GENE REFERENCE / HGNC:11102

SMARCAL1

SNF2 related chromatin remodeling annealing helicase 1

protein-coding gene2q35Gene information

What does this gene do?

The SMARCAL1 gene provides instructions for producing a protein that interacts with DNA. The SMARCAL1 protein helps when the process of making new copies of DNA, called DNA replication, is blocked by DNA damage. When DNA replication stalls, the SMARCAL1 proteins repair DNA damage by reattaching the two strands of DNA's double helix and allowing replication to proceed.

The SMARCAL1 protein is also thought to influence the activity (expression) of other genes through a couple of different mechanisms. One mechanism is by attaching (binding) to certain regions of DNA and turning specific genes on or turning off. The other mechanism is by binding to chromatin, which is the complex of DNA and protein that packages DNA into chromosomes. Research on the function of similar proteins suggests that the SMARCAL1 protein may be involved in a process known as chromatin remodeling. This occurs by changing (remodeling) the structure of chromatin 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.

Source: MedlinePlus, National Library of Medicine. Source publication: 2024-10-01. Source review: 2024-07.

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
SMARCAL1-related tumor predispositionMONDO:1060247 · Evaluated 2026-06-10	Autosomal dominant	StrongChildhood, Adolescent and Young Adult Cancer Predisposition Gene Curation Expert Panel
Schimke immuno-osseous dysplasiaMONDO:0009458 · Evaluated 2021-07-30	Autosomal recessive	DefinitiveSyndromic Disorders 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: 1,424
Submissions for variants in or overlapping this gene: 2,342
Submissions explicitly reporting this gene: 2,290
Alleles reported pathogenic / likely pathogenic: 181
VariationIDs with uncertain significance: 435
VariationIDs with conflicting classifications: 69

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 SMARCAL1?

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 181 alleles in SMARCAL1 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 SMARCAL1.

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

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