BRWD3 p.Pro256=
c.768C>T · VCV4951804
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0088%, sas)
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 -1.3 | GERP -3.6, phastCons 0.001 |
| Overall | ||
| CADD | 3.852 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0088%
South Asian · 5/56,803 alleles
Filtering AF
0.0034%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00217%
Overall
0.00132%
16/1,209,462 alleles · very rare
exomes 15/1,097,775 · genomes 1/111,687 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0088% | 11,361 |
| East Asian | 0.00296% | 33,770 |
| Admixed American | 0.00219% | 45,658 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,600 |
| European (non-Finnish) | 0.000894% | 111,861 |
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.Pro256=
- Coding
- c.768C>T
- MANE Select
- NM_153252
- Type
- single nucleotide variant
- Location
- chrX:80744077 (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-pro256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown