Table 2.

Possible reasons for negative results after gene testing using MPS gene panels or ES

Reason	Examples
Mutations in genes that represent phenocopies of a disease may be missed when using phenotype-associated gene panels	HNF1B-mediated cystic kidney disease can mimic ADPKD/ADTKD   Mutations in GLA (Fabry) can mimic SRNS
Not all genes associated with given phenotype are tested in phenotype-associated gene panels	Currently unknown or very recently identified genes for heterogeneous diseases such as renal ciliopathies and steroid-resistant nephrotic syndrome
Detection of large CNVs from MPS gene panels/ES data is challenging; specific CNV detection algorithms are not automatically performed in diagnostic setting and therefore CNVs might be missed	HNF1B and NPHP1 full gene deletions (CAKUT and nephronophthisis , respectively)
Variants in some genomic regions are poorly discovered with MPS gene panels or ES, such as mutations in regions with high GC content and/or with high sequence homology	High GC content in first exon of COL4A3 (Alport syndrome)   PKD1 (ADPKD) has high GC content and sequence homology with six pseudogenes located nearby
Some pathogenic variants are not discovered by any of the MPS-based techniques	Cytosine insertion in variable number tandem repeat sequences in MUC1 (MUC1-ADTKD)
Variants in non-coding (intronic or regulatory) regions or imprinting defects are not detected with disease-specific gene panels or ES	Deep intronic mutations in DGKE (aHUS)   Imprinting defect in Beckwith–Wiedemann syndrome