Albertine Donker

Chapter 4 154 Table 2. Characteristics of novel TMPRSS6 variants TMPRSS6 defect a Gene Protein Type of variant c.del 118 kb intron 2- exon 3-18 Absent Deletion c.del promotor, exon 1-3 Absent Deletion c.230-6G>A Aberrant Splicing defect c. 52 1T>C p.Leu174Pro Substitution c.863+1G>T del exon 7 Splicing defect c.1228T>C p.Cys410Arg Substitution c.1229G>C p.Cys410Ser Substitution c.1654G>A p.Asp552Asn Substitution c.1832G>A p.Trp611X Stop codon a All novel TMRPSS6 variants, except the defect c.del promotor, exon 1-3 in patient 15, were found in combination with a TMPRSS6 variant that (probably, possibly) affects function, on the other allele. Therefore, the contribution of the novel variant to the clinical phenotype of the patient remains unclear. b This substitution is predicted to introduce a new and more efficient acceptor splice site 4 bases downstream from the original acceptor splice site in intron 2 leading to a frameshift in the open reading frame. Not proven on RNA or protein level (http://www.interactive-biosoftware.com/doc/ alamut-visual/2.7/splicing.html, accessed on July 14 2016). c Align GVGD, web based in silico prediction software program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched deleterious to enriched neutral. A-GVGD scores amino acid substitutions on a 7-scale scoring system, from C0 to C65. An amino acid substitution with a C0 score is considered to be neutral, amino acids with C15 and C25 scores are considered intermediate, as changes to protein structure or function are uncertain, and C35 scores or higher are considered as likely deleterious. 52