CDK11A p.Phe566=
c.1698T>C · rs1136993 · VCV2638055
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0786%, sas)
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 · A>T here scores Δ0.24 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | |
| Overall | ||
| CADD | 0.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0786%
South Asian · 71/90,326 alleles
Filtering AF
0.0639%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0585%
Overall
0.0131%
210/1,603,006 alleles · ultra-rare
exomes 204/1,452,196 · genomes 6/150,810 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0786% | 1,272 |
| Middle Eastern | 0.0738% | 1,356 |
| Remaining individualsnot grpmax-eligible | 0.0274% | 3,644 |
| Admixed American | 0.0134% | 7,439 |
| European (non-Finnish) | 0.00853% | 11,727 |
| Finnishnot grpmax-eligible | 0.00785% | 12,736 |
| African / African-American | 0.00672% | 14,892 |
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
- CDK11A
- Protein
- p.Phe566=
- Coding
- c.1698T>C
- MANE Select
- NM_024011
- dbSNP
- rs1136993
- Type
- single nucleotide variant
- Location
- chr1:1704135 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.94
- Residue 566
- the protein kinase domain
Similar variants
- CDK11A p.Arg247Gln Uncertain significance ★★ ⚠ same type
- CDK11A p.Ala196Val Uncertain significance ★ ⚠ same type
- CDK11A p.Ala558Thr Uncertain significance ★ ⚠ same type
- CDK11A p.Ala590Thr Uncertain significance ★ same type
- CDK11A p.Ala597Val Uncertain significance ★ ⚠ same type
- CDK11A p.Arg131Cys Uncertain significance ★ ⚠ same type
- CDK11A p.Arg132Gln Uncertain significance ★ ⚠ same type
- CDK11A p.Arg132Trp Uncertain significance ★ ⚠ 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/cdk11a-p-phe566 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown