CDK1 p.Phe214=
c.642C>T · rs189255717 · VCV710938
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.825%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 12.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.825%
Admixed American · 484/58,700 alleles
Filtering AF
0.764%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.74%
Overall
0.031%
496/1,600,236 alleles · rare
exomes 448/1,459,178 · genomes 48/141,058 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.825% | 121 |
| Remaining individualsnot grpmax-eligible | 0.0177% | 5,657 |
| African / African-American | 0.00137% | 72,962 |
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
- CDK1
- Protein
- p.Phe214=
- Coding
- c.642C>T
- MANE Select
- NM_001786
- dbSNP
- rs189255717
- Type
- single nucleotide variant
- Location
- chr10:60792042 (GRCh38)
- Gene constraint
- LOEUF 0.565 · pLI 0.90 (gnomAD)
- Structure
- AlphaFold pLDDT 89.52 · 14 PDB
- Residue 214
- the protein kinase domain; an α-helix
Similar variants
- CDK1 p.Arg215Lys Uncertain significance ★ same type
- CDK1 p.Gln28Arg Uncertain significance ★ ⚠ same type
- CDK1 p.His23Asn Uncertain significance ★ ⚠ same type
- CDK1 p.Ile157Leu Uncertain significance ★ ⚠ same type
- CDK1 p.Ile157Val Uncertain significance ★ ⚠ same type
- CDK1 p.Ile190Val Uncertain significance ★ ⚠ same type
- CDK1 p.Leu70Val Uncertain significance ★ ⚠ same type
- CDK1 p.Lys279Arg 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/cdk1-p-phe214 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown