RARB p.Phe82=
c.246C>T · VCV4961526
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 15.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,884 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000496%
8/1,613,932 alleles · very rare
exomes 7/1,461,866 · genomes 1/152,066 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,442 |
| South Asian | 0.00329% | 30,357 |
| European (non-Finnish) | 0.000254% | 393,335 |
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
- RARB
- Protein
- p.Phe82=
- Coding
- c.246C>T
- MANE Select
- NM_000965
- Type
- single nucleotide variant
- Location
- chr3:25461281 (GRCh38)
- Gene constraint
- LOEUF 0.477 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 80.68 · 9 PDB
- Residue 82
- the 'modulating' region
Similar variants
- RARB p.Arg387Cys Pathogenic/Likely pathogenic ★★ same type
- RARB p.Gln404Ter Pathogenic/Likely pathogenic ★★ same type
- RARB p.Gly282Ser Pathogenic/Likely pathogenic ★★ same type
- RARB p.Gly384Asp Likely pathogenic ★★ same type
- RARB p.Leu213Pro Pathogenic/Likely pathogenic ★★ same type
- RARB p.Leu407Pro Likely pathogenic ★★ same type
- RARB p.Ser398Ter Pathogenic/Likely pathogenic ★★ same type
- RARB p.Arg137Ter 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/rarb-p-phe82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown