CDK2AP1 p.Gln57=
c.171G>A · rs143369281 · VCV782568
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.79%, 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 1.4 | GERP -0.15, phastCons 1 |
| Overall | ||
| CADD | 9.474 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.79%
African / African-American · 1,340/75,030 alleles
Filtering AF
1.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.67%
Overall
0.0913%
1,473/1,614,156 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.79% | 56 |
| Middle Eastern | 0.132% | 758 |
| Remaining individualsnot grpmax-eligible | 0.117% | 856 |
| Admixed American | 0.0633% | 1,579 |
| South Asian | 0.00769% | 13,012 |
| European (non-Finnish) | 0.000593% | 168,575 |
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
- CDK2AP1
- Protein
- p.Gln57=
- Coding
- c.171G>A
- MANE Select
- NM_004642
- dbSNP
- rs143369281
- Type
- single nucleotide variant
- Location
- chr12:123265305 (GRCh38)
- Gene constraint
- LOEUF 1.522 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 76.47 · 1 PDB
Similar variants
- CDK2AP1 p.Tyr63= Benign ★★ same type
- CDK2AP1 p.Ala30Ser Uncertain significance ★ ⚠ same type
- CDK2AP1 p.Arg111Trp Uncertain significance ★ ⚠ same type
- CDK2AP1 p.Gly43Arg Uncertain significance ★ ⚠ same type
- CDK2AP1 p.Leu7Phe Uncertain significance ★ ⚠ same type
- CDK2AP1 p.Met11Val Uncertain significance ★ ⚠ same type
- CDK2AP1 p.Pro25His Uncertain significance ★ ⚠ same type
- CDK2AP1 p.Pro45Leu 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/cdk2ap1-p-gln57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown