Table 2 LDLR gene variants with in-Silico analysis on the effect of the variants.
Variant name* | Location | In Silico analysis | Statistical analysis | Miscellaneous | Reference | |||
|---|---|---|---|---|---|---|---|---|
| Â | Â | Non-pathogenic | Pathogenic | Patient n(%)a | Control n(%)b | ** P value | Â | Â |
Nil | promoter | Â | Â | Â | Â | Â | Â | Â |
c.81C>T;p.Cys27Cys | exon 2 | √ |  | 1(0.6) |  |  | rs2228671 | NCBI; UCL*** |
c.190+56G>A | Intron 2 | √ |  | 3(1.9) |  |  | rs3745677 | NCBI; UCL*** |
c.190+58C>T | intron 2 | √ |  | 7 (4.5) | 4(5) | 0.9 | rs3745678 | NCBI |
c.300C>T;p.Asp100Asp | exon 3 | √ |  | 1(0.6) |  |  | Synonymous Unlikely to cause pathogenicity | No reference |
c.910G>A;p.Asp304Asn | exon 6 | √ |  | 7(4.5) |  |  | Changes in amino acid Benign by Poly Phen | UCL*** |
c.940+36G>A | intron 6 | √ |  | 3(1.8) |  |  | rs13306513 | NCBI |
c.1060+7T>C | intron 7 | √ |  | 18(11.7) | 8(10) | 0.7 | rs2738442 | NCBI |
c.1060+10G>C | intron 7 | √ |  | 5(3.2) | 3(3.8) | 0.9 | rs12710260 | NCBI; HGMD**** |
c.1186+41T>A | intron 8 | √ |  | 1(0.6) |  |  | Location is unlikely to cause pathogenicity | No reference |
c.1194C>T;p.Ile398Ile | exon 9 | √ |  | 5(3.2) |  |  | rs13306498 | NCBI |
c.1359-30C>T | intron 9 | √ |  | 2(1.3) |  |  | rs1003723 | NCBI |
c.1411A>G;p.Arg471Gly | exon 10 | √ |  | 17(11.0) |  |  | Changes in amino acid Benign by Poly Phen | No reference |
c.1617C>T;p.Pro539Pro | exon 11 | √ |  | 6 (3.9) | 4(5) | 0.7 | rs5929 | NCBI |
c.1705+56C>T | intron 11 | √ |  | 12 (7.8) | 2 (2.5) | 0.08 | rs4508523 | NCBI |
c.1705+112C>G | intron 11 | √ |  | 1(0.6) |  |  | Location is unlikely to cause pathogenicity | No reference |
c.1706-55A>C | intron 11 | √ |  | 6 (3.9) |  |  | rs2738447 | NCBI |
c.1706-69G>T | intron 11 | √ |  | 1(0.6) |  |  | rs7259278 | NCBI |
c.1705+117T>G | intron 11 | √ |  | 2(1.3) |  |  | Location is unlikely to cause pathogenicity | No reference |
c.1773C>T;p.Asn591Asn | exon 12 | √ |  | 7(4.5) |  |  | rs688 | NCBI |
c.1959T>C;p.Val653Val | exon 13 | √ |  | 1(0.6) |  |  | rs5925 | NCBI |
c.2232A>G;p.Arg744Arg | exon 15 | √ |  | 5 (3.2) | 3(3.8) | 0.8 | rs5927 | NCBI |
c.190+4A>T | intron 2 |  | √ | 1(0.6) |  |  | Possibly pathogenic | UCL** |
c.301G>A;p.Glu101Lys | exon 3 |  | √ | 11(7.1) |  |  | Possibly pathogenic | UniProt; UCL*** |
c.415G>C;p.Asp139His | exon 4 |  | √ | 1(0.6) |  |  | Probably pathogenic | No reference |
c.601G>A;p.Glu201Lys | exon 4 |  | √ | 9(5.8) |  |  | Probably pathogenic | UCL** |
c.763T>A;p.Cys255Ser | exon 5 |  | √ | 10(6.5) |  |  | Probably pathogenic | UCL*** |
c.1706_1845dup;p.Asp616IlefsX96 | exon 12 |  | √ | 2(1.3) |  |  | Pathogenic | No reference |
c.2100C>G;p.Asp700Glu | exon 14 |  | √ | 5(3.2) |  |  | Possibly pathogenic | UniProt; UCL*** |
c.1996_2012del17;p.Trp666ProfsX45 | exon 14 |  | √ | 4(2.6) |  |  | Pathogenic | No reference |