CCNJL

protein-coding

cyclin J like, the group of Cyclins

Gene summary

Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in G1/S transition of mitotic cell cycle. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in cytoplasm; microtubule organizing center; and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001308173.3

Inheritance

—

ClinVar variants

U:66B:6

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr5:160,249,083-160,345,396

External References & Databases

Ensembl (ENSG00000135083)

Transcript & Mutation Effects

hg38 • Region Span ~96.3 kb

Loading mutation effect viewer...

GenCC 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 CCNJL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 3

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001308173.3. 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					1 clinvar	1
missense			64 clinvar	4 clinvar	1 clinvar	69
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	66	4	2	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001308173.3	RefSeq	NP_001295102.1	5	MANE Select
ENST00000257536.13	Ensembl	ENSP00000257536.7	5	MANE Select
NM_024565.8	RefSeq	NP_078841.3	6	Standard
ENST00000393977.7	Ensembl	ENSP00000377547.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

protein kinase activity
cyclin-dependent protein serine/threonine kinase regulator activity
protein kinase binding

Cellular Component

cyclin-dependent protein kinase holoenzyme complex
nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393977
Coding exons: 6
Length: 93745
Individuals with no LoFs: 124792
Homozygous LoFs: 0
Heterozygous LoFs: 39
Defined: 124831
p: 0.000156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.320	220	234	0.941	0.0000137	2797
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00032	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.581
RVIS EVS: 0.15
RVIS percentile EVS: 64.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.260

Gene Damage Prediction

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