CDK2AP1 p.His97=
c.291C>T · VCV3999629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 -1.9 | GERP -3.8 |
| Overall | ||
| CADD | 9.025 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,068 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.000822%
12/1,460,608 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,178 |
| Finnishnot grpmax-eligible | 0.00156% | 64,008 |
| European (non-Finnish) | 0.000424% | 235,771 |
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.His97=
- Coding
- c.291C>T
- MANE Select
- NM_004642
- Type
- single nucleotide variant
- Location
- chr12:123261793 (GRCh38)
- Gene constraint
- LOEUF 1.522 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 76.47 · 1 PDB
- Residue 97
- an α-helix
Similar variants
- CDK2AP1 p.Gln57= Benign ★★ same type
- 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
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-his97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown