Associated disorders

The KCNT1 gene is associated with autosomal dominant nocturnal frontal lobe epilepsy (MedGen UID: 767220) and early infantile epileptic encephalopathy (EIEE) (MedGen UID: 767109).

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KCNT1: Deletion/duplication analysis is not offered for exons 26 or 27.

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Invitae tests that include this gene:

Pathogenic variants in the KCNT1 gene are associated with <5% of clinical cases of autosomal dominant nocturnal frontal lobe epilepsy and are a rare cause of clinical cases of early infantile epileptic encephalopathy (EIEE).

Sodium-activated potassium channels allow potassium ions out of the cell when the intracellular concentration of sodium reaches a critical threshold. The KCNT1 gene, also called Slack in the literature, encodes a sodium-activated potassium channel that is expressed in the brain and participates in sustained and/or repetitive neuronal firing.

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
KCNT1* NM_020822.2

*KCNT1: Deletion/duplication analysis is not offered for exons 26 or 27.