CDK5RAP2 p.Tyr1179=
c.3537C>T · rs555575334 · VCV2420827
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, 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 -6.9 | GERP -4.7 |
| Overall | ||
| CADD | 0.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,086 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.0062%
100/1,614,152 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,554 |
| East Asian | 0.0134% | 7,477 |
| African / African-American | 0.00666% | 15,007 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| Finnishnot grpmax-eligible | 0.00625% | 16,009 |
| European (non-Finnish) | 0.005% | 20,000 |
| Admixed American | 0.00333% | 30,010 |
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.Tyr1179=
- Coding
- c.3537C>T
- MANE Select
- NM_018249
- dbSNP
- rs555575334
- Type
- single nucleotide variant
- Location
- chr9:120439584 (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 1179
- the 'interaction with mapre1' region
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-tyr1179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown