BRPF1 p.Phe682=
c.2046C>T · rs779160179 · VCV2672926
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 4 | GERP -0.41, phastCons 1 |
| Overall | ||
| CADD | 12.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00124%
20/1,614,074 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| South Asian | 0.00329% | 30,358 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.00127% | 78,670 |
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
- BRPF1
- Protein
- p.Phe682=
- Coding
- c.2046C>T
- MANE Select
- NM_001003694
- dbSNP
- rs779160179
- Type
- single nucleotide variant
- Location
- chr3:9742988 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.74 · 66 PDB
- Residue 682
- the bromo domain; the 'interaction with meaf6 and ing5' region; the 'required for runx1 and runx2 transcriptional activation' region; a UniProt-annotated variant site (in idddfp); a UniProt-annotated variant site (in idddfp; decreased histone h3-k23 acetylation; increased localization to the nucleus; decreased expression and assembly of the moz/morf complex); an α-helix
Similar variants
- BRPF1 p.Arg1100Ter Pathogenic/Likely pathogenic ★★ same type
- BRPF1 p.Arg251Ter Pathogenic ★★ same type
- BRPF1 p.Arg455Ter Pathogenic ★★ same type
- BRPF1 p.Trp478Ter Pathogenic/Likely pathogenic ★★ same type
- BRPF1 p.Ala363Thr Uncertain significance ★★ ⚠ same type
- BRPF1 p.Ala601Thr Uncertain significance ★★ ⚠ same type
- BRPF1 p.Arg106Cys Uncertain significance ★★ ⚠ same type
- BRPF1 p.Arg157His 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/brpf1-p-phe682 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown