The Effect of Synonymous Single-Nucleotide Polymorphisms on an Atypical Cystic Fibrosis Clinical Presentation

Abstract

Synonymous single nucleotide polymorphisms (sSNPs), which change a nucleotide, but not the encoded amino acid, are perceived as neutral to protein function and thus, classified as benign. We report a patient who was diagnosed with cystic fibrosis (CF) at an advanced age and presented very mild CF symptoms. The sequencing of the whole cystic fibrosis transmembrane conductance regulator (CFTR) gene locus revealed that the patient lacks known CF-causing mutations. We found a homozygous sSNP (c.1584G>A) at the end of exon 11 in the CFTR gene. Using sensitive molecular methods, we report that the c.1584G>A sSNP causes cognate exon skipping and retention of a sequence from the downstream intron, both of which, however, occur at a relatively low frequency. In addition, we found two other sSNPs (c.2562T>G (p.Thr854=) and c.4389G>A (p.Gln1463=)), for which the patient is also homozygous. These two sSNPs stabilize the CFTR protein expression, compensating, at least in part, for the c.1584G>A-triggered inefficient splicing. Our data highlight the importance of considering sSNPs when assessing the effect(s) of complex CFTR alleles. sSNPs may epistatically modulate mRNA and protein expression levels and consequently influence disease phenotype and progression.

Case Report: A Synonymous Mutation in NF1 Located at the Non-canonical Splicing Site Leading to Exon 45 Skipping

“…Given the characteristics of the genetic code, synonymous mutations are usually considered nonpathogenic (Zhou et al, 2020). Nevertheless, studies proposed that the synonymous mutations could lead to abnormal splicing as well (Bampi et al, 2020;Horinouchi et al, 2020;Knapp et al, 2021;Niersch et al, 2021).…”

Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases

“…A rare synonymous mutation (c.1584G>A) in the cystic fibrosis transmembrane conductance regulator ( CFTR ) gene in a cystic fibrosis (CF) patient ( Table 1 ), who is homozygous for this sSNP, has been recently linked as causal for pathology ( 123 ). This sSNP is located at the last position of exon 11, and the patient presents mild and rather atypical CF clinical symptoms.…”

“…Typically, mutations close to the splicing junctions are associated with splicing aberrancies. This pattern was seen in patient-derived organoids where only very low levels of exon skipping and intron retention were detected ( 123 ), suggesting that these alternative splicing events cannot fully account for pathology. Reconstitution in cell culture models using the copy or complementary DNA containing the sSNP ( i.e., to disentangle the effects on mRNA splicing) shows alterations in the levels of mature functional CFTR.…”

“…The sSNP is a GAG to GAA (Glu) codon. In bronchial epithelial cells, the concentration of tRNA UUC Glu reading GAA is ∼50% higher than that of tRNA CUC Glu ( 61 , 62 ), suggesting that the local acceleration of translation at the mutated codon would alter the translation profile and change CFTR folding and function ( 123 ). The mild splicing aberrations caused by the sSNP appear to be offset by unexpected gains in translation speed to culminate in an atypical mild CF clinical presentation ( 123 ).…”

Features of CFTR mRNA and implications for therapeutics development

“…For example, the following three synonymous SNPs in CFTR exhibit significantly decreased transcript abundance: c.2280G>A ( p .Thr760=), c.3339T>C ( p .Ser1113=), c.3870A>G ( p .Pro1290=) ( Kirchner et al, 2017 ). The synonymous SNP, c.1584G>A ( p .Glu528=), elicits retention of intron-11 and skipping of exon-11, albeit at a low frequency ( Bampi et al, 2020 ). A prevalent silent SNP, c.2562T>G ( p .Thr854=), reduces local ribosome speed through a mechanism dependent on tRNA abundance.…”