Molecular Diagnoses of X-Linked and Other Genetic Hypophosphatemias: Results From a Sponsored Genetic Testing Program

Abstract

X-linked hypophosphatemia (XLH), a dominant disorder caused by pathogenic variants in the PHEX gene, affects both sexes of all ages and results in elevated serum fibroblast growth factor 23 (FGF23) and below-normal serum phosphate. In XLH, rickets, osteomalacia, short stature, and lower limb deformity may be present with muscle pain and/or weakness/fatigue, bone pain, joint pain/stiffness, hearing difficulty, enthesopathy, osteoarthritis, and dental abscesses. Invitae and Ultragenyx collaborated to provide a no-charge sponsored testing program using a 13-gene next-generation sequencing panel to confirm clinical XLH or aid diagnosis of suspected XLH/other genetic hypophosphatemia. Individuals aged ≥6 months with clinical XLH or suspected genetic hypophosphatemia were eligible. Of 831 unrelated individuals tested between February 2019 and June 2020 in this cross-sectional study, 519 (62.5%) individuals had a pathogenic or likely pathogenic variant in PHEX (PHEX-positive). Among the 312 PHEX-negative individuals, 38 received molecular diagnoses in other genes, including ALPL, CYP27B1, ENPP1, and FGF23; the remaining 274 did not have a molecular diagnosis. Among 319 patients with a provider-reported clinical diagnosis of XLH, 88.7% (n = 283) had a reportable PHEX variant; 81.5% (n = 260) were PHEX-positive. The most common variant among PHEX-positive individuals was an allele with both the gain of exons 13-15 and c.*231A>G (3'UTR variant) (n = 66/519). Importantly, over 80% of copy number variants would have been missed by traditional microarray analysis. A positive molecular diagnosis in 41 probands (4.9%; 29 PHEX positive, 12 non-PHEX positive) resulted in at least one family member receiving family testing. Additional clinical or family member information resulted in variant(s) of uncertain significance (VUS) reclassification to pathogenic/likely pathogenic (P/LP) in 48 individuals, highlighting the importance of segregation and clinical data. In one of the largest XLH genetic studies to date, 65 novel PHEX variants were identified and a high XLH diagnostic yield demonstrated broad insight into the genetic basis of XLH. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Keywords: CELL/TISSUE SIGNALING - PARACRINE PATHWAYS - OTHER; DISEASES AND DISORDERS OF/RELATED TO BONE - OTHER; DISORDERS OF CALCIUM/PHOSPHATE METABOLISM- OTHER; GENETIC RESEARCH - HUMAN ASSOCIATION STUDIES; THERAPEUTICS - OTHER.

Fig 1

PHEX and non‐PHEX results from probands. Probands were categorized according to their genetic testing results ‐ PHEX positives (1 P/LP in PHEX). Among PHEX‐negative individuals, those with a positive molecular diagnosis in another gene are indicated. A positive molecular diagnosis was based on the inheritance pattern (AR, 2 P/LP variants; AD, 1 P/LP variant). *Three PHEX‐positive individuals also carried a PHEX VUS and were only counted in the PHEX‐positive group. In addition, one PHEX‐positive individual had a second molecular diagnosis in ALPL, with a single P/LP resulting in the AD form of the disorder. AD = autosomal dominant; AR = autosomal recessive; P/LP = pathogenic/likely pathogenic; VUS = variant of uncertain significance.

Fig 2

Diversity of reported clinical features among unrelated individuals. (A) The number of individuals with each clinician‐reported sign or symptom was calculated and stratified by molecular diagnosis, with proportions based on the number of individuals with each feature noted. (B) For each clinician‐reported sign or symptom, the proportions of PHEX‐positive and non‐PHEX‐positive individuals were calculated. Proportions were calculated based on the number of individuals with the clinical sign or symptom noted (“+”) or not noted (“–”), as indicated in parentheses along the X‐axis.

Fig 3

Distribution of PHEX P/LP variants observed in probands. (A) Distribution of variant types among the 237 unique P/LP variants. (B) Recurrence of PHEX P/LP variants by type observed across all individuals with a positive PHEX molecular diagnosis (n = 585). Note that individuals (n = 65) with the exon 13–15 duplication and c.*231G>A 3′UTR variants in cis were counted in both the CNV and SNV categories. CNVs were defined as >100 base pairs. Small deletions, duplications, and insertions were defined as events involving <100 base pairs. CNV = copy number variant; P/LP = pathogenic/likely pathogenic; SNV = single nucleotide variant.