Identification of variants in pleiotropic genes causing "isolated" premature ovarian insufficiency: implications for medical practice

Abstract

Next-generation sequencing (NGS) is increasingly being used in a clinical setting for the molecular diagnosis of patients with heterogeneous disorders, such as premature ovarian insufficiency (POI). We performed NGS of ~1000 candidate genes in four unrelated patients with POI. We discovered the genetic cause of "isolated" POI in two cases, both of which had causative variants in surprising genes. In the first case, a homozygous nonsense variant in NBN was causative. Recessive function-altering NBN variants typically cause Nijmegen breakage syndrome characterized by microcephaly, cancer predisposition, and immunodeficiency, none of which are evident in the patient. At a cellular level, we found evidence of chromosomal instability. In the second case, compound heterozygous variants in EIF2B2 were causative. Recessive EIF2B2 function-altering variants usually cause leukoencephalopathy with episodic decline. Subsequent MRI revealed subclinical neurological abnormalities. These cases demonstrate that variants in NBN and EIF2B2, which usually cause severe syndromes, can cause apparently isolated POI, and that (1) NGS can precede clinical diagnosis and guide patient management, (2) NGS can redefine the phenotypic spectrum of syndromes, and (3) NGS may make unanticipated diagnoses that must be sensitively communicated to patients. Although there is rigorous debate about the handling of secondary/incidental findings using NGS, there is little discussion of the management of causative pleiotropic gene variants that have broader implications than that for which genetic studies were sought.

Fig. 1

Function-altering variant detected in NBN. a IGV view of c.871C>T NBN (NM_002485.4) variant in Patient 1 (homozygous) and her mother (heterozygous). b Sanger sequencing confirmation of the c.871C>T NBN variant. c Schematic diagram showing patient variant with respect to previously reported variants in patients with Nijmegen breakage syndrome. Patient variant is underlined. Variants found in patients with mild NBS or isolated infertility are shown in italics. Ψ indicates variants that have been shown to also cause alternative protein products. The common founder variant, responsible for most cases of NBS, is shown in bold. Phosphorylation sites are shown as circles. Functional domains are indicated

Fig. 2

The NBN c.871C>T (p.(Gln291*)) (NM_002485.4) variant does not cause aberrant splicing or complete nonsense-mediated decay. a Schematic diagram showing numbered NBN exons and the location of the patient’s variant in the context of the NBN transcript (exons as per NG_008860.1). Primers for cDNA analysis are indicated. b RT-PCR demonstrates a single product comparable to wild-type cDNA from patient lymphoblasts. c Sequencing chromatograms demonstrate that patient lymphoblasts retain some normally spliced NBN transcripts

Fig. 3

Function-altering variants detected in EIF2B2. a IGV view of c.514C>T and c.818A>G (NM_014239.3) variants in Patient 2. b Sanger sequencing of c.514C>T and c.818A>G EIF2B2 variants in Patient 2 and her parents, confirming compound heterozygosity. c Schematic diagram showing patient variants with respect to previously reported variants. Patient variants are underlined. Variant not previously reported is indicated by bold text