Suzanne de Bruijn

52 Chapter 1.2 Besides a phenotypic resemblance, the expected mode of inheritance and the involved pathogenic mechanism of the variant (e.g. haploinsufficiency, loss- or gain-of-function) should also be comparedwith literature reports. For genes that have not been previously associated with the disease of interest, OMIM 104 and GeneCards 116 provide a summary of known clinical and functional information for the gene. For candidate disease genes, it may be valuable to investigate gene expression in the tissue of interest (e.g. SHIELD 117 , gEAR 118 , EyeGEx 119 ) and explore associated protein interaction networks (e.g. STRING 120 ). Additionally, the initiative Genematcher 121 and European Retinal Disease Consortium (ERDC) 122 offer the opportunity for different research groups that share an interest in the same candidate disease gene to collaborate. It is hypothesized that the most prominent genetic causes of diseases have been identified and novel findings appear in few cases or families, which underlines the urgency for collaborations among research groups worldwide. It is of utmost importance to share candidate disease gene data to increase the likelihood of identifying multiple unrelated individuals affected by pathogenic variants in the same gene. 123,124 Computational and predictive data The spectrum of human genetic variation is diverse, and a rich source of bioinformatics tools has been developed to evaluate the different potential consequences of a variant. Although the pathogenicity of SNVs has been most extensively studied, recent efforts into the characterization of SVs have revealed that pathogenic SVs are more abundant than initially thought. 85,125 This has led to a gradual shift of attention from coding variation to structural variation and the non-coding regions of the genome. Null variants Null variants are considered as very strong evidence of pathogenicity and often lead to open reading frame disruption and consequently complete loss of protein function. Null variants include nonsense, frameshift, canonical splice site, and initiation codon variants, as well as out-of-frame single and multi-exon deletions. Available in silico prediction tools are often not designed for the interpretation of null variants as pathogenicity already seems evident in most cases. However, some caveats should be considered, including the presence of alternative transcripts, the position of the variant with respect to the 3’UTR, and the inducement of alternative splicing such as in-frame exon skipping as a putative correction mechanism. 126-128 For each gene, a loss-of-function intolerance (pLI) score is provided in gnomAD 86 , which is based on observed (homozygous) loss-of- function variants in healthy cohorts compared to the expected number based on the gene size.