CDC42 p.Asp170=
c.510C>T · rs200782611 · VCV1596360
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
Conditions
1
Takenouchi-Kosaki syndrome
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 -4.9 | GERP -4.7 |
| Overall | ||
| CADD | 8.701 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/59,948 alleles
Filtering AF
0.00774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00161%
26/1,612,962 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,661 |
| South Asian | 0.00989% | 10,114 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,819 |
| Finnishnot grpmax-eligible | 0.00312% | 32,004 |
| East Asian | 0.00223% | 44,866 |
| European (non-Finnish) | 0.00017% | 589,577 |
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
- CDC42
- Protein
- p.Asp170=
- Coding
- c.510C>T
- MANE Select
- NM_001791
- dbSNP
- rs200782611
- Type
- single nucleotide variant
- Location
- chr1:22091451 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 48 PDB
- Residue 170
- an α-helix
Similar variants
- CDC42 p.Asp170Gly Likely pathogenic ★ same residue
- CDC42 p.Arg66Gly Pathogenic ★★ same condition
- CDC42 p.Arg68Gln Pathogenic ★★ same condition
- CDC42 p.Cys81Phe Likely pathogenic ★★ same condition
- CDC42 p.Glu171Lys Pathogenic ★★ same condition
- CDC42 p.Ser83Pro Pathogenic ★★ same condition
- CDC42 p.Tyr23Cys Pathogenic ★★ same condition
- CDC42 p.Tyr64Cys Pathogenic/Likely pathogenic ★★ 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/cdc42-p-asp170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown