CCNE2

protein-coding

cyclin E2, the group of Cyclins

Gene summary

The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin forms a complex with and functions as a regulatory subunit of CDK2. This cyclin has been shown to specifically interact with CIP/KIP family of CDK inhibitors, and plays a role in cell cycle G1/S transition. The expression of this gene peaks at the G1-S phase and exhibits a pattern of tissue specificity distinct from that of cyclin E1. A significantly increased expression level of this gene was observed in tumor-derived cells. [provided by RefSeq, Jul 2008]

MANE transcript

NM_057749.3

Inheritance

—

ClinVar variants

U:39B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr8:94,879,770-94,896,678

External References & Databases

Ensembl (ENSG00000175305)

Transcript & Mutation Effects

hg38 • Region Span ~16.9 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 CCNE2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_057749.3. 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						0
missense			36 clinvar	2 clinvar		38
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	2	0	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_057749.3	RefSeq	NP_477097.1	11	MANE Select
ENST00000308108.9	Ensembl	ENSP00000309181.4	11	MANE Select
ENST00000396133.7	Ensembl	ENSP00000379437.3	11	Standard
ENST00000396133.8	Ensembl	ENSP00000379437.3	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PI3K-Akt signaling pathway - Homo sapiens (human)
Gastric cancer - Homo sapiens (human)
Cushing,s syndrome - Homo sapiens (human)
Cell cycle - Homo sapiens (human)
Oocyte meiosis - Homo sapiens (human)

Biological Process

regulation of cyclin-dependent protein serine/threonine kinase activity
G1/S transition of mitotic cell cycle
mitotic cell cycle
telomere maintenance
DNA replication initiation

Molecular Function

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

Cellular Component

cyclin-dependent protein kinase holoenzyme complex
nucleus
nucleoplasm
cytoplasm
centrosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000520509
Coding exons: 11
Length: 16909
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125746
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	140	200	0.701	0.00000875	2668
Missense (PolyPhen)		39	72.646	0.53685		1002
Synonymous	0.876	57	66.1	0.863	0.00000306	703
Loss of Function	3.81	4	24.3	0.165	0.00000103	310

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000064	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential for the control of the cell cycle at the late G1 and early S phase.;

Recessive Scores

pRec: 0.168

Intolerance Scores

LoFtool: 0.676
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.872

Gene Damage Prediction

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