Identification of Heterozygous Single- and Multi-exon Deletions in IL7R by Whole Exome Sequencing

Abstract

Purpose We aimed to achieve a retrospective molecular diagnosis by applying state-of-the-art genomic sequencing methods to past patients with T-B+NK+ severe combined immunodeficiency (SCID). We included identification of copy number variations (CNVs) by whole exome sequencing (WES) using the CNV calling method ExomeDepth to detect gene alterations for which routine Sanger sequencing analysis is not suitable, such as large heterozygous deletions. Methods Of a total of 12 undiagnosed patients with T-B+NK+ SCID, we analyzed eight probands by WES, using GATK to detect single nucleotide variants (SNVs) and small insertions and deletions (INDELs) and ExomeDepth to detect CNVs. Results We found heterozygous single-or multi-exon deletions in IL7R, a known disease gene for autosomal recessive T-B+NK+ SCID, in four families (seven patients). In three families (five patients), these deletions coexisted with a heterozygous splice site or nonsense mutation elsewhere in the same gene, consistent with compound heterozygosity. In our cohort, about a quarter of T-B+NK+ SCID patients (26%) had such compound heterozygous IL7R deletions. Conclusions We show that heterozygous IL7R exon deletions are common in T-B+NK+ SCID and are detectable by WES. They should be considered if Sanger sequencing fails to detect homozygous or compound heterozygous IL7R SNVs or INDELs.

Copy Number Variation Disorders

“…CNVs may also reveal recessive disorders, wherein a deletion of one allele of the gene unmasks a point mutation on the other allele, resulting in disease. For example, in three individuals with unexplained intellectual disabilities, the discovery of a CNV that deleted the COH1 gene led to the subsequent identification of a second pathogenic point mutation in COH1, leading to a diagnosis of Cohen syndrome, an autosomal recessive disorder [49] Deletions of the non-mutated allele of IL7R have been uncovered by retrospective analysis of patients with autosomal recessive T-B+NK+ severe combined immunodeficiency (SCID), with a mutation previously detected in only one allele [50]. …”

Deleterious and Oncogenic Mutations in the IL7RA

“…There are only two disease-associated variants found in the intracellular portion of the receptor, at position 356 (p.I356V) and 269 (p.K269fs), and they are associated with increased risk of multiple sclerosis and SCID, respectively [42,53]. Most variations with unknown significance (VUS), classified as pathogenic by computational methods [55], are commonly distributed in the intracellular portion of the receptor, although there are some in the extracellular and transmembrane portions as well.…”

“…Deletions of whole exons of the IL7RA gene have been described in SCID cases, more specifically involving exons 2-4. These deletions inactivate the receptor function by removing entire protein domains and by generating premature stop codons that leads to the production of largely truncated proteins [42]. There are also reports of small frameshift indels at the same exons generating truncated proteins [33,46,48], and nonsense mutations, generating a premature stop codon [35,42].…”

“…These deletions inactivate the receptor function by removing entire protein domains and by generating premature stop codons that leads to the production of largely truncated proteins [42]. There are also reports of small frameshift indels at the same exons generating truncated proteins [33,46,48], and nonsense mutations, generating a premature stop codon [35,42]. Finally, some IL7RA SNPs and mutations are known to impair splicing of the nascent IL7RA transcript, thus contributing to disease also by causing frameshifts that result in protein truncations [33,42,43,45].…”

Pathogenesis and clinical features of congenital stationary night blindness in case of c.283delC NYX gene mutation

“…делеций, так и вариаций числа копийности (CNV) по методу K. Engelhardt и соавт. [9]. Аннотацию вариантов выполняли, следуя методам, описанным ранее [10].…”