CDC42BPB p.Pro1307=
c.3921G>A · rs141912309 · VCV3049207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0397%, 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 -20 | GERP -4.2 |
| Overall | ||
| CADD | 0.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0397%
European (non-Finnish) · 468/1,180,016 alleles
Filtering AF
0.0367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0355%
Overall
0.0311%
501/1,613,152 alleles · ultra-rare
exomes 472/1,460,826 · genomes 29/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0397% | 2,521 |
| Admixed American | 0.015% | 6,668 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| African / African-American | 0.0107% | 9,383 |
| Finnishnot grpmax-eligible | 0.00952% | 10,507 |
| East Asian | 0.00223% | 44,882 |
| South Asian | 0.0022% | 45,537 |
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.Pro1307=
- Coding
- c.3921G>A
- MANE Select
- NM_006035
- dbSNP
- rs141912309
- Type
- single nucleotide variant
- Location
- chr14:102944378 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.28 · 6 PDB
- Residue 1307
- a UniProt-annotated variant site (in chocns); the cnh domain
Similar variants
- 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
- CDC42BPB p.Arg509Ter 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/cdc42bpb-p-pro1307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown