Is BRPF1 p.Asp770fs (c.2308_2309del) pathogenic?

BRPF1 p.Asp770fs (c.23082309del) is classified Pathogenic in BRPF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-12-28). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with BRPF1 p.Asp770fs (c.2308_2309del)?

BRPF1 p.Asp770fs (c.2308_2309del) is associated with Inborn genetic diseases (ClinVar).

How common is BRPF1 p.Asp770fs (c.2308_2309del) in the general population?

BRPF1 p.Asp770fs (c.2308_2309del) is absent from gnomAD (gnomAD).

BRPF1 p.Asp770fs

c.2308_2309del · rs1553696275 · VCV521076

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

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 7 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.4	GERP 0.79, 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.Asp770fs
Coding: c.2308_2309del
MANE Select: NM_001003694
dbSNP: rs1553696275
Type: Deletion
Location: chr3:9743249 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.74 · 66 PDB
Residue 770: 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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BRPF1 p.Lys820fs Pathogenic ★★ same condition
BRPF1 p.Met295fs Pathogenic/Likely pathogenic ★★ same condition
BRPF1 p.Glu472fs Pathogenic ★ same condition
BRPF1 p.Gly306fs Pathogenic ★ same condition
BRPF1 p.Phe10fs Pathogenic ★ same condition
BRPF1 c.3479+3_3479+5del Uncertain significance ★ same condition
BRPF1 p.Phe1154del Likely pathogenic ★★ same condition
BRPF1 p.Arg182Trp Uncertain significance ★★ 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-asp770fs (accessed [today's date]).

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