CDC42 p.Tyr154=
c.462T>C · rs16826536 · VCV790477
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.06%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.85 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.5 | GERP 1.3, phastCons 0.12 |
| Overall | ||
| CADD | 9.327 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.06%
African / African-American · 3,046/75,008 alleles
Filtering AF
3.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.89%
Overall
0.404%
6,524/1,613,946 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.06% | 25 |
| Admixed American | 0.58% | 173 |
| Remaining individualsnot grpmax-eligible | 0.486% | 206 |
| Middle Eastern | 0.313% | 319 |
| East Asian | 0.276% | 362 |
| European (non-Finnish) | 0.22% | 455 |
| South Asian | 0.0823% | 1,214 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0236% | 4,229 |
| Finnishnot grpmax-eligible | 0.0109% | 9,148 |
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.Tyr154=
- Coding
- c.462T>C
- MANE Select
- NM_001791
- dbSNP
- rs16826536
- Type
- single nucleotide variant
- Location
- chr1:22086842 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 48 PDB
- Residue 154
- a β-strand
Similar variants
- CDC42 p.Ala159Val Pathogenic ★★ same type
- CDC42 p.Arg186Cys Pathogenic ★★ ⚠ same type
- CDC42 p.Arg66Gly Pathogenic ★★ same type
- CDC42 p.Arg68Gln Pathogenic ★★ same type
- CDC42 p.Cys81Phe Likely pathogenic ★★ same type
- CDC42 p.Glu171Lys Pathogenic ★★ same type
- CDC42 p.Ser83Pro Pathogenic ★★ same type
- CDC42 p.Tyr23Cys 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/cdc42-p-tyr154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown