RDX p.Ile260=
c.780C>T · rs755824075 · VCV286636
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0027%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.48 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.32 | loss · gain 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -5.2 |
| Overall | ||
| CADD | 8.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0027%
African / African-American · 2/74,014 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000928%
Overall
0.00153%
24/1,573,670 alleles · very rare
exomes 23/1,421,698 · genomes 1/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0027% | 37,007 |
| European (non-Finnish) | 0.00175% | 57,229 |
| Admixed American | 0.00167% | 59,732 |
| South Asian | 0.00111% | 90,016 |
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.Ile260=
- Coding
- c.780C>T
- MANE Select
- NM_002906
- dbSNP
- rs755824075
- Type
- single nucleotide variant
- Location
- chr11:110255304 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 86.98 · 2 PDB
- Residue 260
- the ferm domain
Similar variants
- RDX p.Ile260Val Uncertain significance ★★ ⚠ same residue
- 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
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-ile260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown