Is RDX p.Arg569= (c.1707A>T) pathogenic?

RDX p.Arg569= (c.1707A>T) is classified Likely benign in RDX (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-20). Very rare (popmax 0.00833%, amr).

How common is RDX p.Arg569= (c.1707A>T) in the general population?

RDX p.Arg569= (c.1707A>T) is very rare (popmax 0.00833%, amr) (gnomAD).

RDX p.Arg569=

c.1707A>T · rs1591131619 · VCV666744

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00833%, 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 -0.044	GERP -4.1, phastCons 0.89
Overall
CADD	5.887	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00833% Admixed American · 5/60,014 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00206%

Overall 0.000434% 7/1,613,378 alleles · very rare exomes 5/1,461,164 · genomes 2/152,214 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00833%	12,003
European (non-Finnish)	0.000169%	589,998

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.Arg569=
Coding: c.1707A>T
MANE Select: NM_002906
dbSNP: rs1591131619
Type: single nucleotide variant
Location: chr11:110231914 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.66 (gnomAD)
Structure: AlphaFold pLDDT 86.98 · 2 PDB

Full RDX gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RDX p.Arg569Gln 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-arg569 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown