CCNA1
Chr 13cyclin A1
Also known as: CT146
CCNA1 encodes cyclin A1, which regulates cell cycle transitions at G1/S and G2/M phases by binding and activating CDK2 and CDC2 kinases, with primary functions in germline meiotic cell cycle control and some roles in somatic cell mitosis. Mutations cause autosomal recessive primary male infertility due to meiotic arrest during spermatogenesis. The gene shows low constraint against loss-of-function variants (pLI 0.0004, LOEUF 0.68), consistent with its tissue-specific expression pattern primarily affecting reproductive function.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
133 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 49 | 0 | 49 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 0 | 41 | 21 | 0 | 62 |
Likely Benign | 0 | 1 | 2 | 2 | 5 |
Benign | 0 | 0 | 1 | 3 | 4 |
| Total | 0 | 42 | 73 | 5 | 120 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CCNA1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools