Associated disorders

The SCN1A gene is associated with a spectrum of autosomal dominant SCN1A-related seizure disorders ranging from simple febrile seizures (MedGen UID: 338959) and generalized epilepsy with febrile seizures plus (GEFS+) (MedGen UID: 388117) to Dravet syndrome (MedGen UID: 148243) and intractable childhood epilepsy with generalized tonic-clonic seizures (ICE-GTC) (MedGen UID: 148243). Other SCN1A-related conditions have been reported (OMIM: 182389).

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Pathogenic variants in the SCN1A gene are associated with 5-10% of generalized epilepsy with febrile seizures plus and ~70% of early infantile epileptic encephalopathy (EIEE) (Dravet syndrome).

Voltage-gated sodium channels allow sodium ions into the cell after the application of a current, as in the case of neuron firing (depolarization). The SCN1A gene encodes the alpha subunit of a voltage-gated sodium channel called NaV1.1. These channels are found in the brain and muscles and control the flow of sodium ions into cells. In the brain, the channels are involved in transmitting signals between nerve cells. The flow of sodium ions through NaV1.1 channels regulates the release of neurotransmitters and the communication between neurons.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
SCN1A NM_001165963.1