Table 2. Observed genetic variants in the PSIP1 coding region.
dbSNP rs number | HGVS name | SNP location | African | Caucasian | Amino acid change | SIFT score | POLYPHEN score | ||
NM_033222.3 | MAF exp | MAF obs | MAF exp | MAF obs | |||||
rs2821529 | c.348T>C | Exon2 | 0,169 | 0,107 | 0,042 | 0,039 | S116S | - | - |
rs139433616 | c.402T>C | Exon5 | NA | 0,000 | NA | 0,002 | T134T | - | - |
rs188943134 | c.743C>T | Exon8 | NA | 0,000 | NA | 0,002 | P248L | 0,18 | 0,045 |
rs61744944 | c.1415A>T | Exon13 | 0,034 | 0,059 | NA | 0,002 | Q472L | 0,01 | 0,007 |
rs35678110 | c.1432C>G | Exon14 | 0,025 | 0,000 | NA | 0,004† | L478V | 0,21 | 0,049 |
signifies variants not in accordance with Hardy Weinberg law.
Overview of the observed SNPs in the PSIP1 coding region for LEDGF/p75. Both expected and observed minor allele frequencies (MAF) are shown per ethnicity. The SIFT score ranges from 0 to 1. The amino acid substitution is predicted as damaging if the score is < = 0.05, and tolerated if the score is >0.05. The POLYPHEN score ranges from 0.00 to ≥2.00. The amino acid substitution is predicted possibly damaging if the score is ≥1.50 and probably damaging if the score is ≥2.00.
HGVS = Human Genomic Variation Society; SNP = single nucleotide polymorphism; MAF = minor allele frequency; NA = not assessed; rs = referenced SNP id number; – means no impact due to silent mutation.