RDX p.Glu41=
c.123G>A · rs528740009 · VCV1576464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
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 -0.2 | GERP -3.2, phastCons 0.3 |
| Overall | ||
| CADD | 6.779 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/59,998 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00155%
25/1,613,816 alleles · ultra-rare
exomes 16/1,461,682 · genomes 9/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,750 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| African / African-American | 0.00267% | 37,492 |
| European (non-Finnish) | 0.00017% | 589,967 |
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
- RDX
- Protein
- p.Glu41=
- Coding
- c.123G>A
- MANE Select
- NM_002906
- dbSNP
- rs528740009
- Type
- single nucleotide variant
- Location
- chr11:110264848 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 86.98 · 2 PDB
- Residue 41
- the ferm domain
Similar variants
- RDX c.*156A>G Uncertain significance ★★ same type
- RDX c.*2006A>G Uncertain significance ★★ same type
- RDX c.*79A>C Uncertain significance ★★ same type
- RDX p.Ala126Pro Uncertain significance ★★ ⚠ same type
- RDX p.Ala442Thr Uncertain significance ★★ ⚠ same type
- RDX p.Arg156Cys Uncertain significance ★★ ⚠ same type
- RDX p.Arg342Cys Uncertain significance ★★ ⚠ same type
- RDX p.Arg342His 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/rdx-p-glu41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown