CDC42BPG p.Pro1257=
c.3771G>A · rs55669367 · VCV717710
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, sas)
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 0.21 | GERP -3.6, phastCons 0.028 |
| Overall | ||
| CADD | 4.383 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
South Asian · 993/90,994 alleles
Filtering AF
1.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.492%
7,926/1,611,652 alleles · low-frequency
exomes 7,440/1,459,262 · genomes 486/152,390 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.09% | 92 |
| Middle Eastern | 0.628% | 159 |
| European (non-Finnish) | 0.547% | 183 |
| Remaining individualsnot grpmax-eligible | 0.39% | 257 |
| African / African-American | 0.121% | 825 |
| Ashkenazi Jewishnot grpmax-eligible | 0.102% | 985 |
| Finnishnot grpmax-eligible | 0.0767% | 1,305 |
| Admixed American | 0.0518% | 1,931 |
| East Asian | 0.00446% | 22,427 |
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.Pro1257=
- Coding
- c.3771G>A
- MANE Select
- NM_017525
- dbSNP
- rs55669367
- Type
- single nucleotide variant
- Location
- chr11:64829667 (GRCh38)
- Gene constraint
- LOEUF 1.039 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.90
- Residue 1257
- the cnh domain
Similar variants
- CDC42BPG p.Ile77= Benign ★★ same type
- CDC42BPG p.Lys467Asn 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-pro1257 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown