RECQL4 p.Arg682=
c.2046G>A · rs558318269 · VCV703016
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00409%, afr)
Conditions
2
Baller-Gerold syndrome
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 -0.35 | GERP -3, phastCons 0.094 |
| Overall | ||
| CADD | 3.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00409%
African / African-American · 3/73,302 alleles
Filtering AF
0.00109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000851%
Overall
0.00154%
24/1,556,362 alleles · very rare
exomes 22/1,404,238 · genomes 2/152,124 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00409% | 24,434 |
| Admixed American | 0.00191% | 52,320 |
| European (non-Finnish) | 0.00165% | 60,577 |
| South Asian | 0.00118% | 84,556 |
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
- RECQL4
- Protein
- p.Arg682=
- Coding
- c.2046G>A
- MANE Select
- NM_004260
- dbSNP
- rs558318269
- Type
- single nucleotide variant
- Location
- chr8:144513940 (GRCh38)
- Gene constraint
- LOEUF 1.519 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32 · 2 PDB
Similar variants
- RECQL4 p.Arg682Gly Uncertain significance ★★ ⚠ same residue
- RECQL4 p.Arg682Lys Uncertain significance ★ ⚠ same residue
- RECQL4 c.1132-1G>A Likely pathogenic ★★ same condition
- RECQL4 c.1259-1G>A Pathogenic/Likely pathogenic ★★ same condition
- RECQL4 c.1391-1G>A Pathogenic ★★ same condition
- RECQL4 c.1704+1G>A Pathogenic/Likely pathogenic ★★ same condition
- RECQL4 c.1704+2T>G Likely pathogenic ★★ same condition
- RECQL4 c.1705-1G>A Likely pathogenic ★★ same condition
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/recql4-p-arg682 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown