Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.

少数基因内含子内的基因组序列已被证明可充当影响邻近基因表达的增强子。我们研究了小眼症、无眼症和眼缺损的常染色体隐性表型连续体，没有明显的编码区致病突变。对几个受影响的犹太伊朗家庭进行纯合性作图，结合全基因组序列分析，鉴定出一个 0.5 Mb 的疾病相关染色体 2q35 位点（最大 LOD 评分 6.8），其中包含NHEJ1中的内含子创始人变异，预计不会影响 NHEJ1。人类NHEJ1内含子变体位于邻近基因印度刺猬 (Ihh) 的已知特异性肢体发育增强子内，该基因已知参与小鼠和鸡的眼睛发育。通过小鼠和鸡的分子发育研究，我们证明该变体位于Ihh增强子内，该增强子驱动发育中的眼睛中的基因表达，并且所识别的变体影响这种眼睛特异性增强子活性。因此，我们描述了一种在哺乳动物眼睛发育中活跃的Ihh增强子，其变异会导致人类小眼症、无眼症和眼缺损。这些发现强调了内含子变异影响邻近基因表达的疾病因果关系，描绘了眼睛发育的分子途径。