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  • Alternate specimens:
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CLN3

Alias

BTN1; BTS; JNCL

Associated disorders

The CLN3 gene is associated with autosomal recessive neuronal ceroid lipofuscinosis type 3 (CLN3) (MedGen UID: 155549).

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CLN3

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CLN3: Analysis includes the intronic variant NM_001042432.1; c.461-13G>C.


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Invitae tests that include this gene:

Pathogenic variants in the CLN3 gene are associated with >98% of clinical cases of juvenile-onset neuronal ceroid lipofuscinosis (NCL) (CLN3).

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, then 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 CLN3 gene encodes a protein of unknown function but is thought to play a role in autophagy, endocytosis, and regulation of pH to support normal lysosome function (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 in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

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
CLN3* NM_001042432.1


*CLN3: Analysis includes the intronic variant NM_001042432.1; c.461-13G>C.