CDC42BPG p.Ile77=
c.231C>T · rs56338925 · VCV734169
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.485%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.35 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.22 | gain · loss 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.34 | GERP -2.7, phastCons 0.005 |
| Overall | ||
| CADD | 16.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.485%
European (non-Finnish) · 5,718/1,179,964 alleles
Filtering AF
0.474%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.47%
Overall
0.371%
5,988/1,613,942 alleles · rare
exomes 5,654/1,461,642 · genomes 334/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.485% | 206 |
| Remaining individualsnot grpmax-eligible | 0.253% | 396 |
| African / African-American | 0.076% | 1,316 |
| Finnishnot grpmax-eligible | 0.0532% | 1,879 |
| Admixed American | 0.0283% | 3,531 |
| South Asian | 0.00329% | 30,359 |
| East Asian | 0.00223% | 44,884 |
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
- CDC42BPG
- Protein
- p.Ile77=
- Coding
- c.231C>T
- MANE Select
- NM_017525
- dbSNP
- rs56338925
- Type
- single nucleotide variant
- Location
- chr11:64841834 (GRCh38)
- Gene constraint
- LOEUF 1.039 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.90
- Residue 77
- the protein kinase domain; a binding site
Similar variants
- CDC42BPG p.Lys467Asn Benign ★★ same type
- CDC42BPG p.Pro1257= Benign ★★ same type
- CDC42BPG p.Ala1013Val Uncertain significance ★ ⚠ same type
- CDC42BPG p.Ala1036Val Uncertain significance ★ ⚠ same type
- CDC42BPG p.Ala1071Val Uncertain significance ★ ⚠ same type
- CDC42BPG p.Ala1098Thr Uncertain significance ★ ⚠ same type
- CDC42BPG p.Ala1242Val Uncertain significance ★ ⚠ same type
- CDC42BPG p.Ala1243Thr Uncertain significance ★ ⚠ 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/cdc42bpg-p-ile77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown