RGR p.Ser29=
c.87C>T · rs779017984 · VCV1665471
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
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 |
|---|---|---|
| Pangolin | Δ0.21 | loss · gain 0.18 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -4.9 | GERP -1.8 |
| Overall | ||
| CADD | 5.864 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,086 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.00211%
34/1,614,046 alleles · very rare
exomes 29/1,461,852 · genomes 5/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,121 |
| East Asian | 0.00668% | 14,965 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed American | 0.00333% | 30,007 |
| European (non-Finnish) | 0.00144% | 69,414 |
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.Ser29=
- Coding
- c.87C>T
- MANE Select
- NM_001012720
- dbSNP
- rs779017984
- Type
- single nucleotide variant
- Location
- chr10:84247598 (GRCh38)
- Structure
- AlphaFold pLDDT 62.88
Similar variants
- RGR p.Ser29Tyr 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
- RGR p.Ala251Val 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-ser29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown