Table III.
PLCE1 non-synonymous SNPs in the South African Black population
| SNP identifier | Chr location (build 37), | Amino acid | MAFa | Amino acid conservationb | Polyphen 2 (score) | SIFT (score) |
|---|---|---|---|---|---|---|
| major > minor allele | change | |||||
| rs115135156 | 10:95848924, T>C | Phe25Leu | 0.043 | Rhc, Moc, Doc, Elc, Opc | Benign (0.013) | Damaging (0)d |
| rs17417407 | 10:95931087, G>T | Arg548Leu | 0.178 | Rh, Mo, Do, El, Op, Ch, X_t, Ze | Probably damaging (0.981) | Tolerated (0.12) |
| Novel | 10:96014026, G>A | Gly1120Asp | 0.011 | Rh, Mo, Do, El, Op, Ch, X_t | Probably damaging (0.968) | Damaging (0.04) |
| Novel | 10:96018597, G>A | Gly1199Ser | 0.058 | Rh, Mo, Do, El, Op, Ch, X_t | Probably damaging (0.984) | Tolerated (0.12) |
| rs2274224 | 10:96039597, C>G | Pro1575Arg | 0.318 | Not conserved | Benign (0) | Tolerated (0.53) |
| rs61732525 | 10:96039606, A>G | Asn1578Ser | 0.045 | Rh, Do, El, X_t, Ze | Benign (0.002) | Tolerated (0.42) |
| rs3765524 | 10:96058298, T>C | Ile1777Thr | 0.386 | Not conserved | Benign (0.002) | Tolerated (0.85) |
| rs58539480 | 10:96066230, C>T | Pro1890Leu | 0.087 | Rh, Mo, Do, El, Op, X_t, Ze | Probably damaging (0.999) | Tolerated (0.33) |
| rs2274223 | 10:96066341, A>G | His1927Arg | 0.489 | Ze | Benign (0) | Tolerated (0.83) |
| rs3203713 | 10:96087728, A>G | Lys2304Glu | 0.141 | Rhc, Doc, Elc | Unknown | Damaging (0.01) d |
aMAF calculated from the number of individuals genotyped successfully (n = 43–46).
bAmino acid conservation is shown for Rhesus Macaque (Rh), Mouse (Mo), Dog (Do), Elephant (El), Opossum (Op), Chicken (Ch), Xenopus Tropicalis (X_t) and Zebrafish (Ze).
cConservation only available for nucleotide sequence.
dLow confidence SIFT score indicating that the protein alignment does not have enough sequence diversity and an amino acid may incorrectly be predicted to be damaging.