Fig. 1: Distribution of different types of alleles and deep-intronic variants in ABCA4.

a The contribution of each type of variant or allele in biallelic and monoallelic cases except those carrying c.5603A>T is represented. Protein truncating variants comprise nonsense, frameshift, and canonical splice site variants. The 10% complex alleles only consist of combinations of missense variants, the most frequent of which were c.[1622T>C;3113C>T] (n = 30; 27% of all complex alleles) and c.[4469G>A;5603A>T] (n = 27; 25% of all complex alleles). They do not include the complex alleles that contain noncanonical splice site (NCSS) variants, deep-intronic variants, or protein truncating variants, when present in cis with other variants. If these would have been included, 16% of the alleles would consist of complex alleles. b Deep-intronic variant allele count in this study. Novel deep-intronic variants are highlighted in red. One hundred seventeen causal deep-intronic variants were identified. The deep-intronic variants c.4539+2001G>A (n = 26) and c.4253+43G>A (n = 21) were found most frequently. Most of the novel deep-intronic variants were found in single STGD1 probands.