STAC3 p.Pro237=
c.711T>C · VCV4917385
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 0.32 | GERP -0.24, phastCons 0.55 |
| Overall | ||
| CADD | 8.068 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,028 alleles
Overall
0.000124%
2/1,614,160 alleles · very rare
exomes 2/1,461,866 · genomes 0/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,028 |
| European (non-Finnish) | 8.47e-05% | 1,180,012 |
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.Pro237=
- Coding
- c.711T>C
- MANE Select
- NM_145064
- Type
- single nucleotide variant
- Location
- chr12:57244925 (GRCh38)
- Gene constraint
- LOEUF 0.796 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.06 · 5 PDB
- Residue 237
- the 'disordered' region
Similar variants
- STAC3 p.Lys288Ter Pathogenic/Likely pathogenic ★★ same type
- STAC3 p.Trp284Ser Pathogenic/Likely pathogenic ★★ same type
- STAC3 p.Ala341Val Uncertain significance ★★ ⚠ same type
- STAC3 p.Arg108Gln Uncertain significance ★★ same type
- STAC3 p.Arg173Cys Uncertain significance ★★ ⚠ same type
- STAC3 p.Arg182His Uncertain significance ★★ same type
- STAC3 p.Arg321His Uncertain significance ★★ ⚠ same type
- STAC3 p.Arg351Leu Uncertain significance ★★ ⚠ same type
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-pro237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown