RXRB p.Phe384=
c.1152C>T · rs6531 · VCV1254260
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 98%, eas) — too common for a highly-penetrant pathogenic allele
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 4.1 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 11.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
98%
East Asian · 43,965/44,876 alleles
Filtering AF
97.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96.9%
Overall
74%
1,193,009/1,612,344 alleles · common
exomes 1,075,707/1,460,260 · genomes 117,302/152,084 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 98% | 1 |
| South Asian | 85.8% | 1 |
| African / African-American | 84.1% | 1 |
| Middle Eastern | 82.8% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 80.9% | 1 |
| Admixed American | 79.3% | 1 |
| Remaining individualsnot grpmax-eligible | 75.6% | 1 |
| European (non-Finnish) | 71.2% | 1 |
| Finnishnot grpmax-eligible | 70.3% | 1 |
| Amishnot grpmax-eligible | 60.5% | 2 |
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
- RXRB
- Protein
- p.Phe384=
- Coding
- c.1152C>T
- MANE Select
- NM_021976
- dbSNP
- rs6531
- Type
- single nucleotide variant
- Location
- chr6:33195674 (GRCh38)
- Gene constraint
- LOEUF 0.513 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 72.81 · 7 PDB
- Residue 384
- the nr lbd domain; an α-helix
Similar variants
- RXRB c.235+1G>T Uncertain significance ★ same type
- RXRB p.Ala274Val Uncertain significance ★ ⚠ same type
- RXRB p.Ala292Pro Uncertain significance ★ ⚠ same type
- RXRB p.Ala52Gly Uncertain significance ★ ⚠ same type
- RXRB p.Ala54Gly Uncertain significance ★ ⚠ same type
- RXRB p.Arg242Trp Uncertain significance ★ ⚠ same type
- RXRB p.Arg25Gln Uncertain significance ★ ⚠ same type
- RXRB p.Arg35Pro 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/rxrb-p-phe384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown