CCNI2

protein-coding

cyclin I family member 2, 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 and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001039780.4

Inheritance

—

ClinVar variants

U:61B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr5:132,747,426-132,754,403

External References & Databases

Ensembl (ENSG00000205089)

Transcript & Mutation Effects

hg38 • Region Span ~7.0 kb

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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 CCNI2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039780.4. 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			59 clinvar	2 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	61	3	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039780.4	RefSeq	NP_001034869.1	6	MANE Select
ENST00000378731.6	Ensembl	ENSP00000368005.1	6	MANE Select
NM_001287252.2	RefSeq	NP_001274181.1	6	Standard
NM_001287253.2	RefSeq	NP_001274182.1	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: ENST00000378731
Coding exons: 6
Length: 6720
Individuals with no LoFs: 124911
Homozygous LoFs: 10
Heterozygous LoFs: 826
Defined: 125747
p: 0.00333

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	127	171	0.744	0.00000901	2311
Missense (PolyPhen)		27	32.637	0.82728		463
Synonymous	1.56	61	78.6	0.776	0.00000455	797
Loss of Function	0.0489	11	11.2	0.984	4.78e-7	143

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00087	0.00087	rare
Ashkenazi Jewish	0.0081	0.0082	notable
East Asian	0.00016	0.00016	rare
Finnish	0.0020	0.0020	notable
European (Non-Finnish)	0.0013	0.0013	notable
South Asian	0.017	0.017	notable
Other	0.0036	0.0036	notable

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0204

Gene Damage Prediction

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