Associated disorders

The SCN9A gene is associated with autosomal dominant generalized epilepsy with febrile seizures plus (MedGen UID: 416629) and primary erythermalgia, also referred to as small fiber neuropathy (MedGen UID: 8688). The SCN9A gene is also associated with autosomal recessive congenital insensitivity to pain (CIP), also referred to as hereditary sensory and autonomic neuropathy type 2D (HSAN2D) (MedGen UID: 344563). Other SCN9A-related conditions have also been reported (OMIM: 60345).

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The proportion of HSAN contributed by SCN9A is unknown. However, pathogenic mutations in the SCN9A gene account for approximately 30 percent of cases of small fiber neuropathy.

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 SCN9A gene encodes the alpha subunit of a voltage-gated sodium channel expressed in the peripheral nervous system, and it is required for regulating depolarization and re-establishing resting membrane potential.

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
SCN9A NM_002977.3