CCNYL1

Chr 2

cyclin Y like 1

NCBI Gene: 151195 ENSG00000163249 UniProt: Q8N7R7

CCNYL1 encodes a key regulator of Wnt signaling that activates cyclin-dependent kinase CDK16 and is essential for sperm maturation, embryonic neurogenesis, and cortical development. The gene is highly constrained against loss-of-function variants (LOEUF 0.494), but no definitive human disease associations have been established in the provided data. Given its role in neurogenesis and cortical development, mutations would likely affect brain development and male fertility.

ResearchSummary from RefSeq, UniProt

Predicted to enable protein kinase binding activity. Predicted to be involved in 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, Jul 2025]

ResearchGenerating clinical summary…

LOEUF 0.49

Clinical Summary— CCNYL1

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.59) — some intolerance to loss-of-function variants.

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ClinVar Variants

32 VUS of 43 total submissions

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.49LOEUF

pLI 0.586

Z-score 2.97

OE 0.19 (0.09–0.49)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.62Z-score

OE missense 0.63 (0.54–0.75)

98 obs / 154.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.19 (0.09–0.49)

0≤0.351.4

Missense OE?0.63 (0.54–0.75)

0≤0.61.4

Synonymous OE?0.88

0≤1.21.6

LoF obs/exp: 3 / 15.7Missense obs/exp: 98 / 154.9Syn Z: 0.70

ClinVar Variant Classifications

43 submitted variants in ClinVar

ClinVar

Classification Summary

VUS32

Likely Benign4

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	1	31	0	0	32
Likely Benign	0	1	1	2	4
Benign	0	0	0	0	0
Total	1	32	1	2	36

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

26 pathogenic / likely-pathogenic (of 28) ClinVar copy-number / structural variants overlap CCNYL1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →