A novel synonymous KMT2B variant in a patient with dystonia causes aberrant splicing. Issue 5 (16th March 2022)

• Record Type: Journal Article
• Authors: Grosz, Bianca R.; Tisch, Stephen; Tchan, Michel C.; Fung, Victor S. C.; Darveniza, Paul; Fellner, Avi; Kurian, Manju A.; McLean, Alison; Tomlinson, Susan E.; Smyth, Renee; Devery, Sophie; Wu, Kathy H. C.; Kennerson, Marina L.; Kumar, Kishore R.
• Is Part Of: Molecular genetics & genomic medicine. Volume 10:Issue 5(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-03-16
• Subjects: deep brain stimulation -- dystonia -- KMT2B -- splicing -- synonymous; Medical genetics -- Periodicals; Genomics -- Periodicals; 616.042
• DOI: 10.1002/mgg3.1923
• Languages: English
• ISSNs: 2324-9269

Abstract

Abstract: Background: Heterozygous KMT2B variants are a common cause of dystonia. A novel synonymous KMT2B variant, c.5073C>T (p.Gly1691=) was identified in an individual with childhood‐onset progressive dystonia. Methods: The splicing impact of c.5073C>T was assessed using an in vitro exon‐trapping assay. The genomic region of KMT2B exons 23–26 was cloned into the pSpliceExpress plasmid between exon 2 and 3 of the rat Ins2 gene. The c.5073C>T variant was then introduced through site‐directed mutagenesis. The KMT2B wild‐type and c.5073C>T plasmids were transfected separately into HeLa cells and RNA was extracted 48 hours after transfection. The RNA was reverse transcribed to produce cDNA, which was PCR amplified using primers annealing to the flanking rat Ins2 sequences. Results: Sanger sequencing of the PCR products revealed that c.5073C>T caused a novel splice donor site and therefore a 5‐bp deletion of KMT2B exon 23 in mature mRNA, leading to a coding frameshift and premature stop codon (p.Lys1692AsnfsTer7). Conclusion: To our knowledge, this is the first report of a KMT2B synonymous variant associated with dystonia. Reassessment of synonymous variants may increase diagnostic yield for inherited disorders including monogenic dystonia. This is of clinical importance, given the generally favourable response to deep brain stimulation for KMT2B ‐related dystonia. Abstract : We report a synonymous variant in the KMT2B gene identified on dystonia panel screening. While the variant was predicted to disturb splicing, it was formally reported as a variant of uncertain significance. The patient was reluctant to provide further tissue, however, we were able to confirm aberrant splicing on an exon‐trapping assay, thus changing the classification of the variant to pathogenic.