SMARCE1 p.Ser262=
c.786C>T · rs2143986926 · VCV1158365
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00447%, eas)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.185 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.53 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 19.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00447%
East Asian · 2/44,764 alleles
Filtering AF
0.000741%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000138%
2/1,451,454 alleles · very rare
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
- SMARCE1
- Protein
- p.Ser262=
- Coding
- c.786C>T
- MANE Select
- NM_003079
- dbSNP
- rs2143986926
- Type
- single nucleotide variant
- Location
- chr17:40631622 (GRCh38)
- Gene constraint
- LOEUF 0.318 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 70.72 · 8 PDB
- Residue 262
- an α-helix
Similar variants
- SMARCE1 p.Ser262Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- SMARCE1 p.Arg105Gln Pathogenic/Likely pathogenic ★★ same condition
- SMARCE1 p.Arg158Ter Pathogenic ★★ same condition
- SMARCE1 p.Arg239Ter Pathogenic ★★ same condition
- SMARCE1 p.Arg251Ter Pathogenic/Likely pathogenic ★★ same condition
- SMARCE1 p.Gln225Ter Pathogenic ★★ same condition
- SMARCE1 p.Glu110Ter Pathogenic ★★ same condition
- SMARCE1 p.Glu165Ter Pathogenic ★★ 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/smarce1-p-ser262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown