CDK2 p.Ile275=
c.825T>A · rs147559857 · VCV741794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.112%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 8.564 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.112%
African / African-American · 84/75,038 alleles
Filtering AF
0.0926%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0855%
Overall
0.0057%
92/1,614,152 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.112% | 893 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| Admixed American | 0.00167% | 60,026 |
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
- CDK2
- Protein
- p.Ile275=
- Coding
- c.825T>A
- MANE Select
- NM_001798
- dbSNP
- rs147559857
- Type
- single nucleotide variant
- Location
- chr12:55971553 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.55 · 523 PDB
- Residue 275
- the protein kinase domain; an α-helix
Similar variants
- CDK2 p.Arg199His Uncertain significance ★ ⚠ same type
- CDK2 p.Arg200Gln Uncertain significance ★ ⚠ same type
- CDK2 p.Arg200Trp Uncertain significance ★ ⚠ same type
- CDK2 p.Arg214Gln Uncertain significance ★ ⚠ same type
- CDK2 p.Asp288His Uncertain significance ★ ⚠ same type
- CDK2 p.Cys191Arg Uncertain significance ★ ⚠ same type
- CDK2 p.Glu57Ala Uncertain significance ★ ⚠ same type
- CDK2 p.His268Leu 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/cdk2-p-ile275 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown