SMARCC2 p.Pro1233=
c.3699G>A · rs181267165 · VCV2643069
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.592%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.4 |
| Overall | ||
| CADD | 1.331 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.592%
Middle Eastern · 34/5,744 alleles
Filtering AF
0.435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.382%
Overall
0.0174%
262/1,506,294 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.592% | 169 |
| Ashkenazi Jewishnot grpmax-eligible | 0.303% | 330 |
| Remaining individualsnot grpmax-eligible | 0.0588% | 1,702 |
| Admixed American | 0.0273% | 3,658 |
| African / African-American | 0.0178% | 5,628 |
| Finnishnot grpmax-eligible | 0.00808% | 12,382 |
| South Asian | 0.00799% | 12,515 |
| European (non-Finnish) | 0.00721% | 13,871 |
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
- SMARCC2
- Protein
- p.Pro1233=
- Coding
- c.3699G>A
- MANE Select
- NM_001330288
- dbSNP
- rs181267165
- Type
- single nucleotide variant
- Location
- chr12:56163728 (GRCh38)
- Gene constraint
- LOEUF 0.167 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 9 PDB
Similar variants
- SMARCC2 c.1311-3C>G Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 c.1926+1G>A Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 c.1926+1G>T Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 c.1926+2T>C Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 p.Arg116His Likely pathogenic ★★ same type
- SMARCC2 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 p.Arg269Ter Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 p.Arg474Ter 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/smarcc2-p-pro1233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown