RAC1 p.Ser41Phe
c.122C>T · VCV3341010
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9807 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
3/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9807 | likely pathogenic ✓ concordant with ClinVar · top 4% in RAC1 |
|---|---|---|
| REVEL | 0.875 | moderately pathogenic-leaning |
| SaProt | LLR -15.93 | damaging |
| ⇒ AlphaMissense, REVEL and SaProt all call this damaging. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 4.6, phastCons 1 |
| Overall | ||
| CADD | 29.3 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- RAC1
- Protein
- p.Ser41Phe
- Coding
- c.122C>T
- MANE Select
- NM_002933 · reported on NM_006908
- Type
- single nucleotide variant
- Location
- chr7:6391938 (GRCh38)
- Structure
- AlphaFold pLDDT 92.87 · 12 PDB
- Residue 41
- the 'disordered' region
Similar variants
- RNASE1 p.Met41Thr Uncertain significance ★ same residue
- RAC1 p.Ser41Tyr Likely pathogenic same residue
- RAC1 p.Arg66Ser Likely pathogenic ★★ same type
- RAC1 p.Asn26Ser Pathogenic ★★ ⚠ same type
- RAC1 p.Asn39Ser Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Pro73Leu Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Ser71Phe Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Tyr32His Pathogenic/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/rac1-p-ser41phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown