CDK5RAP2 p.Gln593=
c.1779A>G · rs541039344 · VCV3030676
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0274%, sas)
Conditions
1
CDK5RAP2-related disorder
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 -2.4 | GERP -4.3 |
| Overall | ||
| CADD | 4.631 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0274%
South Asian · 25/91,082 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.00155%
25/1,613,654 alleles · ultra-rare
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
- CDK5RAP2
- Protein
- p.Gln593=
- Coding
- c.1779A>G
- MANE Select
- NM_018249
- dbSNP
- rs541039344
- Type
- single nucleotide variant
- Location
- chr9:120471827 (GRCh38)
- Gene constraint
- LOEUF 0.692 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 60.11 · 5 PDB
Disease context
CDK5RAP2-related disorder
Similar variants
- CDK5RAP2 p.Arg1481Ter Pathogenic/Likely pathogenic ★★ same condition
- CDK5RAP2 p.Arg150Ter Pathogenic ★ same condition
- CDK5RAP2 c.5452-8C>T Conflicting classifications of pathogenicity ★ same condition
- CDK5RAP2 p.Glu225Ter Likely pathogenic same condition
- CDK5RAP2 p.Ser1608Asn Uncertain significance ⚠ same condition
- CDK5RAP2 p.His1182= Likely benign same condition
- CDK5RAP2 p.Pro1587= Likely benign same condition
- CDK5RAP2 p.Ser1064= Likely benign same condition
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/cdk5rap2-p-gln593 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown