Dwarf rats do exist, and it is a simple recessive so yes, they can be born to normal parents. However, as far as I am aware, the population of dwarf rats is still very small, found only among a handful of breeders, and not in pet stores. That said, it is less likely, though not impossible, that your boy is indeed a true genetic dwarf.
That said, there are many other factors that can affect size. Normal "standard" rats, just like people, may be big or small, fat or skinny, and so on. The genes controlling these traits are very complex, not simple and straight forward. It is very possibly to have a smaller-than-average rat born to two "regular" parents. Also, if he recently died from pneumonia, it's possible there was an underlying health problem that could affect his over all size. In other words, although he was genetically predisposed to grow to the size of your average rat, he environmentally was not able to do so due to an unknown health condition (the resources he consumed went to his defenses instead of to growth). This is especially likely if he came from "feeder stock", which are not bred for any trait except productivity (and size can definitely suffer when productivity is the selected trait).
That said, there are many other factors that can affect size. Normal "standard" rats, just like people, may be big or small, fat or skinny, and so on. The genes controlling these traits are very complex, not simple and straight forward. It is very possibly to have a smaller-than-average rat born to two "regular" parents. Also, if he recently died from pneumonia, it's possible there was an underlying health problem that could affect his over all size. In other words, although he was genetically predisposed to grow to the size of your average rat, he environmentally was not able to do so due to an unknown health condition (the resources he consumed went to his defenses instead of to growth). This is especially likely if he came from "feeder stock", which are not bred for any trait except productivity (and size can definitely suffer when productivity is the selected trait).