SMARCA2 p.Pro291=
c.873C>T · rs1339118310 · VCV1637443
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0456%, eas)
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 -0.032 | GERP -1, phastCons 0.61 |
| Overall | ||
| CADD | 10.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0456%
East Asian · 5/10,954 alleles
Filtering AF
0.0179%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0116%
Overall
0.000491%
5/1,018,640 alleles · ultra-rare
exomes 2/872,474 · genomes 3/146,166 · 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
- SMARCA2
- Protein
- p.Pro291=
- Coding
- c.873C>T
- MANE Select
- NM_003070
- dbSNP
- rs1339118310
- Type
- single nucleotide variant
- Location
- chr9:2047311 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 291
- the 'disordered' region
Similar variants
- SMARCA2 p.Pro291Arg Uncertain significance ★★ ⚠ same residue
- SMARCA2 p.Pro291Leu Uncertain significance ★★ ⚠ same residue
- SMARCA2 p.Pro291Ser Uncertain significance ★★ ⚠ same residue
- SMARCA2 p.Pro291_Pro292insGlyGlyArgProSerProAlaPro Uncertain significance ★ same residue
- SMARCA2 p.Ala1138Pro Pathogenic/Likely pathogenic ★★ same type
- SMARCA2 p.Ala1160Gly Pathogenic ★★ same type
- SMARCA2 p.Ala1201Glu Pathogenic/Likely pathogenic ★★ same type
- SMARCA2 p.Ala1201Val Pathogenic/Likely pathogenic ★★ 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/smarca2-p-pro291 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown