Albertine Donker

IRIDA: a Heterogeneous Disease 155 4 In silico findings Conclusion on pathogenicity Patient ID TMPRSS6 domain Absent protein np Pathogenic 1 Absent protein np Pathogenic 2, 15 TM domain Splice site b Most probably pathogenic 18 SEA domain AlignGVGD c : C0 Polyphen d : 0.57 SIFT e : 0.04 Possibly pathogenic 13 CUB domain Skip of exon 7 f Most probably pathogenic 19 CUB domain Align GVGD c : C0 Polyphen d : 0.45 SIFT e : 0.00 Possibly pathogenic 13 CUB2 domain Align GVGD c : C0 Polyphen d : 0.01 SIFT e : 0.00 Possibly pathogenic 12 LDLR domain Align GVGD c : CO Polyphen d : 1.0 SIFT e : 0.00 Possibly pathogenic 20 Serine Protease domain np Most probably Pathogenic g 7 d PolyPhen-2 (Polymorphism Phenotyping v2 HumVar) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. PolyPhen scores range from 0 ≤ 1 ≤ X , outcome scores of 0.00–0.15 are classified as benign, 0.15–1.0 as possibly damaging, 0.85-1.0 as more confidently predicted to be damaging. 53 e The SIFT algorithm combines sequence homology and physical properties of amino acid substitutions to analyze whether or not amino acid substitutions are tolerated, in light of the predicted effect on the protein structure. SIFT score ranges from 0 to 1. The amino acid substitution is predicted damaging if the score is < 0.05 and tolerated if the score is > 0.5. 54 f This substitution is located in the donor splice site of intron 7. The consequence of this change is not predictable, but a skip of exon 7 is very likely as in silico analysis resulting in the loss of a classical splice site. Not proven on mRNA or protein level (http://www.interactive-biosoftware.com/doc/alamut- visual/2.7/splicing.html, accessed on July 14 2016). g Nonsense substitution in exon 15. The reading frame is interrupted by a stop codon. The mRNA produced might be targeted to nonsense-mediated decay (NMD). No formal proof. Abbreviations: np denotes not provided