CCNYL1

cyclin Y like 1, the group of Cyclins|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:207711540-207761839

Links

ENSG00000163249 ∙ NCBI:151195 ∙ ∙ HGNC:26868 ∙ Uniprot:Q8N7R7 ∙ 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 CCNYL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNYL1 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				2		2
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in CCNYL1

This is a list of pathogenic ClinVar variants found in the CCNYL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-207711920-C-G		not specified	Uncertain significance (Nov 30, 2021)
2-207711925-C-T		not specified	Uncertain significance (Feb 21, 2025)
2-207711937-G-C		not specified	Uncertain significance (Nov 28, 2024)
2-207711954-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-207711967-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-207712026-G-A		not specified	Uncertain significance (Oct 29, 2024)
2-207712056-G-T		not specified	Uncertain significance (Jul 09, 2024)
2-207712066-A-G		not specified	Uncertain significance (Jan 03, 2022)
2-207712080-C-T		not specified	Uncertain significance (Aug 12, 2024)
2-207712109-G-A		not specified	Uncertain significance (May 02, 2024)
2-207712110-C-A		not specified	Uncertain significance (Dec 10, 2024)
2-207714418-T-A			Likely benign (Mar 01, 2022)
2-207724814-T-G		not specified	Uncertain significance (Jan 26, 2022)
2-207737424-A-G		not specified	Uncertain significance (Mar 31, 2024)
2-207737436-A-G		not specified	Uncertain significance (Dec 14, 2023)
2-207742292-A-C		not specified	Uncertain significance (Feb 09, 2025)
2-207747128-C-T		not specified	Uncertain significance (Oct 20, 2023)
2-207751014-C-T			Likely benign (Mar 01, 2022)
2-207751045-C-T		not specified	Uncertain significance (Jan 01, 2025)
2-207751049-C-T		not specified	Uncertain significance (Nov 21, 2024)
2-207753633-A-G		not specified	Uncertain significance (Oct 10, 2023)
2-207753652-C-T		not specified	Uncertain significance (Sep 10, 2024)
2-207753676-G-A		not specified	Uncertain significance (Jul 15, 2021)
2-207753681-A-G		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNYL1	protein_coding	protein_coding	ENST00000339882	8	50300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.586	0.414	125526	0	2	125528	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	98	155	0.633	0.00000749	2031
Missense in Polyphen		11	28.942	0.38007		414
Synonymous	0.697	48	54.5	0.880	0.00000273	555
Loss of Function	2.97	3	15.7	0.191	8.22e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0764

Intolerance Scores

• loftool: 0.143
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.623
• hipred: Y
• hipred_score: 0.632
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.420

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnyl1
• Phenotype: cellular 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); reproductive system phenotype

Gene ontology

• Biological process: spermatogenesis;flagellated sperm motility;positive regulation of cyclin-dependent protein serine/threonine kinase activity
• Cellular component: plasma membrane
• Molecular function: protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding