title: Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes.
abstract: 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.
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.
authors.forename: Lucie
authors.initials: L
authors.lastname: Grodecká
authors.affiliation: Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.
authors.forename: Pavla
authors.initials: P
authors.lastname: Hujová
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Kramárek
authors.affiliation: Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.
authors.forename: Tereza
authors.initials: T
authors.lastname: Kršjaková
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Kováčová
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Katarína
authors.initials: K
authors.lastname: Vondrášková
authors.affiliation: Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.
authors.forename: Barbora
authors.initials: B
authors.lastname: Ravčuková
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Kristýna
authors.initials: K
authors.lastname: Hrnčířová
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Přemysl
authors.initials: P
authors.lastname: Souček
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Institute of Clinical Immunology and Allergology, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic. Electronic address: tomas.freiberger@cktch.cz.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Freiberger
mesh_terms: D000077329:Agammaglobulinaemia Tyrosine Kinase; D002648:Child; D002675:Child, Preschool; D003174:Complement C1 Inactivator Proteins / Q000235:genetics; D050718:Complement C1 Inhibitor Protein; D005091:Exons; D006367:HeLa Cells; D056945:Hep G2 Cells; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics*; D007223:Infant; D053631:Interleukin Receptor Common gamma Subunit / Q000235:genetics; D009154:Mutation; D011505:Protein-Tyrosine Kinases / Q000235:genetics; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics; D011993:Recombinant Fusion Proteins / Q000235:genetics; D050796:STAT3 Transcription Factor / Q000235:genetics; D020298:U937 Cells; D051316:Wiskott-Aldrich Syndrome Protein / Q000235:genetics
chemical_list: C526581:CD40LIg fusion protein; D003174:Complement C1 Inactivator Proteins; D050718:Complement C1 Inhibitor Protein; C507941:IL2RG protein, human; D053631:Interleukin Receptor Common gamma Subunit; D012333:RNA, Messenger; D011993:Recombinant Fusion Proteins; C469952:SERPING1 protein, human; D050796:STAT3 Transcription Factor; C494086:STAT3 protein, human; C495767:WAS protein, human; D051316:Wiskott-Aldrich Syndrome Protein; D011505:Protein-Tyrosine Kinases; D000077329:Agammaglobulinaemia Tyrosine Kinase; C000625949:BTK protein, human
keywords: Cryptic splice sites; Primary immunodeficiencies; Splicing prediction; Splicing-affecting variants