Is BRPF1 p.Val351fs (c.1052_1053del) pathogenic?

BRPF1 p.Val351fs (c.10521053del) is classified Pathogenic in BRPF1 (ClinVar, Single submitter, 2 submitters; last evaluated 2016-02-11). Absent from gnomAD; Associated with intellectual disability.

What condition is associated with BRPF1 p.Val351fs (c.1052_1053del)?

BRPF1 p.Val351fs (c.1052_1053del) is associated with intellectual disability, intellectual developmental disorder with dysmorphic facies and ptosis (ClinVar).

How common is BRPF1 p.Val351fs (c.1052_1053del) in the general population?

BRPF1 p.Val351fs (c.1052_1053del) is absent from gnomAD (gnomAD).

BRPF1 p.Val351fs

c.1052_1053del · rs886041090 · VCV268185

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability

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 3 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	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.Val351fs
Coding: c.1052_1053del
MANE Select: NM_001003694
dbSNP: rs886041090
Type: Microsatellite
Location: chr3:9739449 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.74 · 66 PDB
Residue 351: a UniProt-annotated variant site (in idddfp); an α-helix

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

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: intellectual developmental disorder with dysmorphic facies and ptosis

Similar variants

BRPF1 p.Phe1154del Likely pathogenic ★★ same condition
BRPF1 p.Asp1006_Ser1007insTer Pathogenic same condition
BRPF1 p.Glu121fs Pathogenic same condition
BRPF1 p.Ala396fs Pathogenic ★★ same condition
BRPF1 p.Arg1100Ter Pathogenic/Likely pathogenic ★★ same condition
BRPF1 p.Arg251Ter Pathogenic ★★ same condition
BRPF1 p.Arg455Ter Pathogenic ★★ same condition
BRPF1 p.Gln807fs 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-val351fs (accessed [today's date]).

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