title: [Genetic diagnostics of pathogenic splicing abnormalities in the clinical laboratory--pitfalls and screening approaches].
abstract: In recent years, genetic diagnostics of pathogenic splicing abnormalities are increasingly recognized as critically important in the clinical genetic diagnostics. It is reported that approximately 10% of pathogenic mutations causing human inherited diseases are splicing mutations. Nonetheless, it is still difficult to identify splicing abnormalities in routine genetic diagnostic settings. Here, we studied two different kinds of cases with splicing abnormalities. The first case is a protein S deficiency. Nucleotide analyses revealed that the proband had a previously reported G to C substitution in the invariant AG dinucleotide at the splicing acceptor site of intronl/exon2, which produces multiple splicing abnormalities resulting in protein S deficiency. The second case is an antithrombin (AT) deficiency. This proband had a previously reported G to A substitution, at nucleotide position 9788 in intron 4, 14 bp in front of exon 5, which created a de novo exon 5 splice site and resulted in AT deficiency. From a practical standpoint, we discussed the pitfalls, attentions, and screening approaches in genetic diagnostics of pathogenic splicing abnormalities. Due to the difficulty with full-length sequence analysis of introns, and the lack of RNA samples, splicing mutations may escape identification. Although current genetic testing remains to be improved, to screen for splicing abnormalities more efficiently, it is significant to use an appropriate combination of various approaches such as DNA and/or RNA samples, splicing mutation databases, bioinformatic tools to detect splice sites and cis-regulatory elements, and in vitro and/or in vivo experimentally methods as needed.
authors.affiliation: Department of Molecular Genetic Pathology, Clinical Laboratory Center, Toyama University Hospital, Toyama 930-0194, Japan. hiniimi@med.u-toyama.ac.jp
authors.forename: Hideki
authors.initials: H
authors.lastname: Niimi
authors.forename: Tomomi
authors.initials: T
authors.lastname: Ogawa
authors.forename: Rhougou
authors.initials: R
authors.lastname: Note
authors.forename: Shirou
authors.initials: S
authors.lastname: Hayashi
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Ueno
authors.forename: Kenu
authors.initials: K
authors.lastname: Harada
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Uji
authors.forename: Isao
authors.initials: I
authors.lastname: Kitajima
mesh_terms: D000293:Adolescent; D000328:Adult; D020152:Antithrombin III Deficiency / Q000175:diagnosis* / Q000235:genetics*; D001483:Base Sequence; D019411:Clinical Laboratory Techniques; D018076:DNA, Complementary / Q000235:genetics; D006801:Humans; D008297:Male; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D009154:Mutation; D018455:Protein S Deficiency / Q000175:diagnosis* / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger