CCNY

cyclin Y, the group of Cyclins

Basic information

Region (hg38): 10:35247025-35572669

Previous symbols: [ "C10orf9" ]

Links

ENSG00000108100

∙ NCBI:219771 ∙ OMIM:612786 ∙ HGNC:23354 ∙ Uniprot:Q8ND76 ∙ 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 CCNY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNY 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 clinvar		1
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in CCNY

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

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

Position	Phenotype	Significance	ClinVar
10-35337135-C-G	not specified	Uncertain significance (Apr 07, 2023)	2535065
10-35337158-G-C	not specified	Uncertain significance (Nov 21, 2022)	2328842
10-35516524-A-G	not specified	Uncertain significance (Apr 11, 2023)	2516328
10-35516548-A-G	not specified	Uncertain significance (Jun 05, 2023)	2556526
10-35516565-A-G	not specified	Uncertain significance (Jun 18, 2024)	2278597
10-35525968-G-A	not specified	Uncertain significance (Feb 11, 2022)	2222501
10-35529993-T-C	not specified	Uncertain significance (Dec 16, 2023)	3140023
10-35530130-G-A	not specified	Uncertain significance (Jul 12, 2022)	2207268
10-35530174-G-C	not specified	Uncertain significance (Feb 07, 2023)	2481687
10-35530234-C-T	not specified	Likely benign (Aug 15, 2023)	2603049
10-35566081-A-G	not specified	Uncertain significance (May 17, 2023)	2548092
10-35566112-G-A	not specified	Uncertain significance (Aug 16, 2021)	2245439
10-35566153-C-G	not specified	Uncertain significance (Mar 15, 2024)	3264617

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNY	protein_coding	protein_coding	ENST00000374704	10	324900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.807	0.193	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.04	117	198	0.592	0.0000112	2238
Missense in Polyphen		48	85.908	0.55874		957
Synonymous	0.680	69	76.6	0.901	0.00000445	645
Loss of Function	3.35	3	18.6	0.161	8.70e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Positive regulatory subunit of the cyclin-dependent kinases CDK14/PFTK1 and CDK16. Acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase by recruiting CDK14/PFTK1 to the plasma membrane and promoting phosphorylation of LRP6, leading to the activation of the Wnt signaling pathway. Recruits CDK16 to the plasma membrane. Isoform 3 might play a role in the activation of MYC-mediated transcription. {ECO:0000269|PubMed:18060517, ECO:0000269|PubMed:19524571, ECO:0000269|PubMed:20059949, ECO:0000269|PubMed:22184064}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

loftool: 0.319
rvis_EVS: -0.52
rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

pHI: 0.210
hipred: Y
hipred_score: 0.739
ghis: 0.618

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.196

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ccny
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process: G2/M transition of mitotic cell cycle;Wnt signaling pathway;positive regulation of cyclin-dependent protein serine/threonine kinase activity;cell division;regulation of canonical Wnt signaling pathway
Cellular component: cytoplasmic cyclin-dependent protein kinase holoenzyme complex;nucleus;plasma membrane
Molecular function: protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding