GENE REFERENCE / HGNC:11098

SMARCA2

SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2

protein-coding gene9p24.3Gene information

What does this gene do?

The SMARCA2 gene provides instructions for making one piece (subunit) of a group of similar protein complexes known as SWI/SNF complexes. These complexes regulate gene activity (expression) by a process known as chromatin remodeling. Chromatin is the network of DNA and proteins that packages DNA into chromosomes. The structure of chromatin can be changed (remodeled) to alter how tightly DNA is packaged. Chromatin remodeling is one way gene expression is regulated during development; when DNA is tightly packed, gene expression is lower than when DNA is loosely packed. SWI/SNF complexes help with chromatin remodeling by moving parts of chromatin called nucleosomes, which makes DNA more accessible for gene expression. To provide energy for chromatin remodeling, the SMARCA2 protein uses a molecule called ATP.

SWI/SNF complexes regulate genes that are involved in many processes, including repairing damaged DNA; copying (replicating) DNA; and controlling the growth, division, and maturation (differentiation) of cells. The SMARCA2 protein and other SWI/SNF subunits are thought to act as tumor suppressors, which keep cells from growing and dividing too rapidly or in an uncontrolled way.

Source: MedlinePlus, National Library of Medicine. Source publication: 2024-10-01. Source review: 2015-12.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
intellectual disability-sparse hair-brachydactyly syndromeMONDO:0011053 · Evaluated 2020-08-18	Autosomal dominant	DefinitiveIntellectual Disability and Autism Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,875
Submissions for variants in or overlapping this gene: 2,870
Submissions explicitly reporting this gene: 2,576
Alleles reported pathogenic / likely pathogenic: 133
VariationIDs with uncertain significance: 596
VariationIDs with conflicting classifications: 66

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about SMARCA2?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 133 alleles in SMARCA2 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in SMARCA2.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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