Bi-allelic TPP1 variants in neuronal ceroid lipofuscinosis 2: clinical findings from an Iranian cohort of 20 patients, founder effect, and in silico analyses

Abstract

Neuronal Ceroid Lipofuscinosis Type 2 (CLN2) is a rare neurodegenerative disorder. It exhibits an autosomal recessive inheritance pattern and is attributable to pathogenic variants in the TPP1 gene. This study sought to identify and character-ize IPPI variants in eighteen Iranian consanguineous families affected by CLN2 disease. A developmental history, brain imaging, and neurological evaluation were conducted. Exome sequencing (ES) was conducted on the probands DNA. ACMG criteria were used to evaluate pathogenicity, as well as several in silico prediction techniques, protein stability algorithms, and homozygosity mapping. Three-dimensional protein modeling was used to assess structural effects. Shared haplotypes have been determined to assess possible founder alleles and the time to the most recent common ancestor (MRCA). We found twelve different TPP1 bi-allelic variants, six of which had never been reported before, two of which were only listed in ClinVar, and four of which were known to be pathogenic alleles. It contained four various types of variants: missense (33), nonsense (25), frameshift (25), and splice-site (17). The majority of the variants were found within the peptidase 53 domain. All new alleles were found in the "rare-plus-high-CADD" range, which is higher than the gene-specific mutation significance cutoff (MSC). The recurrence of c.729CG (p.Phe243Leu) in several fami-lies, along with a common similar to 2.86 Mb homozygous haplotype and an estimated most recent common ancestor (MRCA) of-16.7 generations (similar to 450 years), strongly indicates a founder effect. Psychomotor regression was universal in clinical settings, seizures usually started between the ages of 3 and 5, and 40 of patients died before the age of 10. No affected patients received enzyme replacement therapy due to financial constraints. This study represents the most extensive Iranian series of CLN2 to date, broadens the TPP1 mutational spectrum with six novel alleles, and reveals a significant founder effect. The results improve genotype-phenotype correlations and show how important it is to do carrier screening that is specific to each population and to make enzyme replacement therapy available quickly in regions with limited funding. ES proved critical for accurate CLN2 diagnosis, precise genetic counseling, and revealing gaps in the availability of broad treatment for rare disorders.