Is USB1 p.Phe260del (c.776TCT[1]) pathogenic?

USB1 p.Phe260del (c.776TCT[1]) is classified Uncertain significance in USB1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-03-24). Absent from gnomAD.

How common is USB1 p.Phe260del (c.776TCT[1]) in the general population?

USB1 p.Phe260del (c.776TCT[1]) is absent from gnomAD (gnomAD).

USB1 p.Phe260del

c.776TCT[1] · rs2142314709 · VCV1338657

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

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.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP -0.37, phastCons 1

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: USB1
Protein: p.Phe260del
Coding: c.776TCT[1]
MANE Select: NM_024598
dbSNP: rs2142314709
Type: Microsatellite
Location: chr16:58020222 (GRCh38)
Gene constraint: LOEUF 1.016 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.91 · 5 PDB
Residue 260: a β-strand

Full USB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

USB1 p.Phe260_Ser261insTer Uncertain significance ★★ same residue
USB1 p.Phe260Leu Uncertain significance ★ ⚠ same residue
USB1 p.Phe260Val Uncertain significance ★ same residue
USB1 c.*317CT[5] Benign/Likely benign ★★ same type
USB1 p.Ser147del Uncertain significance ★ same type
USB1 c.449+12_449+14del Likely benign ★ same type
USB1 c.450-1938_450-1926del Likely benign ★ 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/usb1-p-phe260del (accessed [today's date]).

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