Background: Congenital aniridia is a severe ocular abnormality characterized by incomplete formation of the iris and many other ocular complications. Most cases are caused by the paired box 6 (PAX6) gene mutations generating premature termination codons (PTCs).Methods: Ophthalmic examination was performed on a Chinese pedigree with congenital aniridia. The mutation was identified by targeted next‐generation sequencing. Nonsense suppression therapy was applied on patient‐derived lymphocytes. The PAX6 expression was assayed by real‐time polymerase chain reaction and Western blot.Results: Complete aniridia was complicated with horizontal nystagmus, contract, foveal hypoplasia, and microphthalmia. A novel heterozygous c.702_703delinsAT (p.Tyr234*) mutation was found in exon 9 of PAX6, generating a PTC at the homeodomain. There were about 50% reductions of both full‐length PAX6 protein and PAX6 mRNA in patient‐derived lymphocytes, indicating haploinsufficiency due to nonsense‐mediated mRNA decay. Ataluren (PTC124) and geneticin (G418) could induce about 30%–40% translational readthrough. Nonsense suppression therapy restored PAX6 protein to about 65%–70% of unaffected family controls.Conclusion: Our data expanded the genetic and phenotypic variations of congenital aniridia, and showed the therapeutic effect of nonsense suppression on this disease using patient‐derived cells.

Introduction: Piebaldism is a rare autosomal dominant disorder characterized by congenital white forelock and depigmented patches, which is most commonly caused by deleterious variants in the KIT gene.Methods: Four KIT variants were identified in a piebaldism case series by whole‐exome sequencing. Functional experiments, including in vitro minigene reporter assay and enzyme‐linked immunosorbent assay, were carried out to elucidate the pathogenicity of the variants. The genotype–phenotype correlation was summarized through extensive literature reviewing.Results: All the four cases had severe piebaldism presented with typical white forelock and diffuse depigmentation on the ventral trunk and limbs. Four germline variants at the tyrosine kinase (TK) domains of the KIT gene were identified: two novel variants c.1990+1G>A (p.Pro627_Gly664delinsArg) and c.2716T>C (p.Cys906Arg), and two known variants c.1879+1G>A (p.Gly592_Pro627delinsAla) and c.1747G>A (p.Glu583Lys). Both splicing variants caused exon skipping and inframe deletions in the TK1 domain. The missense variants resided at the TK1 and TK2 domains respectively impairing PI3K/AKT and MAPK/ERK signaling pathways, the downstream of KIT. All severe cases were associated with variants in the TK domains, eliciting a major dominant‐negative mechanism of the disease.Conclusion: Our data expand the mutation spectrum of KIT, emphasized by a dominant‐negative effect of variants in the critical TK domains in severe cases. We also share the experience of prenatal diagnosis and informed reproductive choices for the affected families.

Structural variants (SVs) of unknown significance are great challenges for prenatal risk assessment, especially when involving dose-sensitive genes such asDMD. The pathogenicities of 5′-terminalDMDduplications in the database remain controversial. Four prenatal cases with Xp21.1 duplications were identified by routine prenatal genomic testing, encompassing the 5′-UTR to exons 1–2 in family 1 and family 2, and to exons 1–9 in family 3. The duplication in family 4 was non-contiguous covering the 5′-UTR to exon 1 and exons 3–7. All were traced to unaffected males in the family pedigrees. A new genome-wide approach of optical genome mapping was performed in families 1, 2, and 3 to delineate the breakpoints and orientation of the duplicated fragments. The extra copies were tandemly inserted into the upstream ofDMD, preserving the integrity of ORF from the second copy. The pathogenicities were thus reclassified as likely benign. Our data highlight the importance of structural delineation by optical genome mapping in prenatal risk assessment of incidentally identified SVs involvingDMDand other similar large dose-sensitive genes.

Chromosome 9p21.3 is a locus associated with a rare autosomal dominant cancer predisposition syndrome characterized by early-onset melanoma and a broad spectrum of neural system tumors. Two major tumor-suppressor genes, cyclin-dependent kinase inhibitor 2A and 2B (CDKN2A and CDKN2B), as well as a large non-coding RNA ANRIL, are often co-deleted in the core region. Herein, we report a pregnant woman who had developed more than 20 plexiform neurofibromas since the age of 13 and experienced 11 times of surgical resections. No melanoma or other tumors were found. A germline 9p21.3 deletion involving CDKN2A and the first exon of ANRIL, but not CDKN2B, was identified by whole exome sequencing (WES) and confirmed by quantitative PCR. Prenatal diagnosis was performed through copy number variation-sequencing (CNV-seq), and the pregnancy was terminated with informed choice for an affected fetus. All the eight cases carrying germline 9p21.3 deletions were reviewed for genotype–phenotype correlation, showing that our case with the smallest deletion had plexiform neurofibroma only, and the two cases of Eastern Asian origin had no melanoma. Our data highlight 9p21.3 deletion as a potential differential diagnosis for neurofibroma and emphasize the importance of CNV analysis on the WES data wherein small deletions might be easily overlooked.