CDK5 p.Ser72=
c.216C>T · rs531146226 · VCV3037083
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.283%, 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 -2.2 | GERP -3.5 |
| Overall | ||
| CADD | 7.493 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.283%
South Asian · 257/90,714 alleles
Filtering AF
0.255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.244%
Overall
0.0187%
301/1,612,308 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.283% | 353 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,469 |
| Admixed American | 0.0201% | 4,980 |
| East Asian | 0.00446% | 22,419 |
| African / African-American | 0.00267% | 37,503 |
| European (non-Finnish) | 0.000678% | 147,402 |
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.Ser72=
- Coding
- c.216C>T
- MANE Select
- NM_004935
- dbSNP
- rs531146226
- Type
- single nucleotide variant
- Location
- chr7:151056775 (GRCh38)
- Gene constraint
- LOEUF 0.584 · pLI 0.56 (gnomAD)
- Structure
- AlphaFold pLDDT 91.83 · 12 PDB
- Residue 72
- the protein kinase domain; a modified residue (phosphoserine)
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.Arg50Gln Likely pathogenic ★ same type
- CDK5 c.37+4A>G 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/cdk5-p-ser72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown