Table 2.
Pathogenic Variants in PTEN Exon 5 Identified in the Study Population
| Patients | Nucleotide change | Amino acid change | Variation type | ID rs | Genotype | REVEL score | Clinvar prediction | Reported in | Frequency in breast cancer in other studies |
|---|---|---|---|---|---|---|---|---|---|
| 25 | c.271G>C | E91Q | Missense | - | Heterozygous | 0.733 | - | dbSNP | |
| 24 | c.274G>A | D92N | Missense | - | Heterozygous | 0.924 | - | dbSNP | 20/350 patients, Pakistan (Baig et al., 2011) |
| 8, 10 | c.277C>A | H93N | Missense | rs786204927 | Heterozygous | 0.891 | Likely pathogenic | dbSNP, Clinvar | |
| 21 | c.279T>G | H93Q | Missense | - | Heterozygous | 0.895 | - | RefSeq | |
| 69 | c.298C>T | L100F | Missense | - | Heterozygous | 0.682 | Likely pathogenic | Clinvar | |
| 21 | c.314G>C | C105S | Missense | - | Heterozygous | 0.939 | - | dbSNP | |
| 60 | c.408T>G | C136W | Missense | rs869312776 | Heterozygous | 0.954 | Likely pathogenic | dbSNP, Clinvar | |
| 19 | c.417A>T | L139F | Missense | - | Heterozygous | 0.847 | Uncertain significance | Clinvar | |
| 10.21 | c.423T>G | H141Q | Missense | - | Heterozygous | 0.678 | - | - | |
| 19 | c.424C>G | R142G | Missense | rs746152219 | Heterozygous | 0.731 | Uncertain significance | dbSNP, Clinvar | |
| 44 | c.432del A | Lys144fs | Frameshift | rs1114167657 | Heterozygous | - | Pathogenic | dbSNP, Clinvar | |
| 69 | c.448G>A | E150K | Missense | - | Heterozygous | 0.734 | - | dbSNP | |
| 19 | c.454C>G | L152V | Missense | - | Heterozygous | 0.799 | - | dbSNP | 1/43 patients, Greece (Kechagioglou et al., 2014) |
| 10.21 | c.457G>C | D153H | Missense | rs9651492 | Heterozygous | 0.640 | Uncertain significance | dbSNP, Clinvar | |
| 60 | c.457G>T | p.D153Y | Missense | - | Heterozygous | 0.873 | Uncertain significance | Clinvar | |
| 14, 45 | c.460T>A | F154I | Missense | - | Heterozygous | 0.792 | - | - | |
| 36 | c.463T>A | Y155N | Missense | rs398123325 | Homozygous | 0.911 | Likely pathogenic | dbSNP, Clinvar | |
| 14.45.60 | c.463T>G | Y155D | Missense | - | Heterozygous | 0.960 | - | - | |
| 15 | c.464A>G | Y155C | Missense | rs1060500126 | Heterozygous | 0.968 | Pathogenic | dbSNP, Clinvar | |
| 55 | c.463_464insG | Y155X | Frameshift | - | Homozygous | - | Novel | ||
| 10.25.28.36 | c.465T>G | Y155X | Nonsense | rs1554898206 | Homozygous/ heterozygous | - | Pathogenic | dbSNP, Clinvar | |
| 36 | c.465T>A | Y155X | Nonsense | rs1554898206 | Heterozygous | - | Pathogenic | dbSNP, Clinvar | 1/43 patients, Greece (Kechagioglou et al., 2014) |
| 41 | c.479C>A | T160N | Missense | - | Heterozygous | 0.861 | - | dbSNP | |
| 43 | c.491_492insT | K164 X | Frameshift | - | Homozygous | - | - | Novel |