Skewed X chromosome inactivation in the patient
Because the patient was a girl, we expected that she would express both
wildtype and mutant transcripts in her tissues. However, she only
expressed the defective frameshift BCAP31 transcript and her clinical
features resembled those of X-linked recessive male patients carryingBCAP31 mutations. Haplotype phasing with linked-read sequencing
data around the BCAP31 gene showed that the de novo allele
arose from the paternal X chromosome while the wild type allele came
from the maternal X chromosome (Figure 4). To explain the patient’s
BCAP31 expression pattern and clinical features, we hypothesized that
uneven X chromosome inactivation (XCI) occurred in the patient. We
performed the HUMARA (Human Androgen Receptor Amplification) assay to
assess the methylation ratio of maternal and paternal X chromosome in
WBCs, with the knowledge that XCI patterns between blood and other
analyzed tissues were highly correlated (Echevarria et al., 2016). The
androgen receptor allele profile of triplicate experiments showed skewed
X chromosome inactivation, with the maternal X chromosome (carrying the
wildtype BCAP31 allele) inactivated in 88% ± 2% of the WBCs
(Figure 5). The HUMARA study confirms that the paternal X chromosome
(carrying the de novo mutation) was active in the majority of the
cells and explained the patient’s “X-linked recessive” phenotype.