RDX p.Pro470=
c.1410C>G · rs577555846 · VCV1193938
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0183%, 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 -13 | GERP -4.9 |
| Overall | ||
| CADD | 0.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0183%
Admixed American · 11/59,986 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00785%
Overall
0.00229%
37/1,613,908 alleles · ultra-rare
exomes 35/1,461,828 · genomes 2/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0183% | 5,453 |
| South Asian | 0.00769% | 13,012 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| East Asian | 0.00223% | 44,902 |
| African / African-American | 0.00134% | 74,860 |
| European (non-Finnish) | 0.00119% | 84,285 |
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.Pro470=
- Coding
- c.1410C>G
- MANE Select
- NM_002906
- dbSNP
- rs577555846
- Type
- single nucleotide variant
- Location
- chr11:110233414 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 86.98 · 2 PDB
- Residue 470
- the 'disordered' region
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-pro470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown