Previously Undescribed Gross HACE1 Deletions as a Cause of Autosomal Recessive Spastic Paraplegia

Abstract

Spastic paraplegia and psychomotor retardation with or without seizures (SPPRS, OMIM 616756) is a rare genetic disease caused by biallelic pathogenic variants in the HACE1 gene. Originally, these mutations have been reported to be implicated in tumor predisposition. Nonetheless, via whole exome sequencing in 2015, HACE1 mutations were suggested to be the cause of a new autosomal recessive neurodevelopmental disorder, which is characterized by spasticity, muscular hypotonia, and intellectual disability. To date, 14 HACE1 pathogenic variants have been described; these variants have a loss-of-function effect that leads to clinical presentations with variable severities. However, gross deletions in the HACE1 gene have not yet been mentioned as a cause of spastic paraplegia. Here, we report a clinical case involving a 2-year-old male presenting with spasticity, mainly affecting the lower limbs, and developmental delay. Exome sequencing, chromosomal microarray analysis, and mRNA analysis were used to identify the causative gene. We revealed that the clinical findings were due to previously undescribed HACE1 biallelic deletions. We identified the deletion of exon 7: c.(534+1_535-1)_(617+1_618-1)del (NM_020771.4) and the gross deletion in the 6q16.3 locus, which affected the entire HACE1 gene: g.105018931_105337494del, (GRCh37). A comprehensive diagnostic approach for the patients with originally homozygous mutations in HACE1 is required since false homozygosity results are possible. More than 80% of the described mutations were reported to be homozygous. Initial hemizygosity is hard to detect by quantitative methods, and this may challenge molecular diagnostic identification in patients with spastic paraplegia.

Keywords: HACE1; neurodevelopmental syndrome; spastic paraplegia.

Figure 1

The proband’s facial phenotype.

Figure 2

Spastic paraplegia in the proband’s lower limbs.

Figure 3

The pedigree of the proband.

Figure 4

Molecular genetic testing of the patient by clinical exome sequencing and visualization of the homo/hemizygous deletion of HACE1 exon 7.

Figure 5

Visualization of cDNA amplification products for the proband (F1.1), his parents (F1.2 and F1.3), and reference samples (R1–R5), with primers flanking introns 4 and 9 of the HACE1 gene. Band I (529 bp) includes the sequences of exons 5, 6, 7, 8, and 9 of the HACE1 gene, which corresponds to the canonical protein-coding transcript 1 (isoform a). This amplicon was absent in the proband (F1.1). Band II (446 bp) includes the sequences of exons 5, 6, 8, and 9 of the HACE1 gene without exon 7 (isoform d). Band III (397 bp) corresponds to protein isoforms b and e, whose transcripts do not contain the sequence of HACE1 exon 6, but contain exon 7. Band IV (314 bp) does not include the sequences of exons 6 and 7 of the HACE1 gene, which corresponds to the transcript of HACE1 isoform h. Bands I and III were not registered in the proband (F1.1). In the proband’s father (F1.3), we detected an increase in signal intensity for bands II and IV as compared to the reference samples (R1–R5) and the maternal sample (F1.2).

Figure 6

(a) Nucleotide sequences and lengths of exons 6, 7, and 8 of the HACE1 gene (canonical transcript); (b) Sanger sequencing validation of the homozygous/hemizygous deletion of exon 7 of the HACE1 gene in the proband; (c,d) Sanger sequencing of the patient’s mother’s cDNA, validating the presence of exons 6, 7, and 8 of the HACE1 gene; (e,f) Sanger sequencing of patient’s father’s cDNA, validating the presence of exons 6, 7, and 8 of the HACE1 gene.

Figure 6

(a) Nucleotide sequences and lengths of exons 6, 7, and 8 of the HACE1 gene (canonical transcript); (b) Sanger sequencing validation of the homozygous/hemizygous deletion of exon 7 of the HACE1 gene in the proband; (c,d) Sanger sequencing of the patient’s mother’s cDNA, validating the presence of exons 6, 7, and 8 of the HACE1 gene; (e,f) Sanger sequencing of patient’s father’s cDNA, validating the presence of exons 6, 7, and 8 of the HACE1 gene.

Figure 7

Visualization of the heterozygous deletion of the entire HACE1 gene in the patient by means of chromosomal microarray analysis.

Figure 8

Described pathogenic variants in the HACE1 gene. * = nonsense mutation.

Figure 9

HACE1 protein sequence, as long as exon 7 is deleted, and HACE1 canonical protein sequence (NM_020771.4). *= termination of the protein synthesis.