RAC3 p.Val9=
c.27C>T · VCV4937701
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00357%, afr)
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 0.29 | GERP -3.5, phastCons 0.99 |
| Overall | ||
| CADD | 17.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00357%
African / African-American · 2/55,964 alleles
Filtering AF
0.000593%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000222%
Overall
0.000616%
6/974,194 alleles · very rare
exomes 3/831,820 · genomes 3/142,374 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00357% | 27,982 |
| European (non-Finnish) | 0.000486% | 205,749 |
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.Val9=
- Coding
- c.27C>T
- MANE Select
- NM_005052
- Type
- single nucleotide variant
- Location
- chr17:82031788 (GRCh38)
- Gene constraint
- LOEUF 0.726 · pLI 0.28 (gnomAD)
- Structure
- AlphaFold pLDDT 93.92 · 6 PDB
- Residue 9
- a β-strand
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-val9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown