CDK20 p.His324=
c.972C>T · rs780624824 · VCV751435
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4 | |
| Overall | ||
| CADD | 0.187 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,016 alleles
Filtering AF
0.00508%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00434%
Overall
0.00521%
81/1,555,116 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,016 |
| Admixed American | 0.0117% | 8,568 |
| European (non-Finnish) | 0.00592% | 16,898 |
| East Asian | 0.00486% | 20,574 |
| African / African-American | 0.00273% | 36,614 |
| South Asian | 0.00238% | 42,101 |
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.His324=
- Coding
- c.972C>T
- MANE Select
- NM_001039803
- dbSNP
- rs780624824
- Type
- single nucleotide variant
- Location
- chr9:87967531 (GRCh38)
- Gene constraint
- LOEUF 1.342 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
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-his324 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown