CDK5RAP2 p.Pro1002=
c.3006C>G · rs149463541 · VCV2759963
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.297%, mid)
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 -1.1 | GERP -4.2 |
| Overall | ||
| CADD | 0.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.297%
Middle Eastern · 18/6,060 alleles
Filtering AF
0.192%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.159%
Overall
0.0103%
167/1,613,954 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.297% | 337 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,166 |
| South Asian | 0.011% | 9,106 |
| European (non-Finnish) | 0.0102% | 9,832 |
| Admixed American | 0.00333% | 30,008 |
| Finnishnot grpmax-eligible | 0.00156% | 64,032 |
| African / African-American | 0.00133% | 75,036 |
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.Pro1002=
- Coding
- c.3006C>G
- MANE Select
- NM_018249
- dbSNP
- rs149463541
- Type
- single nucleotide variant
- Location
- chr9:120447914 (GRCh38)
- Gene constraint
- LOEUF 0.692 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 60.11 · 5 PDB
- Residue 1002
- the 'interaction with mapre1' region
Similar variants
- CDK5RAP2 p.Pro1002Ala Uncertain significance ★ ⚠ same residue
- 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
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-pro1002 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown