CCNJL

cyclin J like, the group of Cyclins

Basic information

Region (hg38): 5:160249083-160345396

Links

ENSG00000135083 ∙ NCBI:79616 ∙ ∙ HGNC:25876 ∙ Uniprot:Q8IV13 ∙ 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 CCNJL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNJL 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					1	1
missense			29	2	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	2

Variants in CCNJL

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

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

Position	Type	Phenotype	Significance	ClinVar
5-160253382-C-T		not specified	Uncertain significance (May 24, 2024)
5-160253394-C-A		not specified	Uncertain significance (Aug 26, 2022)
5-160253394-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-160253404-A-G		not specified	Uncertain significance (Oct 16, 2023)
5-160253442-G-T		not specified	Uncertain significance (Jun 06, 2023)
5-160253491-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-160253575-A-G		not specified	Uncertain significance (Mar 01, 2023)
5-160253614-G-A		not specified	Uncertain significance (Sep 16, 2022)
5-160253638-C-T		not specified	Uncertain significance (Nov 08, 2021)
5-160253652-T-C		not specified	Uncertain significance (Mar 24, 2023)
5-160253667-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-160253667-G-C		not specified	Uncertain significance (Apr 17, 2024)
5-160253670-G-A		not specified	Uncertain significance (Dec 13, 2021)
5-160253671-G-C		not specified	Uncertain significance (Jun 21, 2022)
5-160253677-C-T		not specified	Likely benign (Mar 05, 2024)
5-160253685-G-T		not specified	Uncertain significance (Aug 21, 2023)
5-160253722-T-G		not specified	Uncertain significance (Oct 18, 2021)
5-160253743-T-C		not specified	Uncertain significance (Nov 07, 2023)
5-160253749-A-C		not specified	Uncertain significance (Dec 28, 2022)
5-160255577-G-C		not specified	Uncertain significance (Jul 09, 2021)
5-160255595-T-G		not specified	Uncertain significance (Feb 28, 2024)
5-160255603-C-T		not specified	Uncertain significance (Mar 31, 2024)
5-160255681-G-C		not specified	Uncertain significance (Dec 01, 2022)
5-160259529-G-A		not specified	Uncertain significance (Aug 17, 2021)
5-160259566-C-G		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNJL	protein_coding	protein_coding	ENST00000393977	6	93745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-7	0.368	124792	0	39	124831	0.000156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.320	220	234	0.941	0.0000137	2797
Missense in Polyphen		50	70.161	0.71265		846
Synonymous	-0.457	116	110	1.06	0.00000689	904
Loss of Function	0.646	12	14.7	0.818	7.07e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000500	0.000499
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000572	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000218	0.000212
Middle Eastern	0.0000572	0.0000556
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.581
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.170
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnjl

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