
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-3613-3P100.0076.367965
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-9-5P100.0072.282361
HSA-MIR-366299.9973.825684
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-539-3P99.9870.741616
HSA-MIR-485-3P99.9870.681585
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-480399.9871.993117
HSA-MIR-60799.9773.625593
HSA-MIR-568899.9673.234504
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-495-3P99.9672.814197
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AJ-3P99.9673.385345

Functional genomics

gnomAD constraint: pLI 0.43, LOEUF 0.852, missense Z 0.422 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000265260 splits into 4 regions with different missense tolerance; 1 is missense-constrained (≈10% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
3:101,574,216–101,574,27543 / 26.61.62no
3:101,574,276–101,579,8436 / 21.80.28yes (p 7.1e-04)
3:101,579,844–101,579,93446 / 39.31.17no
3:101,579,935–101,592,75066 / 127.80.52no
DepMap (CRISPR cell-line fitness): dependent in 10.8% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): A427 (-0.983), HEC-265 (-0.898), CAL-72 (-0.873), HEC-6 (-0.853), NCI-H226 (-0.845), CI (-0.82), COLO 684 (-0.814), SNU-16 (-0.791), 93T449 (-0.789), SK-HEP-1 (-0.765), 23132/87 (-0.765), SCH (-0.762), NB6 (-0.758), EW-22 (-0.74), MFE-296 (-0.736).

Literature-anchored findings (GeneRIF, showing 5)

  • NIRF has ubiquitination activity, the hallmark of a ubiquitin ligase. PCNP was readily ubiquitinated in 293 and COS-7 cells, and NIRF ubiquitinated PCNP in vitro as well as in vivo. (PMID:14741369)
  • PCNP mediates the proliferation, migration, and invasion of human neuroblastoma cells through mitogen-activated protein kinase and PI3K/AKT/mTOR signaling pathways, implying that PCNP is a therapeutic target for patients with neuroblastoma. (PMID:29716528)
  • PCNP promotes ovarian cancer progression by accelerating beta-catenin nuclear accumulation and triggering EMT transition. (PMID:32548978)
  • TIPE2 and PCNP expression abnormalities in peripheral blood mononuclear cells associated with disease activity in rheumatoid arthritis: a meta-analysis. (PMID:33629294)
  • PCNP is a novel regulator of proliferation, migration, and invasion in human thyroid cancer. (PMID:35813472)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriopcnpENSDARG00000037713
ENSDARG00000116774
mus_musculusPcnpENSMUSG00000071533
rattus_norvegicusPcnpENSRNOG00000028411

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1923552) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 15 distinct phenotype terms.

Mouse phenotype (MP)Records
abnormal heart morphology1
abnormal embryo turning1
abnormal skin morphology1
abnormal neural tube morphology1
abnormal epididymis morphology1
abnormal pharyngeal arch morphology1
abnormal forebrain development1
abnormal optic vesicle formation1
abnormal neural tube closure1
abnormal midbrain development1
embryonic growth retardation1
enlarged epididymis1
abnormal otic vesicle morphology1
preweaning lethality, complete penetrance1
prenatal lethality prior to heart atrial septation1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Bos taurusQ32PF395.5%Diamond
Pongo abeliiQ5RCI994.9%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
TRMT10Cprotein-coding54931
ZBTB11-AS1ncRNA100009676
ZBTB11protein-coding27107
SENP7protein-coding57337

Protein

Protein identifiers

PEST proteolytic signal-containing nuclear protein — Q8WW12 (reviewed: Q8WW12)

All UniProt accessions (3): A0A0B4J1Z9, Q8WW12, G5E9V9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in cell cycle regulation.

Subunit / interactions. Interacts with UHRF2/NIRF.

Subcellular location. Nucleus.

Post-translational modifications. Ubiquitinated; mediated by UHRF2 and leading to its subsequent proteasomal degradation. N-terminally acetylated in a HYPK-dependent manner by the NatA acetyltransferase complex which is composed of NAA10 and NAA15.

Isoforms (3)

UniProt IDNamesCanonical?
Q8WW12-11yes
Q8WW12-22
Q8WW12-33

RefSeq proteins (7): NP_001307324, NP_001307326, NP_001307327, NP_001307328, NP_001307329, NP_001307330, NP_065090* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR029169PCNPFamily

Pfam: PF15473

UniProt features (23 total): modified residue 10, compositionally biased region 4, splice variant 3, region of interest 2, sequence conflict 2, initiator methionine 1, chain 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WW12-F163.430.00

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; nuclear bodies

Antibody reliability (HPA): IH supported · IF enhanced

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 (10)

TypePositions
N6-acetyllysine64, 150, 152
Phosphoserine77, 87, 119, 147, 53
Phosphothreonine139
N-acetylalanine2

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 140 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, AGGAAGC_MIR5163P, TTTGTAG_MIR520D, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGCATT_MIR365, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, MODULE_48, DANG_BOUND_BY_MYC, MODULE_95, GOBP_PROTEIN_CATABOLIC_PROCESS, GOCC_NUCLEAR_BODY, CGTSACG_PAX3_B, GOBP_PROTEOLYSIS

GO Biological Process (2): protein ubiquitination (GO:0016567), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear body (GO:0016604)

GO top-level categories

9 GO namespaces:

CategoryTerms
protein modification by small protein conjugation1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
nucleoplasm1
intracellular membraneless organelle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 6 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO termNSEvidence
proteasome-mediated ubiquitin-dependent protein catabolic processBPdirect assay
protein ubiquitinationBPdirect assay
nuclear bodyCCdirect assay
nucleoplasmCCdirect assay
nucleusCCdirect assay

Protein interactions and networks

STRING

showing 15 of 1,422 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
PCNPHYPKQ9NX55536
PCNPPOLIQ9UNA4509
PCNPUHRF2Q96PU4498
PCNPTULP4Q9NRJ4440
PCNPKLHL2O95198433
PCNPNAA50Q9GZZ1422
PCNPSLC23A3Q6PIS1401
PCNPNPPCP23582398
PCNPFOCADQ5VW36398
PCNPTMEM209Q96SK2398
PCNPBPNT1O95861385
PCNPANAPC15P60006381
PCNPHECW2Q9P2P5370
PCNPUBE3CQ15386370
PCNPCINPQ9BW66369

IntAct

Human interaction partners of PCNP in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

5 partners by confidence:

PartnerInteraction typeMIscoreRecords
KLK6physical association0.5603
TERF2IPphysical association0.5102
HNRNPDLphysical association0.4001
ECE1physical association0.3701
PAPSS2association0.3501

BioGRID (118 interactions; top human partners by supporting records): UHRF2 (Affinity Capture-MS; 5 records), GRIPAP1 (Cross-Linking-MS (XL-MS); 2 records), MYC (Proximity Label-MS; 2 records), YAP1 (Proximity Label-MS; 2 records), ACOT7 (Affinity Capture-MS), AHSA1 (Co-fractionation), ATG16L1 (Affinity Capture-MS), BCL6 (Affinity Capture-MS), BMI1 (Affinity Capture-MS), BPNT1 (Affinity Capture-MS), BRD4 (Affinity Capture-MS), C9orf89 (Affinity Capture-MS), CAND1 (Affinity Capture-MS), CD274 (Affinity Capture-MS), CDC42 (Reconstituted Complex)

SIGNOR signaling

1 signaling interactions:

AEffectBMechanism
UHRF2“down-regulates quantity by destabilization”PCNPpolyubiquitination

Disease & clinical

Genetic variants

Variant evidence for PCNP: 26 ClinVar records (0 pathogenic / likely pathogenic); 1 GWAS association.

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance17
Likely benign0
Benign2

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 33 predictions of 542):

Position(s)EffectΔscoreSites
3:101585423acceptor_gain1.0000
3:101585512–101585513donor_loss1.00006
3:101590213–101590214acceptor_loss1.00004
3:101590268donor_gain1.0000
3:101590271–101590272donor_loss1.00005
3:101592621acceptor_gain1.0000
3:101592624acceptor_gain1.0000
3:101592625–101592626acceptor_loss1.00003
3:101580005–101580006donor_loss0.99005
3:101585435–101585436acceptor_loss0.99006

AlphaMissense

579 missense substitutions predicted likely pathogenic (of 1,162 scored), across 123 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M13290.9981.000
M12490.9951.000
M13090.9951.000
N13481.0001.000
F15580.9991.000
F11380.9961.000
N14680.9900.999
D15780.9880.998
F14880.9821.000
N14980.9270.999
D13880.9090.995
D11880.8910.993
H15380.8420.992
D11680.7830.970
K15070.9981.000
R13170.9971.000
W16270.9960.999
E12270.9950.997
R13770.9951.000
E12370.9920.998

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

CancerPrognosticp-value
Liver Hepatocellular Carcinoma (TCGA)unfavorable6.49e-06
Kidney Renal Clear Cell Carcinoma (TCGA)favorable1.78e-05
Glioblastoma Multiforme (validation)unfavorable0.000417
Pancreatic Adenocarcinoma (validation)unfavorable0.000812

Disease associations

OMIM: gene MIM:615210 | disease phenotypes:

GWAS associations

1 associations:

StudyTraitp-value
GCST008839_283Height7e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067190 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL5653589KD1440 nM

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.70Kd198.9nMCHEMBL5653589
6.70ED50198.9nMCHEMBL5653589

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.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148949: Binding affinity to human PCNP incubated for 45 mins by Kinobead based pull down assaykd0.1989uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression3
sodium arsenitedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression, affects localization, increases expression1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
manganese chlorideincreases abundance, increases expression1
chloropicrinaffects expression1
bisphenol Bincreases expression1
2,2’,4,4’-tetrabromodiphenyl etheraffects expression, affects methylation1
jinfukangdecreases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Air Pollutantsaffects expression, increases abundance1
Aspirinincreases expression1
Benztropineincreases expression1
Cadmiumincreases expression1
Caffeinedecreases phosphorylation1
Clozapineincreases expression1
Diurondecreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydedecreases expression1
Furaldehydeaffects cotreatment, increases expression1
Ivermectindecreases expression1
Ketoconazoledecreases expression1
Manganeseincreases expression, increases abundance1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651991BindingBinding affinity to human PCNP incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — *ChemMedChem*

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B3DKAbcam HEK293T PCNP KOTransformed cell lineFemale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for PCNP across ~30M SureChEMBL compounds — explore on Sugi Predict.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Built deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source. Provided for research and reference, not medical advice or a diagnosis. Data may be incomplete, especially for rare conditions. Consult a qualified clinician.

Generated
Atlas version
v1.12.2
BioBTree
v2.16.1

Sources 95

This page pulls from 95 datasets indexed by BioBTree:

alliance_phenotypealphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruscellphonedbchembl_activitychembl_assaychembl_documentchembl_mechanismchembl_moleculechembl_targetciviccivic_assertioncivic_evidencecivic_variantclingen_dosageclingen_gene_validityclingen_variantclinical_trialsclinvarcollectricorumctd_gene_interactiondepmapdepmap_dependencydiamond_similarityefoensemblentrezexonfantom5_genefantom5_promotergenccgenerifgnomad_constraintgnomad_rmcgogoparentgtex_egenegtopdbgwasgwas_studyhgnchpahpa_expressionhpa_pathologyhpointactinterprointogenjasparmeshmgimimmirdbmondomsigdbneighborentrezorphanetorthologorthologentrezpanelapp_geneparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_var_annotationpharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontaxonomytranscriptufeatureuniprot