CDK20 p.Pro235=
c.705G>A · VCV3489475
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.22 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | |
| Overall | ||
| CADD | 0.297 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00495%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00455%
Overall
0.00533%
86/1,613,778 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,620 |
| European (non-Finnish) | 0.0061% | 16,388 |
| African / African-American | 0.00401% | 24,952 |
| Admixed American | 0.00333% | 29,989 |
| Finnishnot grpmax-eligible | 0.00313% | 31,994 |
| South Asian | 0.0022% | 45,538 |
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.Pro235=
- Coding
- c.705G>A
- MANE Select
- NM_001039803
- Type
- single nucleotide variant
- Location
- chr9:87969332 (GRCh38)
- Gene constraint
- LOEUF 1.342 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
- Residue 235
- the protein kinase domain
Similar variants
- CDK20 p.Pro235Leu Uncertain significance ★ 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
- CDK20 c.76-66T>C 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-pro235 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown