A novel variant in an intron splicing enhancer associated with familial growth hormone deficiency.

Introduction: Variants in the intron splicing enhancer (ISE) of intron 3 in the GH1 gene are implicated in the etiology of isolated growth hormone deficiency Type 2 (Type II IGHD).

Methods: Exome sequencing was performed to screen variants that co-segregated with IGHD in an extended family with Type II IGHD. The causality of the candidate variant was assessed using bioinformatic tools and previous in vitro studies.

Results: Exome sequencing identified a rare intronic variant (NM_000515.5, c.291+34 G>A) in the second XGGG repeat of ISE in intron 3 of GH1, which occurred de novo in the mother with IGHD and was passed onto her two affected children. The variant was previously shown in vitro to cause exon 3 skipping in 50% of the mRNAs and was predicted to create a new binding site for exonic splicing enhancer binding proteins (SR proteins).

Conclusion: Our familial case reiterates the importance of intronic variants in the splicing enhancer region as a cause of IGHD. Consideration should be given to sequencing the splicing enhancer region in intron 3 of GH1 for patients who undergo genetic testing for growth hormone deficiency.