Mutation Spectrum of the Survival of Motor Neuron 1 and Functional Analysis of Variants in Chinese Spinal Muscular Atrophy

Abstract

Proximal spinal muscular atrophy (SMA) is a common fatal autosomal recessive disorder caused by deletion or mutation of the survival of motor neuron 1 (SMN1). Here, we studied SMA molecular pathology in 653 Chinese patients and found approximately 88.2% with homozygous SMN1 exon 7 deletion and 6.3% with heterozygous exon 7 loss using multiplex ligation-dependent probe amplification. SMN1 variants were detected in 34 patients with heterozygous SMN1 loss by clone sequencing. In 27 of them, 15 variants were identified: five were unreported novel variants [c.-7_9del(p.0), p.Tyr109Cys, p.Ile249Tyrfs*16, p.Tyr272Trpfs*35, and c.835-5T>G], five were previously found only in Chinese patients (p.Ser8Lysfs*23, p.Gln14*, p.Val19Glyfs*21, p.Leu228*, and p.Tyr277Cys), and five were reported in other populations [p.Ala2Gly, p.Gln15*, p.Glu134Lys, p.Ser230Leu, and c.863G>T (r.835_*3del, p.Gly279Glufs*5)]. Variants p.Ser8Lysfs*23 and p.Leu228* were the most common in Chinese SMA. Five variants (p.Ser8Lysfs*23, p.Gln14*, p.Gln15*, p.Val19Glyfs*21, and p.Leu228*) resulted in premature stop codons, likely causing SMN1 mRNA nonsense-mediated decay. The novel variant c.-7_9del (p.0) caused deletion of the translation start codon (AUG), resulting in full-length SMN protein loss. The novel variant c.835-5T>G, located in a splice site, resulted in 90% exon 7 skipping. Our study could facilitate early diagnosis for SMA patients in mutation detection and revealed the specific mutation spectrum of SMN1 in Chinese SMA and high genetic heterogeneity in subtle variants observed between patients from China and Caucasians.

Incorporating Spinal Muscular Atrophy Analysis by Next-Generation Sequencing into a Comprehensive Multigene Panel for Neuromuscular Disorders

“…Evidence from the literature supports these ''indeterminate'' variants as either causative for SMA or predicted to be deleterious based on their molecular effect (Supplementary Table S2). We identified the c.815A>G (p.Tyr272Cys) variant, which is a frequent variant in different populations (Wirth, 2000), as well as two other previously reported SMN1 variants: c.5C>G (p.Ala2Gly) and c.283G>C (p.Gly95Arg) (Sun et al, 2005;Bai et al, 2014;Qu et al, 2016). We did not identify any of the other commonly reported variants: c.770-780dup11 (p.Gly261Leufs*8), c.821C>T (p.Thr274Ile), or c.399_402delAGAG (p.Glu134Serfs*14) (Parsons et al, 1996;Clermont et al, 2004;Alias et al, 2009;Prior, 2010).…”

“…Heterozygous loss of SMN1 was detected in 118 patients. Eight of these patients had a probable genetic diagnosis of SMA, and all eight had a heterozygous loss of SMN1 exon 7 and an indeterminate sequence or copy number variant in exons 1-6 that could not be disambiguated to SMN1 or SMN2 ( Supplementary Table S2) (Lefebvre et al, 1995;Parsons et al, 1998;Wirth, 2000;Skordis et al, 2001;Monani et al, 2003;Sun et al, 2005;Kariya et al, 2008;Morse et al, 2011;Bai et al, 2014;Giannopoulou et al, 2015;Qu et al, 2016). These indeterminate variants would be classified as pathogenic if they were determined to be on SMN1, and resolution of the location of these variants would support a diagnosis of SMA in those individuals.…”

Diagnosis of Spinal Muscular Atrophy

“…Among those five subtle SMN1 variants, Ser8Lysfs*23 and Leu228* were the two most common variants in Chinese SMA population. [13] Three novel variants, Tyr276His, Ser143Phefs*5, and Pro218Hisfs*26, were reported in this study for the first time. According to the Standards and Guidelines for the Interpretation of Sequence Variants of American College of Medical Genetics and Genomics ,[14] we classified Tyr276His as pathogenic and weighted as moderate and Ser143Phefs*5 and Pro218Hisfs*26 were classified as pathogenic and weighted as very strong.…”

Genomic Variability in the Survival Motor Neuron Genes (SMN1 and SMN2): Implications for Spinal Muscular Atrophy Phenotype and Therapeutics Development

“…In this scenario, the SMN1 gene actually contains part of SMN2 , in particular within exon 7 [ 46 , 122 , 123 , 124 , 125 , 126 ]. Gene conversion events between SMN1 and SMN2 have been observed by multiple groups using different approaches [ 89 , 93 , 122 , 123 , 124 , 125 , 127 , 128 , 129 , 130 , 131 , 132 , 133 ]. Gene conversion events may account for the inverse relationship between SMN2 copy number and disease severity in SMA ( Figure 2 ).…”

“…There are, however, at least 15 other paralogous structural variants (PSVs) between SMN1 and SMN2 ( Figure 3 ; [ 60 , 108 , 120 , 135 , 136 ]). Gene conversion events at exon 8 ( SMN2c.1155G>A ) as well as those within intron 6 ( SMN2c.835-44G>A ) and intron 7 ( SMN2c.888+100A>G and SMN2c.888+215A>G ) have been observed in SMA, as well as in control populations [ 127 , 129 , 133 ]. Some of these PSVs, such as c.835-44G>A and c.888+100A>G , can affect exon 7 inclusion in spliced SMN mRNAs [ 137 , 138 ].…”