CCNP

cyclin P, the group of Cyclins

Basic information

Region (hg38): 19:40222208-40226697

Previous symbols: [ "CNTD2" ]

Links

ENSG00000105219 ∙ NCBI:79935 ∙ ∙ HGNC:25805 ∙ Uniprot:Q9H8S5 ∙ 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 CCNP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNP 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			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in CCNP

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

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

Position	Type	Phenotype	Significance	ClinVar
19-40223099-G-A		not specified	Uncertain significance (Nov 21, 2024)
19-40223122-C-T		not specified	Likely benign (Jul 12, 2022)
19-40223152-C-T		not specified	Uncertain significance (Sep 08, 2024)
19-40223176-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-40223183-C-T		not specified	Uncertain significance (Aug 14, 2024)
19-40223198-G-A		not specified	Uncertain significance (Nov 03, 2023)
19-40223202-C-A		CCNP-related disorder	Likely benign (Jun 13, 2019)
19-40223236-G-A		not specified	Uncertain significance (Nov 24, 2024)
19-40223240-C-T		not specified	Uncertain significance (Dec 15, 2022)
19-40223248-G-A		not specified	Uncertain significance (Aug 01, 2024)
19-40223428-C-T		not specified	Uncertain significance (Feb 13, 2025)
19-40223450-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-40223503-G-A		not specified	Uncertain significance (Aug 27, 2024)
19-40223533-C-G		not specified	Uncertain significance (Apr 18, 2024)
19-40224498-A-G		not specified	Uncertain significance (Oct 17, 2023)
19-40224499-C-T		not specified	Uncertain significance (Nov 15, 2024)
19-40224570-C-T		not specified	Uncertain significance (Nov 17, 2022)
19-40224575-A-G		CCNP-related disorder	Likely benign (Apr 09, 2024)
19-40224598-G-T		not specified	Uncertain significance (Mar 01, 2023)
19-40224604-C-T		not specified	Uncertain significance (Apr 24, 2024)
19-40224612-T-C		not specified	Uncertain significance (Mar 07, 2024)
19-40224613-A-G		not specified	Uncertain significance (Jan 03, 2025)
19-40224765-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-40224765-G-C		not specified	Uncertain significance (Aug 17, 2022)
19-40224777-C-G		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNP	protein_coding	protein_coding	ENST00000430325	5	4483

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000487	0.693	125724	0	15	125739	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	157	199	0.791	0.0000139	1889
Missense in Polyphen		51	70.214	0.72635		665
Synonymous	0.246	90	93.0	0.967	0.00000683	706
Loss of Function	0.819	6	8.59	0.698	4.66e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000348	0.000348
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.605
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.0514
• hipred: N
• hipred_score: 0.285
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0370

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;mitotic cell cycle;protein phosphorylation;regulation of mitotic nuclear division;positive regulation of cell population proliferation;positive regulation of cell cycle
• Cellular component: cyclin-dependent protein kinase holoenzyme complex;nucleus;cytoplasm
• Molecular function: protein kinase activity;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding