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. 2021 Apr 28;30(14):1293–1304. doi: 10.1093/hmg/ddab122

Figure 1 .

Figure 1

Most frequent haplotypes in STGD1 patients carrying the c.5882G > A, p.(Gly1961Glu) variant. The intronic sequences of the ABCA4 gene in all compound heterozygous and homozygous for the c.5882G > A, p.(Gly1961Glu) variant STGD1 patients were analyzed for possible modifying and haplotype-tagging variants. All c.5882G > A chromosomes share the same DNA segment in the in the 3′ region of the gene, tagged by three frequent variants c.5682G > C, c.5814A > G and c.5844A > G. These common variants with MAFs 0.22–0.18 are benign, non-pathogenic variants with no functional effect, including on splicing. The most frequent haplotype, present in ~80% of all chromosomes, did not contain any modifying variants. Fourteen percent of all chromosomes contain the deep intronic modifier variant in intron 6, c.769-784C > T, and the other two haplotype tagging variants c.769-6109C > T and c.3328 + 645 T > C. The remaining 6% of chromosomes carry, in addition to the p.(Gly1961Glu) variant (shown in bold), the c.67-3166C > T and c.3758C > T, p.(Thr1253Met) variants.