Abnormal Newborn Screening for Severe Combined Immunodeficiency due to CD4 T cell lymphopenia associated with Heterozygous FOXN1 Variants in the Forkhead Domain

Abstract

FOXN1 performs a pivotal role in the development of thymic epithelium. Homozygous FOXN1 deficiency results in T-B+NK+ SCID while FOXN1 haploinsufficiency is associated with T cell lymphopenia and nail dystrophy. We report two patients with variants of uncertain significance (VUS) in FOXN1 who presented with lymphopenia detected on newborn screening.Patient A is a 17-month-old female born to non-consanguineous parents who presented with lowT-cell receptor excision circles (TRECs). At 2 weeks old, her lymphocyte subset panel revealed low T cells, but normal B and NK cells (Table 1). Follow up at 3 months revealed uptrending T cells and significantly decreased B cells. She had no concerning clinical features or infections at that time. By 6 months, her T cells were again downtrending, but her B cells had normalized. She required antibiotics for acute otitis media, which quickly resolved. At 15 months, T cell lymphopenia persisted (Figure 2). Her infection history was reassuring, developmental milestones met and physical exam notable only for spooned nails.Patient B is a 4-month-old female also born to non-consanguineous parents presenting with low TRECs. Initial workup at 5 days revealed T cell lymphopenia, but normal B and NK cells (Table 1). At 2 months, CD4 lymphopenia persisted though CD8T cells normalized (Figure 2). She had a self-limiting upper respiratory infection, but otherwise unremarkable infection history. Development and physical exam were normal.A targeted 429-gene panel for inborn errors of immunity revealed heterozygous FOXN1 VUSs in both Patient A (c.890T > G, p.Ile297Ser) and Patient B (c.890T > C, p.Ile297Thr). Patient A's variant was not present in population databases. Patient B's variant has been observed (gnomAD frequency of 0.007%) but not present in population databases for the patient's ethnicities. Surprisingly, both are located at the same position within the Forkhead domain (Figure 1). Algorithms to predict the effect of missense changes on FOXN1 protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all predicted these variants as likely to be disruptive. Further understanding of the phenotypes associated with heterozygous FOXN1 variants of uncertain significance is crucial to guiding diagnostics, treatment, and prognosis. Table 1Lymphocyte panel results at original presentation (Patient A: 2 weeks old, Patient B: 5 days old). Reference ranges obtained from J Allergy Clin Immunol, Volume 112, Number 5, pp 973–980, November 2003VariantCD4+ CD45RA+ (Naïve CD4+ T Cells, cells/μL)CD4+ CD45RO+ (Memory CD4+ T cells, cells/μL)CD8+ T Cells (cells/μL)CD19+ B Cells (cells/μL)CD16+ CD56+ (NK Cells, cells/μL)Patient Ac.890T>G (p.Ile297Ser)633100518423700Patient Bc.890T>C (p.Ile297Thr)569126122610311Ref range (0–3 months)1200–370060–900560–1700300–2000170–1700 [Display omitted] [Display omitted]