Neuronal Ceroid Lipofuscinosis Type 3 via the CLN3 Gene

Neuronal ceroid lipofuscinosis type three (also known as CLN3 disease) is an inherited neurodegenerative disorder. Characteristic features at onset include deterioration of vision and psychomotor function, followed by seizures and changes in personality and behavior. Vision loss, regression of motor skills, and intellectual decline continue to progress over time, ultimately resulting in total disability, blindness and premature death. Life expectancy typically ranges from teenage years to the third decade. CLN3 disease symptoms usually become apparent in children between 5-10 years of age, yet reported age of first symptoms ranges widely, from infancy to adulthood. Children develop normally prior to onset of disease, which often presents as deterioration of vision and difficulty in school, then loss of the ability to communicate in complete sentences. Psychosis and aggressive outbursts are commonly observed. Motor decline frequently presents as clumsiness, stumbling, rigidity, and decreased movement. More rarely, patients develop cardiac problems such as abnormal heart rythms and hypertrophic cardiomyopathy (Ostergaard. 2016. PubMed ID: 30050370).

CLN3 disease was previously called Batten disease, however the term Batten disease is now more commonly used as a general term for all forms of neuronal ceroid lipofuscinoses (NCLs). CLN3 disease is one of the most common types of NCL, with an estimated prevalence of 1/~220,000. Collectively, NCLs are the most common type of neurodegenerative disorders of childhood, estimated to affect roughly 1 in 100,000 individuals worldwide (Sleat et al. 2016. PubMed ID: 27553520; Mole and Williams. 2013. PubMed ID: 20301601).

While a majority of the reported CLN3 variants cause the classic autosomal recessive CLN3 disease profiled above, some variants cause a milder form of the disorder with a protracted course. In addition, recent studies have reported several CLN3 variants that cause autosomal recessive isolated retinal degeneration that does not progress to the syndromic neurodegenerative course of classic CLN3 disease (Ku et al. 2017. PubMed ID: 28542676). Finally, a handful of variants have been reported in association with both classic CLN3 disease and nonsyndromic retinal disease (Mirza et al. 2019. PubMed ID: 31568712).

Currently, there are no treatments for CLN3 disease, yet advantages of testing may include: 1) prognostic information, including reported genotype-phenotype correlations to predict the expected severity and course of the disorder, 2) early identification and treatment of symptoms such as seizures and psychosis, 3) prenatal testing or pre-implantation genetic diagnosis for future pregnancies, 4) quick access to resource help from schools and social services (Elmerskog et al. 2019. PubMed ID: 31152869), 5) opportunity to join family support groups such as the Batten Disease Support and Research Association (bdsra.org), and 6) ability to participate in clinical trials of new therapies for this disorder, such as the one currently listed at ClinicalTrials.gov (https://clinicaltrials.gov/ct2/show/NCT03770572).

Pathogenic variants in the CLN3 gene cause CLN3 disease, an autosomal recessive disease categorized as a lysosomal storage disorder. Pathogenic CLN3 alteration types include missense, nonsense, frame shift, synonymous, splicing, and gross deletion variants. A ~1 kb deletion of two exons (c.461-280_677+382del) accounts for ~85% of pathogenic alleles and is observed in the homozygous state in ~73% of CLN3 patients. The majority of pathogenic variants in CLN3 lead to premature protein termination, yet other variant types are increasingly reported, and may be associated with the milder isolated retinal-degeneration form of disease, or a protracted course of classic CLN3 disease. To our knowledge, no large duplication events have been reported as causative. Pathogenic variants are spread widely throughout the gene, with some clustering in the predicted lumenal regions of the protein (loops facing the inside of the lysosome or other organelle as opposed to the cell's cytoplasm)(Mirza et al. 2019. PubMed ID: 31568712). Genotype-phenotype correlations are predicted for CLN3, especially based on the recent findings of variants associated with isolated retinal degeneration or protracted disease course; yet the exact relationships have not yet fully come to light (Ku et al. 2017. PubMed ID: 28542676; Adams et al. 2010. PubMed ID: 20187884; Kitzmüller et al. 2008. PubMed ID: 17947292).

Affected individuals inherit one causative variant from each of their parents, resulting in either homozygous or compound heterozygous causative changes. De novo variants are not commonly reported for CLN3. The CLN3 gene is broadly tolerant to heterozygous variation, and carriers do not show any clinical features of the disorder. While the disease is thought to be fully penetrant, some variable expressivity is documented (Mirza et al. 2019. PubMed ID: 31568712). For all types of pathogenic variants combined, the United States carrier frequency is predicted to be ~1/470 individuals, or 0.2% allele frequency (Sleat et al. 2016. PubMed ID: 27553520). The most common single nucleotide variants are reported at an allele frequency of <0.02% in gnomAD, or ~1/5000 carrier frequency (gnomAD database; Human Gene Mutation Database).

One of the cellular hallmarks of disease is the toxic accumulation of materials in lysosomes, instead of being broken down and recycled. The CLN3 protein, called Battenin, is membrane-bound, with a high concentration on the lysosomal membrane, but it is also seen in many other cellular membranes. Battenin is widely expressed throughout the body, yet the central nervous system appears particularly sensitive to the effects of a dysfunctional version. Neuronal death causes the classic features of CLN3 disease, which results when both copies of Battenin are mutated, and subsequently rapidly degraded instead of performing their predicted normal roles in membrane transport, vesicular trafficking, and other cellular functions (Mirza et al. 2019. PubMed ID: 31568712). Numerous mouse and cell culture models have been developed to study the CLN3 gene, and recently these models are increasingly being used to test potential treatments for CLN3 disease (Cotman et al. 2002. PubMed ID: 12374761; Schultz et al. 2018. PubMed ID: 29660499; Mole and Williams. 2013. PubMed ID: 20301601).

CLN3 disease is one of the most common forms of neuronal ceroid lipofuscinosis (NCL). NCLs are clinically divided into 14 subtypes - CLN1-CLN14, resulting from pathogenic variants in thirteen causative genes. Initially CLN9 was thought to be a distinct subtype, but is now attributed to variants in CLN5 (Mole and Williams. 2013. PubMed ID: 20301601; Cárcel-Trullols et al. 2015. PubMed ID: 25962910).

Pathogenic variants in the CLN3 gene are one of the most common causes of juvenile-onset neuronal ceroid lipofuscinosis worldwide. Incidence for the different NCL subtypes ranges between ethnicities, yet a recent estimate for United States disease incidence of the CLN3 subtype suggests that it accounts for ~25% of NCL disease (Sleat et al. 2016. PubMed ID: 27553520). Therefore, this test is expected to identify biallelic pathogenic variants in at least a quarter of tested individuals, and is likely to have a higher diagnostic yield when combined with careful clinical phenotyping and completion of other recommended tests (see the NCL diagnostic algorithm in Schulz et al. 2013. PubMed ID: 23602993). To increase clinical sensitivity, the Neuronal Ceroid Lipofuscinoses (Batten disease) Gene Panel could be considered as an alternative test.

Analytical sensitivity of this test is expected to be very high (>98%), as this test will detect the vast majority of known pathogenic variants in CLN3, including large copy number variants (CNVs), such as the common 1 kb deletion (Munroe et al. 1997. PubMed ID: 9311735; Mole and Williams. 2013. PubMed ID: 20301601).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the CLN3 genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing.