Compound heterozygous c.598_612del and c.1746-20C > G CAPN3 genotype cause autosomal recessive limb-girdle muscular dystrophy-1: a case report

Abstract

Background Autosomal recessive limb–girdle muscular dystrophy-1 (LGMDR1), also known as calpainopathy, is a genetically heterogeneous disorder characterised by progression of muscle weakness. Homozygous or compound heterozygous variants in the CAPN3 gene are known genetic causes of this condition. The aim of this study was to confirm the molecular consequences of the CAPN3 variant NG_008660.1(NM_000070.3):c.1746-20C > G of an individual with suspected LGMDR1 by extensive complementary DNA (cDNA) analysis. Case presentation In the present study, we report on a male with proximal muscular weakness in his lower limbs. Compound heterozygous NM_000070.3:c.598_612del and NG_008660.1(NM_000070.3):c.1746-20C > G genotype was detected on the CAPN3 gene by targeted next-generation sequencing (NGS). To confirm the pathogenicity of the variant c.1746-20C > G, we conducted genetic analysis based on Sanger sequencing of the proband’s cDNA sample. The results revealed that this splicing variant disrupts the original 3′ splice site on intron 13, thus leading to the skipping of the DNA fragment involving exon 14 and possibly exon 15. However, the lack of exon 15 in the CAPN3 isoforms present in a blood sample was explained by cell-specific alternative splicing rather than an aberrant splicing mechanism. In silico the c.1746-20C > G splicing variant consequently resulted in frameshift and formation of a premature termination codon (NP_000061.1:p.(Glu582Aspfs*62)). Conclusions Based on the results of our study and the literature we reviewed, both c.598_612del and c.1746-20C > G variants are pathogenic and together cause LGMDR1. Therefore, extensive mRNA and/or cDNA analysis of splicing variants is critical to understand the pathogenesis of the disease.

HINT1 neuropathy in Lithuania: clinical, genetic, and functional profiling

“…Several in silico prediction programs (PolyPhen-2 [ 16 ], MutationTaster [ 17 ], SIFT [ 18 ]) were used to predict the functional effect as well as the genomic evolutionary rate profiling (GERP) [ 28 ] score. Segregation analysis was performed by Sanger sequencing [ 29 ].…”

Two novel variants of the CAPN3 gene in Chinese patients with Limb-Girdle Muscular Dystrophy Recessive 1

“…Although we reported two novel pathogenic mutations in LGMD patients for the first time, the shortcoming of this study is that the influence of mRNA level after mutation is not further verified through appropriate experiments. DNA sequence variants affect pre-mRNA processing through exon skipping, cryptic splicing, intron inclusion, leaky splicing, and other methods [30]. Therefore, it is difficult to accurately predict the specific cause of pathogenicity by artificial intelligence.…”

Next generation sequencing panel as an effective approach to genetic testing in patients with a highly variable phenotype of neuromuscular disorders

“…However, Mroczek et al (2022) showed that this variant is hypomorphic causing LGMDR1 when occurs in trans position with another pathogenic/likely pathogenic variant [ 26 ]. Many studies confirm that this variant is causal when occurs in the compound heterozygous state [ 25 , 27 , 28 ]. According to these findings, we can hypothesize that one of our patients, in whom compound heterozygous CAPN3: c.[700G > A];[1746-20C > G] variants together with heterozygous POLG likely pathogenic variant: c.2243G > C (p.Trp748Ser) were identified can be diagnosed with LGMDR1.…”