RB1 Sequence Variants in Retinoblastoma: Analysis of RB1 Variants in a Database for Correlation with pRB Protein Domains and Clinical Presentation.
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Background: Retinoblastoma (RB) is the most common pediatric ocular tumor that occurs due to the biallelic inactivation of the RB1 tumor suppressor gene. RB may be unilateral or bilateral and is hereditary in 50% of cases. An inactivation of the RB1 gene may occur due to gross rearrangements (20%) or due to small-length changes (80%): single nucleotide substitutions (SNVs) and insertions/deletions (INDELs). Objectives: Our objective was to study the frequency of the different RB1 variants present in patients with retinoblastoma and to correlate them with the functional domains of the pRb protein and with the clinical presentation. Methods: For this purpose, we analyzed all the clinically validated germline SNVs and INDELs annotated in the database. They were grouped into the pRb domains; contingency tables were made, and figures were constructed to compare the types of variants in the different domains between bilateral and unilateral patients. Results: The number of variants analyzed was 2103; 34% of them were nonsense, 34% INDELs, 22% splice-site and 10% missense. All these variants mainly gave rise to bilateral RB (88%); their frequency and distribution in relation to pRb domains varied between bilateral (Bi) and unilateral hereditary (Ug) RB. Nonsense variants occurred more frequently in Bi vs. Ug, whereas missense variants were more frequent in Ug vs. Bi. Indels and splice-site variants were not significantly different between Bi and Ug. The most frequent pRB location of variants was in the Pocket domain (the binding site of the E2F transcription factor). The slice-site of the consensus sequence most mutated was the first nucleotide of the donor, which is the driver of the splicing process. Conclusions: The highest percentage of variants in RB corresponded to nonsense substitutions and indels, mainly affecting the Pocket domain, which is the major functional site for the pRb regulatory process. These results indicate the predominance of the most pathogenic variants related to the bilateral presentation of retinoblastoma.