A novel likely pathogenic variant in the FBXO32 gene associated with dilated cardiomyopathy according to whole‑exome sequencing

Abstract

Background: Familial dilated cardiomyopathy (DCM) is a genetic heart disorder characterized by progressive heart failure and sudden cardiac death. Over 250 genes have been reported in association with DCM; nonetheless, the genetic cause of most DCM patients has been unknown. The goal of the present study was to determine the genetic etiology of familial DCM in an Iranian family.

Methods: Whole-exome sequencing was performed to identify the underlying variants in an Iranian consanguineous family with DCM. The presence of the candidate variant was confirmed and screened in available relatives by PCR and Sanger sequencing. The pathogenic effect of the candidate variant was assessed by bioinformatics analysis, homology modeling, and docking.

Results: One novel likely pathogenic deletion, c.884_886del: p.Lys295del, in F-box only protein 32 (muscle-specific ubiquitin-E3 ligase protein; FBXO32) was identified. Based on bioinformatics and modeling analysis, c.884_886del was the most probable cause of DCM in the studied family.

Conclusions: Our findings indicate that variants in FBXO32 play a role in recessive DCM. Variants in FBXO32 may disturb the degradation of target proteins in the ubiquitin-proteasome system and lead to severe DCM. We suggest considering this gene variants in patients with recessively inherited DCM.

Keywords: Dilated cardiomyopathy; FBXO32; Genetic; Variant; Whole-exome sequencing.

Fig. 1

The image presents the pedigree of the family with dilated cardiomyopathy (DCM), as well as the results of magnetic resonance imaging (MRI) and the sequencing chromatograms of the mutated nucleotide in the FBXO32 gene. A The pedigree of the family with DCM is presented herein. The proband (indicated by the arrow) was a candidate for heart transplantation. B The MRI of the proband (III-4) is presented herein. C The Sanger sequencing results of the FBXO32 gene in the patient and her family members are shown here. The patients carried a homozygous missense variant: c.884_886del: p.Lys295del

Fig. 2

The image depicts the potential mechanism of FBXO32, as well as the location and conservation of the mutated amino acid. A The different domains of FBXO32 are illustrated here. The image presents a schematic representation of the FBXO32 structure, containing the leucine zipper domain, the leucine-charged residue-rich domain (LCD), nuclear export signal (NES-like motif) in the LCD domain, 2 highly conserved nuclear localization signals (NLS), the F-Box domain (F-Box), the PDZ domain (PDZ), and the Cytochrome c-like domain (CytC). B The mechanism of the importin α3/β-mediated nuclear import of FBXO32 is depicted here. The NLS domain is bound to importin α3; then, importin β binds to importin α3 for transmission through the nuclear pore complex (NPC). C The alignment of conserved NLS residues from different FBXO32 orthologs was compared using the CLUSTALW Web Server. The lysine amino acids are shown in the box

Fig. 3

The image presents the top complex structures for normal and mutant FBXO32 in interaction with importin α3 (PDB ID: 6BW9), as well as their HADDOCK scores and related energies. A The binding site of wild-type FBXO32 is surrounded by 8 amino acids including Lys288, Gln290, Lys295, Lys299, Arg282, Lys281, Glu261, and Asp287 that binds to importin α3. The panel shows the 3D strong interaction between importin α3 (green) and the wild-type FBXO32 (blue). B The panel shows the 3D weak interaction between importin α3 (green) and the mutant FBXO32 (pink). The binding site of Lys295del FBXO32 is surrounded by 4 amino acids including Lys294, Lys288, Val258, and Asp292 that binds to importin α3. The images were obtained by using PyMOL v.2.5.2. (The yellow dashed lines represent the hydrogen bonds)

Fig. 4

The image demonstrates the molecular interactions between the normal (A) and mutant (B) FBXO32 and importin α3 generated by LigPlus+ v.2.2.4. (The dotted green line indicates hydrogen bonding, with bond distance). In the wild-type FBXO32, 8 amino acids (Lys288, Gln290, Lys295, Lys299, Arg282, Lys281, Glu261, and Asp287) formed hydrogen bonds with 11 amino acids importin α3 (Asp261, Trp222, Arg218, Asn219, Trp179, Gln176, Glu1754, Ser101, Arg103, Ser100, and Lys299), whereas in the Lys295del FBXO32, just four 4 amino acids (Lys294, Lys288, Val258, and Asp292) formed hydrogen bonds with 5 amino acids importin α3 (Ser144, Gly145, Glu175, Asn104, and Arg103)