CCNI2

cyclin I family member 2, the group of Cyclins

Basic information

Region (hg38): 5:132747425-132754403

Links

ENSG00000205089 ∙ NCBI:645121 ∙ ∙ HGNC:33869 ∙ Uniprot:Q6ZMN8 ∙ 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 CCNI2 gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNI2 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in CCNI2

This is a list of pathogenic ClinVar variants found in the CCNI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-132747525-G-C		not specified	Uncertain significance (Dec 27, 2023)
5-132747583-C-A		not specified	Uncertain significance (Sep 22, 2023)
5-132747587-A-G		not specified	Uncertain significance (Dec 15, 2022)
5-132747626-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-132747634-C-T		not specified	Likely benign (Oct 06, 2021)
5-132747715-G-T		not specified	Uncertain significance (Oct 28, 2023)
5-132747730-C-G		not specified	Uncertain significance (Aug 17, 2021)
5-132747765-C-A		not specified	Uncertain significance (Feb 28, 2024)
5-132747802-C-T		not specified	Uncertain significance (Dec 11, 2023)
5-132747803-C-G		not specified	Uncertain significance (Jan 03, 2024)
5-132747824-C-T		not specified	Uncertain significance (Jun 05, 2023)
5-132747848-A-T		not specified	Uncertain significance (Mar 14, 2023)
5-132747849-C-A		not specified	Uncertain significance (Mar 14, 2023)
5-132748392-C-T		not specified	Uncertain significance (Oct 02, 2023)
5-132748446-A-G		not specified	Uncertain significance (Feb 15, 2023)
5-132750891-A-G		not specified	Uncertain significance (Sep 16, 2021)
5-132750928-G-A		not specified	Uncertain significance (Oct 29, 2021)
5-132750963-T-C		not specified	Uncertain significance (Apr 27, 2023)
5-132750975-C-T		not specified	Uncertain significance (Feb 27, 2024)
5-132750976-G-A			Likely benign (Apr 01, 2022)
5-132750978-C-T		not specified	Uncertain significance (Jun 24, 2022)
5-132751993-C-A		not specified	Uncertain significance (Aug 22, 2023)
5-132752100-G-C		not specified	Uncertain significance (Oct 06, 2021)
5-132752107-A-C		not specified	Uncertain significance (Feb 15, 2023)
5-132752141-A-G		not specified	Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNI2	protein_coding	protein_coding	ENST00000378731	6	6720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.84e-8	0.162	124911	10	826	125747	0.00333

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	127	171	0.744	0.00000901	2311
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00118
Ashkenazi Jewish	0.00813	0.00817
East Asian	0.000163	0.000163
Finnish	0.00199	0.00199
European (Non-Finnish)	0.00128	0.00128
Middle Eastern	0.000163	0.000163
South Asian	0.0169	0.0166
Other	0.00358	0.00359

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0974
• hipred: N
• hipred_score: 0.204

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0204

Gene Damage Prediction

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

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