CDC42 p.Gln162=
c.486G>A · rs1645666283 · VCV1491948
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.52 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.32 | gain · loss 0.12 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 24.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,012 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.000753%
11/1,460,412 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,012 |
| European (non-Finnish) | 0.000848% | 117,876 |
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.Gln162=
- Coding
- c.486G>A
- MANE Select
- NM_001791
- dbSNP
- rs1645666283
- Type
- single nucleotide variant
- Location
- chr1:22086866 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 48 PDB
- Residue 162
- a turn
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-gln162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown