High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency

Am J Hum Genet. 2021 Aug 5;108(8):1526-1539. doi: 10.1016/j.ajhg.2021.06.013. Epub 2021 Jul 15.

Abstract

Pituitary hormone deficiency occurs in ∼1:4,000 live births. Approximately 3% of the cases are due to mutations in the alpha isoform of POU1F1, a pituitary-specific transcriptional activator. We found four separate heterozygous missense variants in unrelated individuals with hypopituitarism that were predicted to affect a minor isoform, POU1F1 beta, which can act as a transcriptional repressor. These variants retain repressor activity, but they shift splicing to favor the expression of the beta isoform, resulting in dominant-negative loss of function. Using a high-throughput splicing reporter assay, we tested 1,070 single-nucleotide variants in POU1F1. We identified 96 splice-disruptive variants, including 14 synonymous variants. In separate cohorts, we found two additional synonymous variants nominated by this screen that co-segregate with hypopituitarism. This study underlines the importance of evaluating the impact of variants on splicing and provides a catalog for interpretation of variants of unknown significance in POU1F1.

Keywords: PIT-1; alternative splicing; growth hormone deficiency; hypopituitarism; massively parallel splicing assay; multiplexed assays of variant effects; transcriptional regulation; variants of uncertain significance.

Publication types

  • Case Reports
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Child
  • Child, Preschool
  • High-Throughput Screening Assays / methods*
  • Humans
  • Hypopituitarism / etiology
  • Hypopituitarism / metabolism
  • Hypopituitarism / pathology*
  • Male
  • Mutation*
  • Pedigree
  • Pituitary Hormones / deficiency*
  • RNA Splicing / genetics*
  • Transcription Factor Pit-1 / genetics*

Substances

  • POU1F1 protein, human
  • Pituitary Hormones
  • Transcription Factor Pit-1