BRPF1 p.Ser260=
c.780T>C · rs767757496 · VCV3057358
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000932%, nfe)
Conditions
1
BRPF1-related disorder
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 0.66 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 9.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000932%
European (non-Finnish) · 11/1,179,742 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000753%
11/1,461,534 alleles · very rare
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.Ser260=
- Coding
- c.780T>C
- MANE Select
- NM_001003694
- dbSNP
- rs767757496
- Type
- single nucleotide variant
- Location
- chr3:9739179 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.74 · 66 PDB
- Residue 260
- a UniProt-annotated variant site (in idddfp)
Disease context
BRPF1-related disorder
Similar variants
- BRPF1 p.Ser260Arg Uncertain significance ★ ⚠ same residue
- BRPF1 p.Arg251Ter Pathogenic ★★ same condition
- BRPF1 p.Arg455Ter Pathogenic ★★ same condition
- BRPF1 p.Gln643His Uncertain significance ★★ ⚠ same condition
- BRPF1 p.Tyr1149Cys Uncertain significance ★★ ⚠ same condition
- BRPF1 c.2921-1G>C Likely pathogenic ★ same condition
- BRPF1 p.Pro1130Leu Likely pathogenic ★ same condition
- BRPF1 p.Tyr1105Ter Likely pathogenic ★ same condition
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-ser260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown