BRWD3 p.Pro586=
c.1758T>A · rs1418379224 · VCV2416363
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0963%, 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 -0.84 | GERP -3.8 |
| Overall | ||
| CADD | 5.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0963%
Admixed American · 44/45,672 alleles
Filtering AF
0.0737%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0657%
Overall
0.00422%
51/1,207,990 alleles · ultra-rare
exomes 26/1,096,251 · genomes 25/111,739 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0963% | 1,038 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,546 |
| European (non-Finnish) | 0.000672% | 148,916 |
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
- BRWD3
- Protein
- p.Pro586=
- Coding
- c.1758T>A
- MANE Select
- NM_153252
- dbSNP
- rs1418379224
- Type
- single nucleotide variant
- Location
- chrX:80722680 (GRCh38)
- Structure
- AlphaFold pLDDT 65.11
Similar variants
- BRWD3 c.4006-1G>A Likely pathogenic ★★ same type
- BRWD3 p.Arg1240Ter Pathogenic/Likely pathogenic ★★ same type
- BRWD3 p.Arg1694Ter Pathogenic ★★ same type
- BRWD3 p.Arg190Ter Pathogenic ★★ same type
- BRWD3 p.Arg750Ter Pathogenic/Likely pathogenic ★★ same type
- BRWD3 p.Trp1138Ter Pathogenic/Likely pathogenic ★★ same type
- BRWD3 c.2232-3T>C Uncertain significance ★★ same type
- BRWD3 c.90+5G>A 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/brwd3-p-pro586 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown