Is STAC3 p.Arg321= (c.963C>T) pathogenic?

STAC3 p.Arg321= (c.963C>T) is classified Likely benign in STAC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-25). Very rare (popmax 0.000932%, nfe); Associated with Bailey-Bloch congenital myopathy.

What condition is associated with STAC3 p.Arg321= (c.963C>T)?

STAC3 p.Arg321= (c.963C>T) is associated with Bailey-Bloch congenital myopathy (ClinVar).

How common is STAC3 p.Arg321= (c.963C>T) in the general population?

STAC3 p.Arg321= (c.963C>T) is very rare (popmax 0.000932%, nfe) (gnomAD).

STAC3 p.Arg321=

c.963C>T · rs988981364 · VCV838844

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000932%, nfe)

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 -4.1	GERP -4.3
Overall
CADD	4.08	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000932% European (non-Finnish) · 11/1,180,032 alleles

Filtering AF 0.0005% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000366%

Overall 0.000682% 11/1,613,994 alleles · very rare exomes 9/1,461,884 · genomes 2/152,110 · joint denominator

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.Arg321=
Coding: c.963C>T
MANE Select: NM_145064
dbSNP: rs988981364
Type: single nucleotide variant
Location: chr12:57244121 (GRCh38)
Gene constraint: LOEUF 0.796 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.06 · 5 PDB
Residue 321: the sh3 2 domain; an α-helix

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.Arg321His 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.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-arg321 (accessed [today's date]).

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