STAC3 p.Pro155=
c.465A>C · VCV3703190
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
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 -0.11 | GERP -2.1, phastCons 0.83 |
| Overall | ||
| CADD | 9.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,968 alleles
Overall
0.000124%
2/1,613,736 alleles · very rare
exomes 1/1,461,844 · genomes 1/151,892 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,968 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
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.Pro155=
- Coding
- c.465A>C
- MANE Select
- NM_145064
- Type
- single nucleotide variant
- Location
- chr12:57248166 (GRCh38)
- Gene constraint
- LOEUF 0.796 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.06 · 5 PDB
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-pro155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown