Table 5:
PATH/LPATH Variant Test Set and Criteria
| PTEN Variant | Round 1 review – criteria applied | Initial Classification | Round 2 review - criteria added following PM2 adjustment, additional de novo/proband phenotype specificity levels of evidence | Final EP classification |
|---|---|---|---|---|
| c.50_51delAA (p.Q17RfsX26) | PVS1, PS4_P | VUS | PM2 | PATH |
| c.511C>T (p.Q171X) | PVS1, PM2, PM6, PS4_P | PATH | PS4_P→PS4_M | PATH |
| c.892C>T (p.Q298X) | PVS1, PM2, PS4_P | PATH | PATH | |
| c.964A>T (p.K322X) | PVS1, PM2 | LPATH | LPATH | |
| c.987_990delTAAA (p.N329KfsX14) | PVS1, PM2, PS4_P | PATH | PATH | |
| c.80-1G>C (IVS1-1G>C) | PVS1, PM2 | LPATH | LPATH | |
| c.165-1G>A (IVS2-1G>A) | PVS1, PM2 | LPATH | LPATH | |
| c.493-2A>G (IVS5-2A>G) | PVS1, PM6_S, PM2 | PATH | PATH | |
| c.801+1delG (IVS7+1delG) | PVS1, PM2 | LPATH | LPATH | |
| c.802-2A>T (IVS7-2A>T) | PVS1, PM2, PS4_P | PATH | PATH | |
| c.1026+1G>A (IVS8+1G>A) | PVS1, PM2, PS4_P | PATH | PS4_P→PS4_M | PATH |
| c.103A>G (p.M35V) | PS2, PM2, PP2, PS4_P | LPATH | PS4_P→PS4_M | LPATH |
| c.389G>A (p.R130Q) | PS3, PM6_S, PM1, PM2, PP2, PS4_P | PATH | PS4_P→PS4, PM6_S→PM6_VS | PATH |
| c.407G>A (p.C136Y) | PS2, PS3, PM2, PP2, PS4_P | PATH | PATH | |
| c.517C>T (p.R173C) | PS3, PM6_S, PM2, PP1, PP2, PS4_P | PATH | PS4_P→PS4_M, PM6_S→PM6_VS | PATH |
| c.737C>T (p.P246L) | PS2, PM2, PP2, PS4_P | LPATH | PS4_P→PS4, PS2→PS2_VS | PATH |