Is BRD9 p.Ser278= (c.834C>T) pathogenic?

BRD9 p.Ser278= (c.834C>T) is classified Likely benign in BRD9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-03). Very rare (popmax 0.00534%, afr).

How common is BRD9 p.Ser278= (c.834C>T) in the general population?

BRD9 p.Ser278= (c.834C>T) is very rare (popmax 0.00534%, afr) (gnomAD).

BRD9 p.Ser278=

c.834C>T · VCV4646634

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.4	GERP 1.7, phastCons 1
Overall
CADD	14.33	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00534% African / African-American · 4/74,918 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000248% 4/1,612,588 alleles · very rare exomes 0/1,460,424 · genomes 4/152,164 · joint denominator

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: BRD9
Protein: p.Ser278=
Coding: c.834C>T
MANE Select: NM_023924
Type: single nucleotide variant
Location: chr5:884070 (GRCh38)
Gene constraint: LOEUF 0.927 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.72 · 57 PDB

Full BRD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BRD9 c.1526-6A>G Benign ★★ same type
BRD9 p.Pro272= Benign ★★ same type
BRD9 p.Ala10Asp Uncertain significance ★ ⚠ same type
BRD9 p.Ala20Gly Uncertain significance ★ ⚠ same type
BRD9 p.Ala232Thr Uncertain significance ★ ⚠ same type
BRD9 p.Ala306Thr Uncertain significance ★ ⚠ same type
BRD9 p.Ala346Thr Uncertain significance ★ ⚠ same type
BRD9 p.Ala537Val 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/brd9-p-ser278 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown