RAC3 p.Pro69=
c.207A>G · VCV4937704
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, 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 -9.9 | GERP -3.9 |
| Overall | ||
| CADD | 0.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,068 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000434%
7/1,612,630 alleles · very rare
exomes 7/1,460,656 · genomes 0/151,974 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,534 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.000339% | 294,976 |
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
- RAC3
- Protein
- p.Pro69=
- Coding
- c.207A>G
- MANE Select
- NM_005052
- Type
- single nucleotide variant
- Location
- chr17:82032810 (GRCh38)
- Gene constraint
- LOEUF 0.726 · pLI 0.28 (gnomAD)
- Structure
- AlphaFold pLDDT 93.92 · 6 PDB
- Residue 69
- an α-helix
Similar variants
- RAC3 p.Asp63Asn Pathogenic/Likely pathogenic ★★ same type
- RAC3 p.Glu62Lys Pathogenic ★★ same type
- RAC3 p.Lys116Asn Pathogenic/Likely pathogenic ★★ same type
- RAC3 p.Tyr64Cys Likely pathogenic ★★ same type
- RAC3 p.Arg120Cys Uncertain significance ★★ ⚠ same type
- RAC3 p.Arg130Gln Uncertain significance ★★ ⚠ same type
- RAC3 p.Arg174Cys Uncertain significance ★★ ⚠ same type
- RAC3 p.Asn92Lys 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/rac3-p-pro69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown