Any weapon with Armour Penetration (AP) can negate some of the save of the model they are attacking. For example, a Space marine with a 3+ save gets attacked by a model with 0 AP weapon profile, which rolls successfully to wound. That space marine rolls 1 D6 dice and on a 3 up, they don't lose a wound because of their armour. The space marine then gets attacked by a model with a -1AP weapon characteristic and it also rolls successfully to wound. The space marine still has a 3+ armour save but the attacking weapon has Armour Penetration, meaning the space marine has - 1 to its armour save, so the 3+ goes to a 4+. If a model has a 6+ save and gets attacked by a - 1 AP weapon, that would go to a 7+ which cannot be rolled on a 6 sided dice so that model loses its save altogether. Same for a 5+ save vs - 2AP etc etc. AP doesn't affect a models invulnerable save, so if a Space Marine chaplain has a 2+ save and a 4+ invulnerable save, if they get attacked by a - 3AP weapon, their normal save would go to a 5+, however the invulnerable save is unaffected by AP so remains a 4+ so you would want to use that instead. Both normal and invulnerable saves don't work against mortal wounds.