RGR p.Asp86=
c.258C>T · rs561362389 · VCV1088771
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0602%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.059 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.27 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -13 |
| Overall | ||
| CADD | 0.082 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0602%
East Asian · 27/44,878 alleles
Filtering AF
0.0424%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.00607%
98/1,614,106 alleles · ultra-rare
exomes 88/1,461,790 · genomes 10/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0602% | 1,662 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,250 |
| Admixed American | 0.0133% | 7,502 |
| African / African-American | 0.00666% | 15,010 |
| European (non-Finnish) | 0.00381% | 26,223 |
| South Asian | 0.0022% | 45,543 |
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
- RGR
- Protein
- p.Asp86=
- Coding
- c.258C>T
- MANE Select
- NM_001012720
- dbSNP
- rs561362389
- Type
- single nucleotide variant
- Location
- chr10:84248943 (GRCh38)
- Structure
- AlphaFold pLDDT 62.88
Similar variants
- RGR p.Asp86Gly Uncertain significance ★ ⚠ same residue
- RGR p.Asp86fs Uncertain significance ★ same residue
- RGR c.358+1G>A Uncertain significance ★★ same type
- RGR p.Ala110Thr Uncertain significance ★★ ⚠ same type
- RGR p.Ala186Thr Uncertain significance ★★ ⚠ same type
- RGR p.Ala217Gly Uncertain significance ★★ ⚠ same type
- RGR p.Ala234Thr Uncertain significance ★★ ⚠ same type
- RGR p.Ala251Thr 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/rgr-p-asp86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown