• Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit



Associated disorders

The PPT1 gene is associated with autosomal recessive forms of neuronal ceroid lipofuscinosis including classic infantile, late-infantile, juvenile and adult CLN1 disease. [MedGen UID: 340540]

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Order this gene as a single gene test.

PPT1: Analysis includes the large, mostly intronic deletion NM_000310.3:c.124+1215_235-102del3627.

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Invitae tests that include this gene:

Pathogenic variants in the PPT1 gene are associated with >98% of clinical cases of neuronal ceroid lipofuscinosis (NCL) type 1 (CLN1).

The cell is continually producing essential building blocks for life, such as proteins, metabolites, sugars, and lipids. These components are also continually degraded, as they become damaged, overabundant, or unnecessary. If this balance is disrupted, excess components can accumulate in the cell, interfering with normal function and causing toxicity. Defects in lysosomes, acidic cellular organelles that degrade cellular components, cause a group of conditions known as lysosomal storage disorders. The PPT1 gene, also called CLN1 in the literature, encodes a protein involved in vesicle recycling, cholesterol metabolism, and cell death (PMID: 25962910).

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
PPT1* NM_000310.3

*PPT1: Analysis includes the large, mostly intronic deletion NM_000310.3:c.124+1215_235-102del3627.