SMARCE1
Chr 17ADSWI/SNF related BAF chromatin remodeling complex subunit E1
Also known as: BAF57, CSS5
The encoded protein is a component of the SWI/SNF chromatin remodeling complex that binds to 4-way junction DNA and enables transcriptional activation of genes normally repressed by chromatin. Loss-of-function mutations cause Coffin-Siris syndrome 5, a neurodevelopmental disorder characterized by intellectual disability, distinctive facial features, and hypoplastic fifth fingernails and toenails, following an autosomal dominant inheritance pattern. Mutations also predispose to familial meningioma.
Definitive — sufficient evidence for diagnostic panels
2 total gene-disease associations curated
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Moderately missense-constrained (top ~2.5%)
This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Literature Evidence
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
300 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 10 | 4 | 2 | 0 | 16 |
Likely Pathogenic | 5 | 1 | 0 | 0 | 6 |
VUS | 4 | 150 | 11 | 3 | 168 |
Likely Benign | 0 | 4 | 40 | 48 | 92 |
Benign | 0 | 0 | 3 | 0 | 3 |
Conflicting | — | 2 | |||
| Total | 19 | 159 | 56 | 51 | 287 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SMARCE1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools