| Description: |
Incontinentia pigmenti (IP) is a rare hereditary disorder affecting 1.2 in 100,000 live births, predominantly females. Genetic analysis of IP is complicated by a homologous pseudogene, making conventional short‐read sequencing challenging. While long‐range PCR is typically used to overcome this, skewed X‐inactivation detection can also aid in assigning variants to IKBKG . We employed a comprehensive approach, incorporating whole‐exome sequencing (WES), long‐range PCR, RT‐PCR, X‐inactivation analysis, and nanopore sequencing, to identify and accurately phase a small heterozygous deletion, NM_001099857.5: c.363_367del, p.(Leu122Glyfs ∗ 14), in the IKBKG gene in an IP‐affected family. The deletion was initially detected via WES, with skewed X‐inactivation observed in both the proband and her mother. Long‐range PCR specific to IKBKG confirmed the variant’s location in the IKBKG gene, not in the pseudogene. On the RNA level, the variant was undetectable, suggesting nonsense‐mediated decay of the transcript. Nanopore sequencing precisely mapped the variant to IKBKG and analyzed the methylation status of both alleles, confirming the skewed X‐inactivation, with the variant‐carrying allele predominantly inactivated. This demonstrates the nanopore sequencing’s value in genetic diagnosis, enabling precise variant localization and analysis of X chromosome activation status in females with skewed X‐inactivation, aiding in accurate diagnosis and understanding of IP. |