RDX p.Ile359=
c.1077T>C · rs780179701 · VCV3021182
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0988%, mid)
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 2.8 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 7.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0988%
Middle Eastern · 6/6,070 alleles
Filtering AF
0.043%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0293%
Overall
0.0062%
100/1,612,098 alleles · ultra-rare
exomes 97/1,459,886 · genomes 3/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0988% | 1,012 |
| South Asian | 0.0298% | 3,361 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,802 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,395 |
| European (non-Finnish) | 0.00424% | 23,591 |
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.Ile359=
- Coding
- c.1077T>C
- MANE Select
- NM_002906
- dbSNP
- rs780179701
- Type
- single nucleotide variant
- Location
- chr11:110247716 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 86.98 · 2 PDB
Similar variants
- RDX p.Ile359Val Likely benign ★ same residue
- RDX p.Ile359fs Pathogenic/Likely pathogenic ★★ 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
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-ile359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown