SMARCD1
Chr 12ADSWI/SNF related BAF chromatin remodeling complex subunit D1
Also known as: BAF60A, CRACD1, CSS11, Rsc6p
The encoded protein is a component of the SWI/SNF chromatin remodeling complex that uses ATP-dependent mechanisms to alter chromatin structure and regulate gene transcription. Heterozygous loss-of-function mutations cause Coffin-Siris syndrome 11, an autosomal dominant disorder characterized by developmental delay, intellectual disability, and distinctive facial features. The high constraint scores (pLI 0.999, LOEUF 0.206) indicate the gene is highly intolerant to loss-of-function variants, consistent with haploinsufficiency as the disease mechanism.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Highly missense-constrained (top ~0.1%)
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
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
134 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 | 3 | 4 | 4 | 0 | 11 |
Likely Pathogenic | 0 | 2 | 0 | 0 | 2 |
VUS | 7 | 79 | 3 | 0 | 89 |
Likely Benign | 0 | 4 | 3 | 4 | 11 |
Benign | 0 | 1 | 8 | 0 | 9 |
Conflicting | — | 1 | |||
| Total | 10 | 90 | 18 | 4 | 123 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SMARCD1 · 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