Associated disorders

The SPTLC1 gene is associated with autosomal dominant hereditary sensory and autonomic neuropathy type 1A (HSAN1A) (MedGen UID: 5645).

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Invitae tests that include this gene:

Pathogenic variants in SPTLC1 account for 12% of patients with hereditary sensory and autonomic neuropathy.

SPTLC1 encodes a subunit of serine palmitoyltransferase (SPT). SPT is located at the outer membrane of the endoplasmic reticulum and is the initial enzyme in sphingolipid biosynthesis. Sphingolipids, having both a structural and a signaling function, are essential for all eukaryotic cells.

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
SPTLC1 NM_006415.3