CDK5 p.Arg50=
c.150G>T · VCV3670461
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0367%, 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 0.084 | GERP -0.97, phastCons 0.91 |
| Overall | ||
| CADD | 10.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0367%
Admixed American · 22/59,978 alleles
Filtering AF
0.0248%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0209%
Overall
0.0018%
29/1,613,634 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0367% | 2,726 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,229 |
| European (non-Finnish) | 0.000424% | 235,963 |
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.Arg50=
- Coding
- c.150G>T
- MANE Select
- NM_004935
- Type
- single nucleotide variant
- Location
- chr7:151056952 (GRCh38)
- Gene constraint
- LOEUF 0.584 · pLI 0.56 (gnomAD)
- Structure
- AlphaFold pLDDT 91.83 · 12 PDB
- Residue 50
- the protein kinase domain; an α-helix
Similar variants
- CDK5 p.Arg50Gln Likely pathogenic ★ same residue
- 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
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-arg50 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown