ESPE Abstracts (2018) 89 FC11.5

A Recurrent 6-bp Intronic Deletion in NESP55 with Reduced Penetrance in Pseudohypoparathyroidism Type 1b

Dong Li, Hakon Hakonarson & Michael Levine


The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA


Background: Pseudohypoparathyroidism type 1b (PHP1b) is caused by epigenetic errors on the maternal GNAS allele at differentially methylated regions (DMRs) associated with exons A/B, XL, and NESP that lead to reduced production of Gαs transcripts most notably in the renal proximal tubule and thyroid follicular cells. Most PHP1b cases appear sporadically, few of which can be explained by paternal uniparental disomy involving chromosome 20q, leading to global methylation defects at all three DMRs. Familial PHP1b is most frequently associated with loss of methylation at GNAS exon A/B and heterozygous STX16 deletions. A minority of familial PHP1b patients have global methylation defects at DMRs associated with exons A/B, XL, and NESP (Low-Low-High methylation) due to heterozygous deletions affecting maternal NESP and/or AS exons.

Objective and hypotheses: To identify the underlying genetic defect for PHP1b in patients with normal microarrays.

Method: Whole genome sequencing (WGS) was applied to two patients within a multigenerational kindred with clinical diagnosis of PHP1b and Sanger was used to confirm the identified variant in the entire family and screen 14 additional sporadic PHP1b patients.

Results: In a previously described PHP1b family with global methylation defects in affected subjects, WGS revealed a 6-bp intronic deletion (chr20:g.57, 419, 071-57, 419, 076) between exons AS3 and AS2 in two affecteds. Subsequent Sanger confirmed that the deletion was maternally inherited and the deletion was present in all four affecteds and one obligate carrier. However, three subjects with the maternal deletion had normal methylation and normal PTH responsiveness. We screened additional 14 sporadic PHP1b patients and found the same mutation in one patient with global methylation defects. His unaffected mother and brother both carried the same heterozygous 6-bp deletion but had normal methylation patterns and normal PTH responsiveness. The mutation was absent from 1000 Genomes Projects, gnomAD dataset with >15 000 genomes, and >10 000 samples with genome-sequencing data in Human Longevity database.

Conclusion: Our analysis indicate that this very small deletion is a recurrent GNAS mutation with reduced penetrance, and when maternally inherited leads to a global methylation defect (L-L-H) in only some patients. PHP1b occurs only when the methylation defect is present, indicating that the epigenetic defect rather than the genetic mutation is an accurate predictor of PTH resistance. The incomplete penetrance of this 6-bp deletion may define the limit of a cis-acting element on the maternal allele that is required for normal methylation of GNAS DMRs.

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