Is BRPF1 p.Asp800fs (c.2398del) pathogenic?

BRPF1 p.Asp800fs (c.2398del) is classified Likely pathogenic in BRPF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-09). Absent from gnomAD.

How common is BRPF1 p.Asp800fs (c.2398del) in the general population?

BRPF1 p.Asp800fs (c.2398del) is absent from gnomAD (gnomAD).

BRPF1 p.Asp800fs

c.2398del · rs2125509502 · VCV1335931

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 8 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BRPF1
Protein: p.Asp800fs
Coding: c.2398del
MANE Select: NM_001003694
dbSNP: rs2125509502
Type: Deletion
Location: chr3:9743663 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.74 · 66 PDB
Residue 800: 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)

Full BRPF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BRPF1 p.Ala396fs Pathogenic ★★ same type
BRPF1 p.Gln807fs Pathogenic ★★ same type
BRPF1 p.Lys820fs Pathogenic ★★ same type
BRPF1 p.Met295fs Pathogenic/Likely pathogenic ★★ same type
BRPF1 p.Pro933fs Pathogenic ★★ same type
BRPF1 p.Arg739_Ala742del Uncertain significance ★★ same type
BRPF1 c.3069-1del Likely pathogenic ★ same type
BRPF1 p.Arg200fs Pathogenic ★ 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-asp800fs (accessed [today's date]).

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