Expanding the phenotypic and genetic landscape of congenital neutropenia through whole-exome and genome sequencing

Abstract

Congenital neutropenia (CN) comprises a heterogeneous group of rare genetic disorders. While some CN cases present only with neutropenia, others present with additional extra-hematological manifestations. The most common cause of CN is variants in ELANE; however, approximately 30 other genes have been implicated. Despite this, the genetic basis remains unknown in roughly 30% of cases. The clinical and genetic heterogeneity of CN makes diagnosis particularly challenging. To address this, we conducted exome or genome sequencing of 60 patients with a suspected diagnosis of CN that remained unresolved following targeted sequencing. A genetic diagnosis was established in 25 patients (42%). Variants were identified in 15 different genes. Half of these cases involved genes traditionally associated with hereditary immunodeficiencies (GINS4, CARD11, ADA2, GINS1, LCP1, SASH3, and WAS). One-third of the cases carried variants in genes linked to syndromic disorders (VPS13B, TAFAZZIN, CLPB, and TONSL), demonstrating variable penetrance of extra-hematological phenotypes. A smaller subset (15%) harbored variants in genes associated with inherited bone marrow failure syndromes (BLM, RPL18, SAMD9, and SRP72), identified incidentally due to atypical presentations. Compared to patients with ELANE-CN, these individuals were diagnosed later, had fewer severe bacterial infections and gingivitis, exhibited less profound neutropenia, lacked monocytosis, and had a granulocytic maturation arrest, often beyond the promyelocytic stage. A shared feature among these cases was a tendency toward reduced lymphocyte subsets, particularly NK cells. This study highlights the significant contribution of exome and genome sequencing in diagnosing CN, given the phenotypic overlap, genetic heterogeneity, and variable penetrance of immunological and extra-hematological features.

Figure 1

Pedigrees with disease‐causing variants and associated mode of inheritance. (A) Autosomal recessive, (B) autosomal dominant, and (C) X‐linked genetic subtypes. Squares, males; circles, females; filled black symbols, clinical diagnosis of CN; symbols with a black dot, confirmed obligate heterozygotes; arrow indicates the proband in large families; NA, genotype not available; NN, wild‐type genotype. By default, variants are described at protein level except promoter and intronic variants described at nucleotide level; genotypes of recessive forms are indicated in brackets. Nomenclature and classification of variants are detailed in Supporting Information S2: Table 1. In pedigree F25, gray filled symbols, neutropenia and thrombocytopenia phenotypes; hatched symbols, myelodysplastic syndrome phenotype.

Figure 2

Gene defect distribution and classification. (A) The numbers and (B) percentages of patients with disease‐causing variants identified by exome and genome sequencing. Gene defects were classified into three subgroups: immunodeficiency disorders, inherited bone marrow failure syndrome (IBMFS), and rare genetic disorders with syndromic features (rare syndromes).

Figure 3

Analysis of neutrophil precursors in the bone marrow of patients with disease‐causing variants. Patients were classified according to gene defect subgroup and compared to patients with ELANE‐CN.

Figure 4

Immunophenotype of patients according to gene defect subgroup. (A) Total lymphocytes; (B) lymphocyte subsets including CD3⁺CD4⁺ and CD3⁺CD8⁺ T lymphocytes, CD19⁺ B lymphocytes, and CD16⁺56⁺ NK lymphocytes; (C) immunoglobulins IgG, IgA, and IgM. The gray area corresponds to the normal range observed in controls.