In point comes from French. World Wide Words explains it as follows:
[I]t was once possible to say in point by itself, meaning something appropriate, relevant or pertinent, but it survives only in phrases like this one.
It derives from the French à point, meaning the same as à propos, something relevant or to the point. The first example of the English form seems to be this from 1658: “Some play or other is in point”. It was beginning to look old fashioned by the time this next was published in 1888: “I recall another humble incident somewhat in point”. [...]
Here’s an example cited in the Oxford English Dictionary from 1769 that shows how the modern set phrase case in point may have come about: “Some case or cases, strictly in point, must be produced”.