GENE REFERENCE / HGNC:10588

SCN2A

sodium voltage-gated channel alpha subunit 2

protein-coding gene2q24.3Gene information

What does this gene do?

The SCN2A gene belongs to a family of genes that provide instructions for making sodium channels. These channels, which transport positively charged atoms (ions) of sodium into cells, play a key role in a cell's ability to generate and transmit electrical signals.

The SCN2A gene provides instructions for making one part (the alpha subunit) of a sodium channel called NaV1.2. These channels are primarily found in the brain, where they control the flow of sodium ions into nerve cells (neurons). NaV1.2 channels are involved in transmitting signals from one neuron to another. Communication between neurons depends on chemicals called neurotransmitters, which are released from one neuron and taken up by neighboring neurons. The flow of sodium ions through NaV1.2 channels helps determine when neurotransmitters will be released.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-07-01. Source review: 2025-07.

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
complex neurodevelopmental disorderMONDO:0100038 · Evaluated 2019-05-07	Autosomal dominant	DefinitiveEpilepsy 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: 3,175
Submissions for variants in or overlapping this gene: 5,298
Submissions explicitly reporting this gene: 5,158
Alleles reported pathogenic / likely pathogenic: 746
VariationIDs with uncertain significance: 1,314
VariationIDs with conflicting classifications: 151

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 SCN2A?

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 746 alleles in SCN2A 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 SCN2A.

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

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