CDK5RAP2 p.Asp490=
c.1470C>T · rs375317489 · VCV2723869
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, 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 1.8 | GERP -1.6, phastCons 0.96 |
| Overall | ||
| CADD | 8.167 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,990 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00681%
Overall
0.00682%
110/1,612,650 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 5,999 |
| European (non-Finnish) | 0.0078% | 12,816 |
| African / African-American | 0.00534% | 18,720 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,809 |
| South Asian | 0.0011% | 90,966 |
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.Asp490=
- Coding
- c.1470C>T
- MANE Select
- NM_018249
- dbSNP
- rs375317489
- Type
- single nucleotide variant
- Location
- chr9:120491319 (GRCh38)
- Gene constraint
- LOEUF 0.692 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 60.11 · 5 PDB
Similar variants
- CDK5RAP2 c.4005-1G>A Pathogenic ★★ same type
- CDK5RAP2 c.4963+1G>A Likely pathogenic ★★ same type
- CDK5RAP2 p.Arg1403Ter Pathogenic/Likely pathogenic ★★ same type
- CDK5RAP2 p.Arg1481Ter Pathogenic/Likely pathogenic ★★ same type
- CDK5RAP2 p.Arg1558Ter Pathogenic ★★ same type
- CDK5RAP2 p.Arg427Ter Pathogenic ★★ same type
- CDK5RAP2 p.Gln1301Ter Pathogenic/Likely pathogenic ★★ same type
- CDK5RAP2 p.Gln1474Ter 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/cdk5rap2-p-asp490 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown