CDC42BPB p.Ser595=
c.1785C>G · rs138149940 · VCV722986
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.032%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.62 | GERP -4.2, phastCons 0.001 |
| Overall | ||
| CADD | 2.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.032%
African / African-American · 24/75,062 alleles
Filtering AF
0.022%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0187%
Overall
0.00204%
33/1,614,200 alleles · ultra-rare
exomes 18/1,461,872 · genomes 15/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.032% | 3,128 |
| Admixed American | 0.01% | 10,004 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| European (non-Finnish) | 8.47e-05% | 1,180,018 |
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.Ser595=
- Coding
- c.1785C>G
- MANE Select
- NM_006035
- dbSNP
- rs138149940
- Type
- single nucleotide variant
- Location
- chr14:102972018 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.28 · 6 PDB
Similar variants
- CDC42BPB p.Ser595Thr 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-ser595 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown