Figure 6.

Homozygous Tier 1 deletions. Each illustrates a unique feature of homozygous deletions. (A) The hypotonia-cystinuria syndrome (HCS) region (top) is homozygously deleted in subject 163 (middle, light gray shading on probe log₂ plot). Twelve heterozygous Tier 1 deletions affect SLC3A1 (bottom) in our cohort, demonstrating diverse sizes and locations of carrier alleles. Each is plotted by minimum (thick line) and maximum (thin line) boundaries. No Tier 1 CNV affected solely PREPL. (B) NPHP1, the disease gene for juvenile nephronophthisis 1 and other conditions, is homozygously deleted as part of a compound heterozygous deletion, likely mediated by the complex repeat architecture of this region (colored bars above RefSeq genes track). Arrow indicates heterozygously deleted region. (C) Six homozygous deletions of a noncoding alternative exon 1 of LEPREL1. This CNV is mostly likely not pathogenic (see text). Database of Genomic Variant CNVs are shown (“table browser query on dgv”).