Is STAC3 p.Phe92= (c.276C>T) pathogenic?

STAC3 p.Phe92= (c.276C>T) is classified Likely benign in STAC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-16). Absent from gnomAD v4.1; Associated with Bailey-Bloch congenital myopathy.

What condition is associated with STAC3 p.Phe92= (c.276C>T)?

STAC3 p.Phe92= (c.276C>T) is associated with Bailey-Bloch congenital myopathy (ClinVar).

How common is STAC3 p.Phe92= (c.276C>T) in the general population?

STAC3 p.Phe92= (c.276C>T) is absent from gnomAD v4.1 (gnomAD).

STAC3 p.Phe92=

c.276C>T · rs2548121195 · VCV2744024

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Bailey-Bloch congenital myopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 0.32, phastCons 1
Overall
CADD	13.49	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: STAC3
Protein: p.Phe92=
Coding: c.276C>T
MANE Select: NM_145064
dbSNP: rs2548121195
Type: single nucleotide variant
Location: chr12:57249099 (GRCh38)
Gene constraint: LOEUF 0.796 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.06 · 5 PDB
Residue 92: a β-strand

Full STAC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bailey-Bloch congenital myopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

STAC3 p.Lys288Ter Pathogenic/Likely pathogenic ★★ same condition
STAC3 p.Trp284Ser Pathogenic/Likely pathogenic ★★ same condition
STAC3 p.Ala341Val Uncertain significance ★★ ⚠ same condition
STAC3 p.Arg108Gln Uncertain significance ★★ same condition
STAC3 p.Arg173Cys Uncertain significance ★★ ⚠ same condition
STAC3 p.Arg182His Uncertain significance ★★ same condition
STAC3 p.Arg321His Uncertain significance ★★ ⚠ same condition
STAC3 p.Arg351Leu 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/stac3-p-phe92 (accessed [today's date]).

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