CEP104 and CEP290; Genes with Ciliary Functions Cause Intellectual Disability in Multiple Families

Background: Neurodevelopmental and intellectual impairments are extremely heterogeneous disorders caused by a diverse variety of genes involved in different molecular pathways and networks. Genetic alterations in cilia, highly-conserved organelles with sensorineural and signal transduction roles can compromise their proper functions and lead to so-called ciliopathies featuring intellectual disability (ID) or neurodevelopmental disorders as frequent clinical manifestations. Here, we report several Iranian families affected by ID and other ciliopathy-associated features carrying known and novel variants in two ciliary genes; CEP104 and CEP290. Methods: Whole exome and targeted exome sequencing were carried out on affected individuals. Lymphoblastoid cell lines (LCLs) derived from the members of affected families were established for two families carrying CEP104 mutations. RNA and protein expression studies were carried out on these cells using qPCR and Western blot, respectively. Results: A novel homozygous variant; NM_025114.3:c.7341_7344dupACTT p.(Ser2449Thrfs*8) and four previously reported homozygous variants; NM_025114.3:c.322C> T p.(Arg108*), NM_025114.3:c.4393C >T p.(Arg1465*), NM_025114.3:c.5668C; >T p.(Gly1890*) and NM_025114.3:c.1666dupA p.(Ile556Asnfs*20) were identified in CEP290. In two other families, two novel homozygous variants; NM_014704:c.2356_2357insTT p.(Cys786Phefs*11) and NM_014704:c.1901_1902insT. p.(Leu634Phefs*33) were identified in CEP104, another ciliary gene. qPCR and Western blot analyses showed significantly lower levels of CEP104 transcripts and protein in patients compared to heterozygous or normal family members. Conclusion: We emphasize the clinical variability and pleiotropic phenotypes due to the variants of these genes. In conclusion, our findings support the pivotal role of these genes in cognitive and neurodevelopmental features.

Automated summary

This study identified known and novel variants in ciliary genes CEP104 and CEP290 in Iranian families affected by intellectual disabilities and ciliopathy-associated features. Analysis of RNA and protein expression levels in affected individuals showed significant differences compared to normal family members. These findings highlight the clinical variability and importance of these genes in cognitive and neurodevelopmental features.