UC San Diego

After exome and whole genome sequencing failed to reveal any potential causative variants in two large consanguineous Pakistani pedigrees with members affected by retinal degeneration, subsequent examination of low frequency noncoding variants was performed. Homozygosity mapping and segregation of rare variants with disease identified a rare homozygous variant (chr11:61,392,563G>A) in the intergenic region of TMEM216 and TMEM138 segregating with disease in affected members. Based on FIMO transcription factor (TF) motif analysis, the variant is predicted to impact binding of CHIP-seq validated TFs that bind to this region of DNA. Additionally, the variant is located in an ATAC-seq peak, suggesting a regulatory role. Available individuals from these two pedigrees underwent ophthalmic evaluation including fundoscopy and ERG analysis. Affected individuals show a phenotype consistent with a diagnosis of early-onset retinal degeneration. To validate the functional impact of the variant, genome editing of hTERT-RPE1 cells resulted in cells heterozygous for the variant (G/A), and homozygous (A/A) for the variant and an additional variant two bases away. qRT-PCR analysis of these cells revealed significantly reduced expression of TMEM216 and TMEM138 expression, and immunocytochemistry showed abnormal ciliary morphology in cells with the variant. These results suggest that silencing the expression of TMEM216 and TMEM138 may lead to abnormal photoreceptor ciliogenesis and may underlie the retinal degeneration pathology observed.