Utility of two SMN1 variants to improve spinal muscular atrophy carrier diagnosis and genetic counselling

Abstract

Spinal muscular atrophy (SMA) is caused by deletions/mutations in SMN1. Most heterozygous SMA carriers have only one SMN1 copy in one of the alleles (1/0 carriers). However, a few carriers lack SMN1 in one of their chromosomes, but present two gene copies in the other. These "2/0 carriers" are undistinguishable from non-carrier individuals (1/1) with currently available methods. Previous association of SMN1 variants c.*3 + 80 T > G and c.*211_*212del with two SMN1 copies in cis in Ashkenazi population prompted us to analyze them in 270 Spanish individuals (SMA carriers, patients and general population). Both variants were much more frequently detected in chromosomes with 2 SMN1 copies in cis in comparison with chromosomes carrying one copy (17.9 vs. 0.7%; p < 0.001). In particular, one-fifth of 2/0 SMA carriers harboured one or both variants compared to none of 99 non-carriers with two SMN1 copies (p < 0.001). The c.*211_*212del variant was also much more frequent in exon 8 of SMN2-SMN1 hybrids than in that of intact SMN1 genes (20 vs. 0.83%, p < 0.001), suggesting its association with chromosomal rearrangements. Although absence of these variants does not exclude that a particular individual is a 2/0 SMA carrier, their presence is valuable to substantially increase residual risk in putative carriers, thus improving genetic counselling.

Fig. 1

Identification and genetic analyses of special SMA carriers. a Familial haplotype and SMN1 quantitative analyses in a family with a 3/0 carrier. The family requested carrier studies because of the previous death of a son with clinical manifestations compatible with type I SMA. Due to the informative potential of the D5F149S1 and D5S1556 polymorphic markers and allele segregation, the more likely explanation is that the three copies of the SMN1 gene detected in the mother (I:2) were located in cis in the same chromosome. Her non-carrier daughter (II:1) harboured 4 SMN1 copies, three of them inherited from her maternal chromosome and the other one from her father. The carrier daughter (II:2) showed a single SMN1 copy inherited from her father (shared also with her sister) and the SMN1 deletion from her mother. The haplotype of SMA patient (II:3) is inferred. Black bars represent the chromosome that lacks SMN1. Each box represents a single SMN1 copy. The number of each marker allele corresponds to the CA repeats. b Association between the presence of the c.*3 + 80 T > G variant in intron 7 of the SMN1 gene and a chromosome carrier of two copies of this gene. By quantitative studies, we detected the presence of three SMN1 copies in the father (I:1) and one copy in the mother (I:2). Haplotype analyses revealed that both siblings inherited the same maternal chromosome without the SMN1 gene, while the paternal chromosome was different. The older daughter (II:1) was diagnosed as a 2/0 carrier with 2 copies of the SMN1 gene and the presence of the c.*3 + 80 T > G variant inherited from her father, while the younger son (II:2) showed one copy of the gene without the variant