CDC42BPG p.Thr673=
c.2019G>A · rs141739556 · VCV2641936
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.3%, 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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.615 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.3%
South Asian · 273/91,032 alleles
Filtering AF
0.271%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.259%
Overall
0.0628%
1,006/1,601,208 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.3% | 333 |
| African / African-American | 0.144% | 694 |
| European (non-Finnish) | 0.0489% | 2,044 |
| Remaining individualsnot grpmax-eligible | 0.0433% | 2,310 |
| Middle Eastern | 0.0333% | 3,004 |
| Admixed American | 0.0267% | 3,746 |
| Finnishnot grpmax-eligible | 0.00383% | 26,083 |
| East Asian | 0.00223% | 44,776 |
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.Thr673=
- Coding
- c.2019G>A
- MANE Select
- NM_017525
- dbSNP
- rs141739556
- Type
- single nucleotide variant
- Location
- chr11:64835088 (GRCh38)
- Gene constraint
- LOEUF 1.039 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.90
- Residue 673
- the 'disordered' region
Similar variants
- CDC42BPG p.Thr673Met Uncertain significance ★ ⚠ same residue
- CDC42BPG p.Ile77= Benign ★★ same type
- 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
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-thr673 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown