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Neuronal Ceroid Lipofuscinosis 5 via the CLN5 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
CLN5 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7601CLN581479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Renee Bend, PhD

Clinical Features and Genetics

Clinical Features

The neuronal ceroid lipofuscinoses (NCLs) are inherited neurodegenerative lysosomal storage disorders caused by the accumulation of ceroid and lipofuscin in various cell types, mainly cells of the cerebral cortex, cerebellar cortex, and retina (Dyken et al. 1988; Williams and Mole 2012). Characteristic features at onset include clumsiness; deterioration of vision and psychomotor functions; seizures and behavioral changes. Progression of clinical features results ultimately in total disability, blindness and premature death. Although NCL affects primarily children, age of onset of symptoms varies from infancy to adulthood. The incidence of NCL is variable and ranges from 1.3 to 7 per 100,000 (Mole and Williams 2013). However, it is more common in the northern European populations, particularly Finland where the incidence may reach 1 in 12,500 individuals and a carrier frequency of 1 in 70 (Rider and Rider 1988; Vesa et al. 1995). NCLs are clinically and genetically heterogeneous. A nomenclature and classification based both on the age of onset of symptoms and the disease-causing gene has been recently developed, which classifies NCLs into thirteen subtypes (CLN1-8, 10-14) (Williams and Mole 2012). The causative gene for the CLN9 phenotype has not been identified yet (Schulz et al. 2004). Of note, NCLs were previously known as Batten disease. However, in recent nomenclature, Batten disease only applies to NCL caused by mutations in CLN3.

CLN5 is further divided into three subgroups based on the age of onset of symptoms.

1) CLN5 disease, variant late infantile, previously known as Finnish variant late infantile, is the most common of the three. It is characterized by onset between 4-7 years of age and death in the third decade of life. Motor decline is usually the first manifestation followed by seizures and psychomotor and visual decline (Santavuori et al. 1982; Holmberg et al. 2000).

2) CLN5 disease, juvenile, is characterized by onset during childhood. Motor and visual decline and tremor of the lower limbs are usually the first symptoms. Additional features develop later in age and include seizures, cognitive decline and behavioral changes (Pineda-Trujillo et al. 2005; Xin et al. 2010).

3) CLN5 disease, adult, has been reported in a few cases only. In these patients, symptoms began during the late teens and survival was prolonged into the fourth decade of life. Cognitive and motor decline were the first reported symptoms. Epileptic seizures developed in later age. Visual impairment was absent in some cases (Goebel et al. 1998; Sleat et al. 2009; Xin et al. 2010).


Most CLNs are inherited in an autosomal recessive manner. Thirteen genes have been implicated in the disorder: PPT1, TPP1, CLN3, CLN5, CLN6, MFSD8, CLN8, CTSD, DNAJC5, CTSF, ATP13A2, GRN, and KCTD7 (Mole and Williams 2013). Pathogenic variants in the CLN5 gene, which were first documented in Finnish families, cause CLN5 (Savukoski et al. 1998). Subsequently, about 40 CLN5 pathogenic variants have been reported in patients of various ethnic and geographical origins such as Northern European, Chinese, Asian Indian, Hispanic, Pakistani, south American and Arabic (Xin et al. 2010; Al-Kowari et al. 2011). Pathogenic variants include missense, nonsense, small insertions or deletions, and one large deletion. Most of these variants are predicted to result in truncated proteins.

The CLN5 gene encodes a soluble lysosomal glycoprotein of unknown function. Mutations in the CLN5 gene appear to affect the normal lysosomal trafficking of the mutated proteins (Schmiedt et al, 2010).

Clinical Sensitivity - Sequencing with CNV PG-Select

This test will detect pathogenic variants in the CLN5 gene in about 20% of patients of various ethnicities with a clinical diagnosis of CLN and without pathogenic variants in the CLN1, CLN2, CLN3, CLN6, and CLN8 genes (Xin et al. 2010).

Testing Strategy

This test provides full coverage of all coding exons of the CLN5 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients, regardless of their ethnic or geographical origins, with a clinical diagnosis of: 1-CLN5 disease, variant late infantile. 2-CLN5 disease, juvenile. 3-CLN5 disease, adult with or without visual impairment. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CLN5.


Official Gene Symbol OMIM ID
CLN5 608102
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Ceroid Lipofuscinosis Neuronal 5 AR 256731

Related Test

Neuronal Ceroid Lipofuscinoses (Batten Disease) Panel


  • Al-Kowari MK, Hassan S, El-Said MF, Ben-Omran T, Hedin L, Mole SE, Badii R. 2011. Neuronal ceroid lipofuscinosis in Qatar: report of a novel mutation in ceroid-lipofuscinosis, neuronal 5 in the Arab population. J Child Neurol. 26:625-629. PubMed ID: 21447811
  • Dyken PR, Opitz JM, Reynolds JF, Pullarkat RK. 1988. Reconsideration of the classification of the neuronal ceroid-lipofuscinoses. American Journal of Medical Genetics 31: 69–84. PubMed ID: 3146331
  • Goebel HH, Schochet SS, Jaynes M, Gutmann L. 1998. Ultrastructure of the retina in adult neuronal ceroid lipofuscinosis. Acta Anat (Basel) 162:127-132.
    PubMed ID: 9831759
  • Holmberg V, Lauronen L, Autti T, Santavuori P, Savukoski M, Uvebrant P, Hofman I, Peltonen L, Järvelä I. 2000. Phenotype-genotype correlation in eight patients with Finnish variant late infantile NCL (CLN5). Neurology 55:579-581. PubMed ID: 10953198
  • Mole S.E., Williams R.E. 2013. Neuronal Ceroid-Lipofuscinoses. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301601
  • Pineda-Trujillo N, Cornejo W, Carrizosa J, Wheeler RB, Múnera S, Valencia A, Agudelo-Arango J, Cogollo A, Anderson G, Bedoya G, Mole SE, Ruíz-Linares A. 2005. A CLN5 mutation causing an atypical neuronal ceroid lipofuscinosis of juvenile onset. Neurology 64:740-742. PubMed ID: 15728307
  • Rider J.A., Rider D.L. 1988. American journal of medical genetics. Supplement. 5: 21-6. PubMed ID: 3146319
  • Santavuori P, Rapola J, Sainio K, Raitta C. 1982. A variant of Jansky-Bielschowsky disease. Neuropediatrics 13:135-141. PubMed ID: 7133332
  • Savukoski M, Klockars T, Holmberg V, Santavuori P, Lander ES, Peltonen L. 1998. CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis. Nat Genet 19:286-288. PubMed ID: 9662406
  • Schmiedt ML, Bessa C, Heine C, Ribeiro MG, Jalanko A, Kyttälä A. 2010.  The neuronal ceroid lipofuscinosis protein CLN5: new insights into cellular maturation, transport, and consequences of mutations. Hum Mutat 31:356-365. PubMed ID: 20052765
  • Schulz A. et al. 2004. Annals of neurology. 56: 342-50. PubMed ID: 15349861
  • Sleat DE, Ding L, Wang S, Zhao C, Wang Y, Xin W, Zheng H, Moore DF, Sims KB, Lobel P. 2009. Mass spectrometry-based protein profiling to determine the cause of lysosomal storage diseases of unknown etiology. Mol Cell Proteomics. 8:1708-81718. PubMed ID: 19383612
  • Vesa J, Hellsten E, Verkruyse LA, Camp LA, Rapola J, Santavuori P, Hofmann SL, Peltonen L. 1995. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis. Nature 376:584-587. PubMed ID: 7637805
  • Williams R.E., Mole S.E. 2012. Neurology. 79: 183-91. PubMed ID: 22778232
  • Xin W, Mullen TE, Kiely R, Min J, Feng X, Cao Y, O PubMed ID: 20157158


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

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