CDC42 p.Gln116=
c.348A>G · rs772882822 · VCV1900448
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0209%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.91 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.59 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 0.21, phastCons 1 |
| Overall | ||
| CADD | 22.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0209%
South Asian · 19/91,088 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00211%
34/1,613,982 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0209% | 4,794 |
| Middle Eastern | 0.0164% | 6,084 |
| African / African-American | 0.004% | 24,970 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| East Asian | 0.00223% | 44,892 |
| Admixed American | 0.00167% | 59,996 |
| European (non-Finnish) | 0.000593% | 168,571 |
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.Gln116=
- Coding
- c.348A>G
- MANE Select
- NM_001791
- dbSNP
- rs772882822
- Type
- single nucleotide variant
- Location
- chr1:22086728 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 48 PDB
- Residue 116
- a binding site
Similar variants
- CDC42 p.Gln116Glu Likely pathogenic ★ same residue
- 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
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-gln116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown