PCNP
protein-codingPEST proteolytic signal containing nuclear protein
Gene summary
Involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Located in nuclear body. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PCNP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020357.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 16 | 1 | 17 | |||
| nonsense | 1 | 1 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 22 | 0 | 1 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065090.1 | 5 | MANE Select | |
| Ensembl | ENSP00000265260.3 | 5 | MANE Select | |
| RefSeq | NP_001307324.1 | 4 | Standard | |
| RefSeq | NP_001307326.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell cycle
- protein ubiquitination
- proteasome-mediated ubiquitin-dependent protein catabolic process
Molecular Function
- protein binding
Cellular Component
- nucleus
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000265260
- Coding exons
- 5
- Length
- 20343
- Individuals with no LoFs
- 125106
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125107
- p
- 0.00000400
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 62 | 93.8 | 0.661 | 0.00000454 | 1157 |
| Missense (PolyPhen) | 11 | 14.131 | 0.77845 | 208 | ||
| Synonymous | -0.0982 | 33 | 32.3 | 1.02 | 0.00000167 | 343 |
| Loss of Function | 2.55 | 1 | 9.45 | 0.106 | 5.65e-7 | 116 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in cell cycle regulation.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- RVIS EVS
- 0.5
- RVIS percentile EVS
- 79.79
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |