PCNP

PEST proteolytic signal containing nuclear protein

Basic information

Region (hg38): 3:101574180-101594465

Links

ENSG00000081154 ∙ NCBI:57092 ∙ OMIM:615210 ∙ HGNC:30023 ∙ Uniprot:Q8WW12 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCNP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2			2
Total	0	0	12	0	1

Variants in PCNP

This is a list of pathogenic ClinVar variants found in the PCNP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-101574240-G-C		not specified	Uncertain significance (Nov 17, 2022)
3-101574241-A-T		not specified	Uncertain significance (Dec 07, 2021)
3-101574245-G-C		not specified	Uncertain significance (Dec 16, 2021)
3-101574245-G-T		not specified	Uncertain significance (Jul 25, 2024)
3-101574253-A-G			Benign (Jun 26, 2018)
3-101579886-C-T		not specified	Uncertain significance (Jan 16, 2024)
3-101579909-C-G		not specified	Uncertain significance (Dec 15, 2022)
3-101579951-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-101585441-C-T		not specified	Uncertain significance (May 24, 2023)
3-101585455-C-G		not specified	Uncertain significance (Jun 02, 2023)
3-101585479-T-G		not specified	Uncertain significance (Jul 13, 2022)
3-101585504-A-G		not specified	Uncertain significance (Mar 01, 2024)
3-101590212-T-C			Benign (Jun 26, 2018)
3-101592637-A-T		not specified	Uncertain significance (May 18, 2023)
3-101592737-A-G		not specified	Uncertain significance (Dec 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCNP	protein_coding	protein_coding	ENST00000265260	5	20343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.786	0.213	125106	0	1	125107	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	62	93.8	0.661	0.00000454	1157
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.746
• hipred: Y
• hipred_score: 0.783
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcnp

Gene ontology

• Biological process: cell cycle;protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: nucleus;nuclear body
• Molecular function: protein binding