Is USP7 p.Glu83fs (c.247_250del) pathogenic?

USP7 p.Glu83fs (c.247250del) is classified Pathogenic in USP7 (ClinVar, No assertion criteria, 1 submitter). No gnomAD frequency available for this variant; Associated with Hao-Fountain syndrome.

What condition is associated with USP7 p.Glu83fs (c.247_250del)?

USP7 p.Glu83fs (c.247_250del) is associated with Hao-Fountain syndrome (ClinVar).

How common is USP7 p.Glu83fs (c.247_250del) in the general population?

USP7 p.Glu83fs (c.247_250del) is no gnomAD frequency available for this variant (gnomAD).

USP7 p.Glu83fs

c.247_250del · rs2549250330 · VCV1713161

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Hao-Fountain syndrome

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 31
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.7	GERP 2.3, 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: USP7
Protein: p.Glu83fs
Coding: c.247_250del
MANE Select: NM_003470
dbSNP: rs2549250330
Type: Microsatellite
Location: chr16:8923348 (GRCh38)
Gene constraint: LOEUF 0.085 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 86.50 · 86 PDB
Residue 83: the math domain; the 'interaction with tspyl5' region; the 'interaction with p53/tp53, mdm2 and ebna1' region; the 'necessary for nuclear localization' region

Full USP7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Hao-Fountain syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hao-Fountain syndrome (Orphanet):

Onset: Infancy, Neonatal

Similar variants

USP7 p.Arg723fs Likely pathogenic ★ same condition
USP7 p.Gln617fs Likely pathogenic ★ same condition
USP7 p.Glu83Ala Uncertain significance ★ ⚠ same residue
USP7 p.Arg745fs Likely pathogenic same condition
USP7 p.Gln866Ter Pathogenic/Likely pathogenic ★★ same condition
USP7 c.3039+3A>G Uncertain significance ★★ same condition
USP7 c.852-4A>G Uncertain significance ★★ same condition
USP7 p.Thr177Asn 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/usp7-p-glu83fs (accessed [today's date]).

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