CDK5 p.Arg260=
c.780G>A · VCV3619262
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
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 3.2 | GERP 0.46, phastCons 1 |
| Overall | ||
| CADD | 11.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,836 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000892%
Overall
0.000274%
4/1,460,622 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,945 |
| European (non-Finnish) | 8.48e-05% | 1,179,473 |
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
- CDK5
- Protein
- p.Arg260=
- Coding
- c.780G>A
- MANE Select
- NM_004935
- Type
- single nucleotide variant
- Location
- chr7:151054224 (GRCh38)
- Gene constraint
- LOEUF 0.584 · pLI 0.56 (gnomAD)
- Structure
- AlphaFold pLDDT 91.83 · 12 PDB
- Residue 260
- the protein kinase domain; an α-helix
Similar variants
- CDK5 p.Met230Val Uncertain significance ★★ ⚠ same type
- CDK5 c.194+12G>A Benign/Likely benign ★★ same type
- CDK5 c.312+3G>A Benign ★★ same type
- CDK5 c.408+9T>C Likely benign ★★ same type
- CDK5 c.483+11A>C Benign ★★ same type
- CDK5 p.Pro240= Likely benign ★★ same type
- CDK5 p.Ser72= Benign/Likely benign ★★ same type
- CDK5 p.Arg50Gln Likely pathogenic ★ 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/cdk5-p-arg260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown