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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) and non-syndromic retinitis pigmentosa (PMID: 28542676, 24154662).

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 and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
CLN3 NM_001042432.1