Is MYO7A p.Thr54fs (c.160_164del) pathogenic?

MYO7A p.Thr54fs (c.160164del) is classified Likely pathogenic in MYO7A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-22). Associated with Usher syndrome type 1B.

What condition is associated with MYO7A p.Thr54fs (c.160_164del)?

MYO7A p.Thr54fs (c.160_164del) is associated with Usher syndrome type 1B (ClinVar).

MYO7A p.Thr54fs

c.160_164del · VCV4818014

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Usher syndrome type 1B

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 49
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.9	GERP -0.45, phastCons 1

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

Variant & gene context

Gene: MYO7A
Protein: p.Thr54fs
Coding: c.160_164del
MANE Select: NM_000260
Type: Microsatellite
Location: chr11:77147819 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB

Full MYO7A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Usher syndrome type 1B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYO7A p.Thr54Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
MYO7A p.Glu1716del Pathogenic/Likely pathogenic ★★ same condition
MYO7A p.Phe1963del Pathogenic/Likely pathogenic ★★ same condition
MYO7A p.Ser423fs Likely pathogenic ★★ same condition
MYO7A p.Val1501fs Pathogenic/Likely pathogenic ★★ same condition
MYO7A c.3924+31_3924+46del Benign/Likely benign ★★ same condition
MYO7A p.Ala601fs Likely pathogenic ★ same condition
MYO7A p.Leu2130del 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/myo7a-p-thr54fs (accessed [today's date]).

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