Table 1.
The 22 candidate positions for paralogous sequence variants (PSVs) between SMN1 and SMN2 are shown
| SMN1 position | SMN2 position | Gene location | Ref SMN1 | Ref SMN2 | Categorization | Conversion nomenclature SMN2>SMN1 | Source of information |
|---|---|---|---|---|---|---|---|
| 70231509 | 69356085 | Intron 1 | G | A | SNPa | c.82‐3157A>G | BLAT |
| 70240028 | 69364605 | Intron 4 | G | A | SNPa | c.628‐457A>G | BLAT |
| 70242435 | 69367010 | Intron 6 | T | C | SNPa | c.834+432C>T | BLAT |
| 70242978 | 69367553 | Intron 6 | A | G | SNVb | c.834+975G>A | BLAT |
| 70244142 | 69368717 | Intron 6 | A | G | SNPa | c.834+2139G>A | Monani et al. /BLAT |
| 70245876 | 69370451 | Intron 6 | T | C | PSV | c.835‐1897C>T | Monani et al. /BLAT |
| 70246016 | 69370591 | Intron 6 | G | A | PSV | c.835‐1757A>G | Monani et al. /BLAT |
| 70246019 | 69370594 | Intron 6 | T | C | PSV | c.835‐1754C>T | Monani et al. /BLAT |
| 70246156 | 69370731 | Intron 6 | G | A | PSV | c.835‐1617A>G | Monani et al. /BLAT |
| 70246167 | 69370742 | Intron 6 | T | C | PSV | c.835‐1606C>T | BLAT |
| 70246320 | 69370895 | Intron 6 | G | A | PSV | c.835‐1453A>G | Monani et al. /BLAT |
| 70246793 | 69371368 | Intron 6 | G | A | PSV c | c.835‐980A>G | Monani et al. /BLAT |
| 70246872 | 69371448 | Intron 6 | ‐ | AGGCA | PSV c | c.835‐900_835‐896del | Monani et al. /BLAT |
| 70246919 | 69371499 | Intron 6 | A | C | PSV c | c.835‐849C>A | Monani et al. /BLAT |
| 70247219 | 69371799 | Intron 6 | G | A | PSV c | c.835‐549A>G | Monani et al. /BLAT |
| 70247290 | 69371870 | Intron 6 | T | C | PSV | c.835‐478C>T | Monani et al. /BLAT |
| 70247401 | 69371981 | Intron 6 | C | A | SNVb, c | c.835‐367A>C | Monani et al. /BLAT |
| 70247724 | 69372304 | Intron 6 | G | A | PSV c | c.835‐44A>G | Monani et al. /BLAT |
| 70247773 | 69372353 | Exon 7 | C | T | PSV c | c.840T>C | Monani et al. /BLAT |
| 70247921 | 69372501 | Intron 7 | A | G | PSV c | c.*3+100G>A | Monani et al. /BLAT |
| 70248036 | 69372616 | Intron 7 | A | G | PSV c | c.*3+215G>A | Monani et al. /BLAT |
| 70248501 | 69373081 | Exon 8 | G | A | PSV c | c.*239A>G | Monani et al. /BLAT |
Note: These positions were obtained from a previous bibliographic compilation (Monani et al., 1999) and were complemented with a BLAT between the two genes, as deposited in the reference genome Hg19. Repetitive regions (polyA, polyT, and polyGT) were discarded. The candidate positions were genotyped in the patients studied in this study (n = 53) and in samples with at least one SMN1 (n = 3) to check for consistency. From the 22 candidates, six were discarded as PSVs, four of them are listed as SNPs instead, and the remaining two as rare SNV. Therefore, a total of 16 nucleotides (in bold in the Table) differentiate SMN1 and SMN2 genes, 10 of which had been previously described and validated, 5 had been described but not validated, and 1 is considered here as a PSV for the first time.
Abbreviations: BLAT, BLAST‐like alignment tool; SNP, single‐nucleotide polymorphism; SNV, single‐nucleotide variant.
These positions show high variability between samples and were therefore classified as SNPs (including position c.835‐367C/A previously validated by Monani et al., 1999).
In these positions, the same nucleotide has always been found in both SMN1 and SMN2. Thus, G>A and A>C exchanges appears to be very rare SNV found in the reference genome.
These 11 positions were previously classified as bona fide PSVs, after being tested in a control population of 15 individuals (Monani et al., 1999).