Genotyping of Sp110 variants and novel variants identified by DNA sequencing
| Localisation | Exchange | AF | Assay | Inclusion criterium | GenBank accession number |
|---|---|---|---|---|---|
| AC009950.6 is the Sp110 reference sequence. Tagging SNPs 1–10 were genotyped following the selection of bins provided by LDSelect software. The numbering of tagging SNPs (1–10) refers to the order of SNPs as given in haplotypes in table 4. AF, allele frequency. GenBank accession numbers are given only for novel variants identified in this study by re-sequencing. | |||||
| *SNPs included in Sp110 genotyping; †novel Sp110 variants identified in this study; ‡AF as observed in 24 samples that underwent DNA sequencing; ¶putative transcription factor binding site predicted by a matrix search for transcription factor binding sites (Match). | |||||
| 5′-UTR | *g.394T>C (at −2653 of the ATG) | 0.10 | rs6756352 | Tagging SNP (1) | |
| *g.2302C>T (at −745 of the ATG) | 0.20 | rs1346311 | Transcription factor binding site¶ | ||
| *g.2755A>G (at −292 of the ATG) | 0.34 | rs1966555 | Transcription factor binding site¶ | ||
| *g.2804C>T (at −243 of the ATG)† | 0.18 | This report (table 2) | More frequent among patients | DQ124709 | |
| g.2978C>T (at −69 of the ATG)† | 0.02‡ | – | DQ124709 | ||
| *g.3009C>A (at −38 of the ATG)† | 0.09 | This report (table 2) | 5′-UTR; transcription factor binding site¶ | DQ124709 | |
| Intron 2 | *g.3305+112C>T | 0.34 | rs7580900 | Tagging SNP (2) | |
| Exon 4 | *g.7013C>T [p.Val128Ala] | 0.01 | rs11556887 | Non-synonymous mutation | |
| Exon 4 | g.7152C>T [p.Pro174Pro]† | 0.02‡ | – | DQ124710 | |
| Intron 4 | g.7213+322C>T† | 0.35‡ | – | DQ124711 | |
| Exon 5 | *g.7577C>T [p.Ala206Val]† | 0.20 | This report (table 2) | Non-synonymous mutation | DQ124711 |
| *g.7579A>G [p.Lys207Glu] | 0.06 | rs11556888 | Non-synonymous mutation | ||
| Intron 5 | *g.8400-21G>T | 0.42 | rs3820974 | Tagging SNP (3) | |
| Intron 5 | g.7627+726T>C† | 0.04‡ | – | DQ124712 | |
| Exon 8 | *g.11980G>A [p.Gly299Arg] | 0.98 | rs1365776 | Non-synonymous mutation | |
| Intron 8 | *g.12828+845T>C | 0.10 | rs10167116 | Tagging SNP (4) | |
| Exon 9 | *g.17384G>C [p.Ser346Ser] | 0.30 | rs7606916 | Tagging SNP (5) | |
| Intron 9 | g.17394+1573T>A† | 0.21‡ | – | DQ124713 | |
| Exon 10 | *g.19059C>T [p.Thr367Met]† | 0.09 | This report (table 2) | Non-synonymous mutation | DQ124713 |
| Intron 10 | *g.20220+1132C>T | 0.24 | rs1124534 | Tagging SNP (6) | |
| Exon 11 | *g.33974C>T [p.Ser425Leu] | 0.14 | rs3948464 | Tagging SNP (7); non-synonymous mutation | |
| Intron 11 | *g.34120+141C>T | 0.46 | rs2114591 | Tagging SNP (8) | |
| Intron 13 | *g.41816+71G>A | 0.15 | rs2241525 | More frequent among controls | |
| Exon 14 | *g.42413T>C [p.Thr523Met] | 0.19 | rs1804027 | Tagging SNP (9); non-synonymous mutation | |
| Exon 15a | g.47070C>T [p.Cys549Cys]† | 0.04‡ | – | DQ124714 | |
| Intron 15 | g.47129+77G>A† | 0.04‡ | – | DQ124714 | |
| g.47129+115C>T† | 0.02‡ | – | DQ124714 | ||
| Exon 16 | *g.47823C>T [p.Cys577Cys] | 0.06 | rs13018234 | More frequent among patients | |
| Intron 16 | g.47906+28C>T† | 0.15‡ | – | DQ124715 | |
| Intron 17 | *g.50165+813G>T | 0.28 | rs6436915 | Tagging SNP (10) | |