Is STAC3 p.Val293= (c.879C>A) pathogenic?

STAC3 p.Val293= (c.879C>A) is classified Likely benign in STAC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-30). Ultra-rare (popmax 0.0164%, mid); Associated with Bailey-Bloch congenital myopathy.

What condition is associated with STAC3 p.Val293= (c.879C>A)?

STAC3 p.Val293= (c.879C>A) is associated with Bailey-Bloch congenital myopathy (ClinVar).

How common is STAC3 p.Val293= (c.879C>A) in the general population?

STAC3 p.Val293= (c.879C>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

STAC3 p.Val293=

c.879C>A · rs367701062 · VCV753557

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

Bailey-Bloch congenital myopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.86	GERP -4.5
Overall
CADD	6.098	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000186% 3/1,614,032 alleles · ultra-rare exomes 2/1,461,884 · genomes 1/152,148 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
European (non-Finnish)	0.000169%	590,012

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: STAC3
Protein: p.Val293=
Coding: c.879C>A
MANE Select: NM_145064
dbSNP: rs367701062
Type: single nucleotide variant
Location: chr12:57244205 (GRCh38)
Gene constraint: LOEUF 0.796 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.06 · 5 PDB
Residue 293: the sh3 1 domain; 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.Val293Ile Uncertain significance ★ ⚠ same residue
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

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-val293 (accessed [today's date]).

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