CCNYL1

protein-coding

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

Gene summary

Predicted to enable cyclin-dependent protein serine/threonine kinase activator activity. Predicted to be involved in neurogenesis and regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within flagellated sperm motility; regulation of protein kinase activity; and spermatogenesis. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001330218.2

Inheritance

—

ClinVar variants

U:32B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr2:207,711,540-207,761,839

External References & Databases

Ensembl (ENSG00000163249)

Transcript & Mutation Effects

hg38 • Region Span ~50.3 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 CCNYL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330218.2. 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				2 clinvar		2
missense			32 clinvar	1 clinvar		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	3	0	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330218.2	RefSeq	NP_001317147.1	10	MANE Select
ENST00000295414.8	Ensembl	ENSP00000295414.3	10	MANE Select
NM_001142300.2	RefSeq	NP_001135772.1	8	Standard
NM_152523.3	RefSeq	NP_689736.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
flagellated sperm motility
positive regulation of cyclin-dependent protein serine/threonine kinase activity

Molecular Function

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

Cellular Component

plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339882
Coding exons: 8
Length: 50300
Individuals with no LoFs: 125526
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125528
p: 0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.62	98	155	0.633	0.00000749	2031
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0764

Intolerance Scores

LoFtool: 0.143
RVIS EVS: -0.36
RVIS percentile EVS: 28.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.420

Gene Damage Prediction

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