RDX p.Pro259=
c.777A>G · rs142773831 · VCV286303
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0151%, nfe)
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 -0.94 | GERP -2.6, phastCons 0.006 |
| Overall | ||
| CADD | 9.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0151%
European (non-Finnish) · 173/1,148,968 alleles
Filtering AF
0.0132%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0125%
Overall
0.0117%
184/1,579,036 alleles · ultra-rare
exomes 174/1,426,864 · genomes 10/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0151% | 6,641 |
| Remaining individualsnot grpmax-eligible | 0.0131% | 7,663 |
| Admixed American | 0.00334% | 29,906 |
| African / African-American | 0.00135% | 74,210 |
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.Pro259=
- Coding
- c.777A>G
- MANE Select
- NM_002906
- dbSNP
- rs142773831
- Type
- single nucleotide variant
- Location
- chr11:110255307 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 86.98 · 2 PDB
- Residue 259
- 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-pro259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown