CDK5 p.Pro243=
c.729G>A · rs754772887 · VCV2084412
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
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 -8.8 | GERP -3.2 |
| Overall | ||
| CADD | 1.719 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/59,962 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00155%
25/1,613,620 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00667% | 14,991 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,229 |
| European (non-Finnish) | 0.00153% | 65,544 |
| African / African-American | 0.00134% | 74,876 |
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.Pro243=
- Coding
- c.729G>A
- MANE Select
- NM_004935
- dbSNP
- rs754772887
- Type
- single nucleotide variant
- Location
- chr7:151054275 (GRCh38)
- Gene constraint
- LOEUF 0.584 · pLI 0.56 (gnomAD)
- Structure
- AlphaFold pLDDT 91.83 · 12 PDB
- Residue 243
- 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-pro243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown