A De Novo Noncoding RARB Variant Associated with Complex Microphthalmia Alters a Putative Regulatory Element

Figure 2

Assessment of pathogenicity by in silico analysis. (a) UCSC Genome Browser output highlighting a 4,143 bp region including the RARB gene promoter, exon 1, and the conserved region 1 (CR1) within RARB intron 1-2 carrying the c.157+1895G>A variant (hg38; variant coordinates 3:25430783). RARB promoter region included in the reporter construct is indicated with a green box; the CR1 region is shown as a red box with c.157+1895G>A variant marked with an orange line. PhyloP histogram and Multiz Alignment illustrate high conservation of CR1 (black asterisk). ENCODE track shows predicted promoter (red rectangle) and candidate cis-regulatory elements (orange rectangles) including E2186460/enhD element located within CR1 and overlapping the c.157+1895G>A variant. H3K27Ac track shows CR1 is acetylated. The triangle plot indicates areas of interaction identified within the region (adapted from the Micro-C chromatin track), including between CR1 and the RARB promoter region (arrowhead). ReMap track demonstrates enrichment of transcription factor binding sites within CR1. (b) A multispecies alignment of the 50 bp fragment of CR1 surrounding the c.157+1895G nucleotide (red box). Nucleotides conserved across all species are indicated in black, while divergent nucleotides are shown in grey.

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