RXRA p.Pro44=
c.132G>A · rs200082299 · VCV713755
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.43%, amr)
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 -12 | GERP -3.2 |
| Overall | ||
| CADD | 0.876 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.43%
Admixed American · 258/60,016 alleles
Filtering AF
0.387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.37%
Overall
0.0171%
276/1,613,088 alleles · rare
exomes 140/1,460,852 · genomes 136/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.43% | 233 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,831 |
| Finnishnot grpmax-eligible | 0.00476% | 21,028 |
| South Asian | 0.00329% | 30,360 |
| African / African-American | 0.00267% | 37,509 |
| European (non-Finnish) | 0.000593% | 168,567 |
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
- RXRA
- Protein
- p.Pro44=
- Coding
- c.132G>A
- MANE Select
- NM_002957
- dbSNP
- rs200082299
- Type
- single nucleotide variant
- Location
- chr9:134401735 (GRCh38)
- Gene constraint
- LOEUF 0.266 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.67 · 110 PDB
- Residue 44
- the 'modulating' region; the 'disordered' region
Similar variants
- RXRA c.28+1G>A Uncertain significance ★ same type
- RXRA p.Ala391Val Uncertain significance ★ ⚠ same type
- RXRA p.Ala457Thr Uncertain significance ★ ⚠ same type
- RXRA p.Ala457Val Uncertain significance ★ ⚠ same type
- RXRA p.Arg191Cys Uncertain significance ★ ⚠ same type
- RXRA p.Arg211Cys Uncertain significance ★ ⚠ same type
- RXRA p.Asn114Ser Uncertain significance ★ ⚠ same type
- RXRA p.Asn216Lys 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/rxra-p-pro44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown