CDC42 p.Asn92=
c.276C>T · rs16826534 · VCV730778
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.282%, eas)
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 5.1 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 13.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.282%
East Asian · 126/44,742 alleles
Filtering AF
0.242%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.226%
Overall
0.142%
2,278/1,607,852 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.282% | 355 |
| Middle Eastern | 0.215% | 465 |
| Remaining individualsnot grpmax-eligible | 0.182% | 551 |
| European (non-Finnish) | 0.154% | 648 |
| Admixed American | 0.109% | 919 |
| African / African-American | 0.0882% | 1,134 |
| South Asian | 0.0739% | 1,353 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0237% | 4,220 |
| Finnishnot grpmax-eligible | 0.0109% | 9,140 |
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.Asn92=
- Coding
- c.276C>T
- MANE Select
- NM_001791
- dbSNP
- rs16826534
- Type
- single nucleotide variant
- Location
- chr1:22086536 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 48 PDB
- Residue 92
- an α-helix
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-asn92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown