CDK20 p.Ala95=
c.285C>A · rs3750491 · VCV3050464
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.296%, eas)
Conditions
1
CDK20-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.51 | GERP -0.65, phastCons 1 |
| Overall | ||
| CADD | 7.286 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.296%
East Asian · 133/44,864 alleles
Filtering AF
0.255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.24%
Overall
0.01%
162/1,614,124 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.296% | 337 |
| South Asian | 0.0253% | 3,960 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,419 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDK20
- Protein
- p.Ala95=
- Coding
- c.285C>A
- MANE Select
- NM_001039803
- dbSNP
- rs3750491
- Type
- single nucleotide variant
- Location
- chr9:87971240 (GRCh38)
- Gene constraint
- LOEUF 1.342 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
- Residue 95
- the protein kinase domain
Disease context
CDK20-related disorder
Similar variants
- CDK20 p.Tyr215His Uncertain significance ★ ⚠ same condition
- CDK20 p.Val91Met Uncertain significance ⚠ same condition
- CDK20 c.190-6C>A Likely benign same condition
- CDK20 c.-10C>T Likely benign same condition
- CDK20 p.Arg158Cys Likely benign same condition
- CDK20 p.Arg179Cys Likely benign ⚠ same condition
- CDK20 p.Asp256= Likely benign same condition
- CDK20 p.Glu345= Likely benign same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdk20-p-ala95 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown