CDC42BPB p.Ala313=
c.939G>A · VCV3770431
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.261%, nfe)
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 -6.6 | GERP -5.2 |
| Overall | ||
| CADD | 1.269 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.261%
European (non-Finnish) · 3,078/1,180,044 alleles
Filtering AF
0.253%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.25%
Overall
0.216%
3,487/1,614,156 alleles · rare
exomes 3,225/1,461,856 · genomes 262/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.261% | 383 |
| Remaining individualsnot grpmax-eligible | 0.219% | 456 |
| Admixed American | 0.138% | 723 |
| South Asian | 0.124% | 806 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0743% | 1,345 |
| African / African-American | 0.052% | 1,924 |
| Middle Eastern | 0.033% | 3,031 |
| Finnishnot grpmax-eligible | 0.0203% | 4,923 |
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
- CDC42BPB
- Protein
- p.Ala313=
- Coding
- c.939G>A
- MANE Select
- NM_006035
- Type
- single nucleotide variant
- Location
- chr14:102980974 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.28 · 6 PDB
- Residue 313
- the protein kinase domain; an α-helix
Similar variants
- CDC42BPB p.Ala313Val Uncertain significance ★ ⚠ same residue
- CDC42BPB c.2726+1G>A Pathogenic/Likely pathogenic ★★ same type
- CDC42BPB p.Ala177Val Likely pathogenic ★★ same type
- CDC42BPB p.Arg122Ter Pathogenic/Likely pathogenic ★★ same type
- CDC42BPB p.Arg867Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDC42BPB p.Arg876Pro Likely pathogenic ★★ ⚠ same type
- CDC42BPB p.Asp175Tyr Likely pathogenic ★★ same type
- CDC42BPB p.Ser1530Ter Likely 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/cdc42bpb-p-ala313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown