CDK20 p.Pro205=
c.615G>A · rs28364959 · VCV768313
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.18%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.33 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.3 | |
| Overall | ||
| CADD | 15.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.18%
African / African-American · 3,131/74,816 alleles
Filtering AF
4.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.01%
Overall
0.235%
3,780/1,607,388 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.18% | 24 |
| Middle Eastern | 0.432% | 232 |
| Remaining individualsnot grpmax-eligible | 0.404% | 248 |
| Admixed American | 0.385% | 260 |
| South Asian | 0.0211% | 4,739 |
| European (non-Finnish) | 0.0102% | 9,804 |
| East Asian | 0.00447% | 22,371 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00344% | 29,054 |
| Finnishnot grpmax-eligible | 0.00313% | 31,929 |
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.Pro205=
- Coding
- c.615G>A
- MANE Select
- NM_001039803
- dbSNP
- rs28364959
- Type
- single nucleotide variant
- Location
- chr9:87969868 (GRCh38)
- Gene constraint
- LOEUF 1.342 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
- Residue 205
- the protein kinase domain
Similar variants
- 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
- CDK20 c.76-66T>C Benign ★★ same type
- CDK20 c.*153C>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-pro205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown