SMARCC1

Chr 3AD

SWI/SNF related BAF chromatin remodeling complex subunit C1

Also known as: BAF155, CRACC1, HYC5, Rsc8, SRG3, SWI3

NCBI Gene: 6599ENSG00000173473UniProt: Q92922OMIM: 601732

SMARCC1 encodes a component of SWI/SNF chromatin remodeling complexes that alters chromatin structure in an ATP-dependent manner and is essential for neural stem cell proliferation and neuronal differentiation. Mutations cause autosomal dominant congenital hydrocephalus with susceptibility to this condition. The gene is highly constrained against loss-of-function variants (pLI >0.99), reflecting its critical role in neurodevelopment.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 0.121 OMIM phenotype
Clinical Summary— SMARCC1
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Gene-Disease Validity (ClinGen)
SMARCC1-associated developmental dysgenesis syndrome · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.12LOEUF
pLI 1.000
Z-score 7.23
OE 0.04 (0.02–0.12)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
2.45Z-score
OE missense 0.72 (0.67–0.78)
438 obs / 607.7 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.04 (0.02–0.12)
0≤0.351.4
Missense OE0.72 (0.67–0.78)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 3 / 66.7Missense obs/exp: 438 / 607.7Syn Z: 0.24
DN
0.2698th %ile
GOF
0.2796th %ile
LOF
0.82top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.12

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

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SMARCC1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients