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Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes
L. Grodecká, P. Hujová, M. Kramárek, T. Kršjaková, T. Kováčová, K. Vondrášková, B. Ravčuková, K. Hrnčířová, P. Souček, T. Freiberger,
Language English Country United States
Document type Journal Article
Grant support
NV16-34414A
MZ0
CEP Register
- MeSH
- Hep G2 Cells MeSH
- Child MeSH
- Exons MeSH
- HeLa Cells MeSH
- Infant MeSH
- Complement C1 Inactivator Proteins genetics MeSH
- Humans MeSH
- RNA, Messenger genetics MeSH
- Mutation MeSH
- Child, Preschool MeSH
- Wiskott-Aldrich Syndrome Protein genetics MeSH
- Interleukin Receptor Common gamma Subunit genetics MeSH
- Recombinant Fusion Proteins genetics MeSH
- RNA Splicing * MeSH
- Immunologic Deficiency Syndromes genetics MeSH
- STAT3 Transcription Factor genetics MeSH
- Protein-Tyrosine Kinases genetics MeSH
- U937 Cells MeSH
- Check Tag
- Child MeSH
- Infant MeSH
- Humans MeSH
- Child, Preschool MeSH
- Publication type
- Journal Article MeSH
Both variants affecting splice sites and those in splicing regulatory elements (SREs) can impair pre-mRNA splicing, eventually leading to severe diseases. Despite the availability of many prediction tools, prognosis of splicing affection is not trivial, especially when SREs are involved. Here, we present data on 92 in silico-/55 minigene-analysed variants detected in genes responsible for the primary immunodeficiencies development (namely BTK, CD40LG, IL2RG, SERPING1, STAT3, and WAS). Of 20 splicing-affecting variants, 16 affected splice site while 4 disrupted potential SRE. The presence or absence of splicing defects was confirmed in 30 of 32 blood-derived patients' RNAs. Testing prediction tools performance, splice site disruptions and creations were reliably predicted in contrast to SRE-affecting variants for which just ESRseq, ΔHZEI-scores and EX-SKIP predictions showed promising results. Next, we found an interesting pattern in cryptic splice site predictions. These results might help PID-diagnosticians and geneticists cope with potential splicing-affecting variants.
References provided by Crossref.org
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