CCNJ

cyclin J, the group of Cyclins

Basic information

Region (hg38): 10:96043394-96060870

Links

ENSG00000107443 ∙ NCBI:54619 ∙ ∙ HGNC:23434 ∙ Uniprot:Q5T5M9 ∙ 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 CCNJ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNJ 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in CCNJ

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

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

Position	Type	Phenotype	Significance	ClinVar
10-96044407-G-T		not specified	Uncertain significance (Apr 06, 2024)
10-96044422-G-A		not specified	Uncertain significance (Jun 26, 2024)
10-96050280-G-A		not specified	Uncertain significance (Mar 01, 2024)
10-96050364-G-A		not specified	Uncertain significance (Aug 01, 2024)
10-96056806-A-G		not specified	Uncertain significance (Jul 21, 2021)
10-96056893-C-G		not specified	Uncertain significance (May 23, 2023)
10-96057160-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-96057192-C-T		not specified	Uncertain significance (Mar 14, 2023)
10-96057195-C-G		not specified	Uncertain significance (Jul 25, 2024)
10-96057198-A-T		not specified	Uncertain significance (Oct 22, 2024)
10-96057202-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-96057841-A-T		not specified	Uncertain significance (Jan 16, 2024)
10-96057895-A-C		not specified	Uncertain significance (Jul 19, 2022)
10-96057930-C-T		not specified	Uncertain significance (Apr 25, 2023)
10-96057931-G-A		not specified	Uncertain significance (Dec 23, 2024)
10-96057939-C-G		not specified	Uncertain significance (Nov 13, 2024)
10-96058006-C-T		not specified	Uncertain significance (Sep 22, 2023)
10-96058012-A-C		not specified	Uncertain significance (Nov 18, 2024)
10-96058037-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
10-96058085-C-G		not specified	Uncertain significance (Jan 06, 2023)
10-96058090-C-T		not specified	Uncertain significance (Oct 08, 2024)
10-96058093-G-A		not specified	Uncertain significance (Jul 29, 2022)
10-96058095-G-A		not specified	Uncertain significance (Nov 18, 2024)
10-96058105-T-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNJ	protein_coding	protein_coding	ENST00000465148	5	17477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00204	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	144	209	0.689	0.0000115	2484
Missense in Polyphen		37	73.382	0.50421		948
Synonymous	1.50	62	78.9	0.786	0.00000415	761
Loss of Function	3.94	0	18.1	0.00	8.71e-7	214

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)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.152
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.518
• hipred: Y
• hipred_score: 0.673
• ghis: 0.693

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnj

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