Haemophilia B, severe childhood obesity and other extra‐haematological features associated with similar 4Mb‐deletions on Xq27: Clinical findings, molecular insights and literature update

Abstract

Introduction: Haemophilia B (HB) is associated with pathogenic variants in F9. Hemizygous deletions encompassing the entire F9 and proximate genes may express extra-haematological clinical phenotypes. Aim: To analyse the genotype/phenotype correlations in two unrelated boys with severe early childhood obesity (SCO), global developmental delay (GDD) and similar bleeding phenotype associated with comparable Xq27 deletions spanning the entire F9 and proximate genes, and characterise the pathogenic events estimating the most likely mutational mechanism involved. Methods: Entire F9-deletions were detected in three hemizygous unrelated probands with HB: two cases, C#1/C#2, presented SCO and GDD and a control patient (Co), who only had severe bleeding symptoms. Dense SNP-array and case-specific STS walking scan allowed characterisation of the deletion breakpoints. Extensive use of bioinformatics, statistics and clinical databases allowed the investigation of genotype-phenotype associations. Results: Patients C#1/C#2 and Co resulted in a complete F9 and additional gene deletions of variable extensions on Xq26.3-Xq27.2 (C#1/C#2/Co: 4.3Mb/3.9Mb/160Kb). C#1/C#2 common deleted gene SOX3 is directly associated with SCO, GDD and pituitary hypothyroidism (PH) whilst C#2 extra-deleted gene MAGEC2 indirectly relates to anal atresia (AA). Breakpoint analysis revealed the involvement of the mechanisms of Alu/Alu recombination for the first time in HB and non-homologous or alternative end-joining. Conclusion: Our results represent the first report of unrelated patients with HB, SCO and GDD. This study and the literature update expand the spectrum of clinical findings

Complete F9 Gene Deletion, Duplication, and Triplication Rearrangements: Implications for Factor IX Expression and Clinical Phenotypes

“…According to Radic et al patients develop extra-hematologic phenotypes such as partial hypopituitarism, intellectual disability, and developmental delay when the deletion region encompasses the SOX3 gene. 15 However, proband 1 had a chromosomal deletion affecting multiple genes, including SOX3 , but did not exhibit any unique medical history records beyond HB. One possible explanation could be attributed to compensatory mechanisms within the genome that can mitigate the functional loss of the SOX3 gene.…”

“…Previous studies have suggested the involvement of DNA repair-based mechanisms, such as nonhomologous end joining and nonallelic homologous recombination (NAHR), and DNA replication-based mechanisms like Fork Stalling and Template Switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR) in F9 -related SVs. 15 16 17 However, recurrent NAHR rearrangements mediated by low-copy repeats (LCRs), similar to the intron 22 inversion of F8 , have not been identified in structural rearrangements involving F9 to date.…”

“…Understanding the specific breakpoints of F9-related SVs can provide valuable insight into the underlying rearrangement mechanisms and help to predict microhomology-mediated break-induced replication (FoSTeS/ MMBIR) in F9-related SVs. [15][16][17] However, recurrent NAHR rearrangements mediated by low-copy repeats (LCRs), similar to the intron 22 inversion of F8, have not been identified in structural rearrangements involving F9 to date.…”