RGR p.Ile236=
c.708C>T · VCV3432855
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -6.4 | GERP 0.1 |
| Overall | ||
| CADD | 5.715 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,882 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000434%
7/1,614,204 alleles · very rare
exomes 7/1,461,872 · genomes 0/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,882 |
| South Asian | 0.0022% | 45,541 |
| European (non-Finnish) | 0.000339% | 295,010 |
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.Ile236=
- Coding
- c.708C>T
- MANE Select
- NM_001012720
- Type
- single nucleotide variant
- Location
- chr10:84257970 (GRCh38)
- Structure
- AlphaFold pLDDT 62.88
- Residue 236
- the ras-gef domain
Similar variants
- 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
- RGR p.Ala61Val 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-ile236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown