CDK20 p.Lys281=
c.843G>A · VCV4852897
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0143%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.075 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.51 | donor loss at this position · masked 0 · deltas |
| Pangolin | Δ0.67 | loss · gain 0.07 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | phastCons 1 |
| Overall | ||
| CADD | 18.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0143%
South Asian · 13/91,064 alleles
Filtering AF
0.00844%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00661%
Overall
0.000868%
14/1,613,670 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0143% | 7,005 |
| European (non-Finnish) | 8.48e-05% | 1,179,814 |
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.Lys281=
- Coding
- c.843G>A
- MANE Select
- NM_001039803
- Type
- single nucleotide variant
- Location
- chr9:87969194 (GRCh38)
- Gene constraint
- LOEUF 1.342 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
- Residue 281
- the protein kinase domain; a UniProt-annotated variant site (in)
Similar variants
- CDK20 p.Lys281Glu Uncertain significance ★ ⚠ same residue
- CDK20 p.Lys281Arg Benign same residue
- CDK20 p.Phe204Leu Uncertain significance ★★ ⚠ same type
- CDK20 c.189+23G>C Benign ★★ same type
- CDK20 c.378+19C>T Benign ★★ same type
- CDK20 c.564-44C>T Benign ★★ same type
- CDK20 c.688-214G>A Benign ★★ same type
- CDK20 c.76-20G>T Benign ★★ same type
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-lys281 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown