In the actual 12 sons of Jacob and the 12 Tribes, Levi is removed as a tribe, Joseph is given a double portion with Ephraim and Manasseh. In Revelation 7, however, Dan is not mentioned, and Manasseh but not Ephraim is mentioned. Why?
It’s probably a symbolic choice. In the OT the tribes of Dan and Ephraim became infamous because of their association with idolatry (for example, the story of Micah’s silver idol in Judges 17-18). This reputation is partly why some of the early Fathers thought that the Antichrist would come from the tribe of Dan.
There was a man
of the hill country of Ephraim, whose name was Micah. And he said to his mother, “The 1,100 pieces of silver that were taken from you, about which you uttered a curse, and also spoke it in my ears, behold, the silver is with me; I took it.” And his mother said, “Blessed be my son by the Lord.” And he restored the 1,100 pieces of silver to his mother. And his mother said, “I dedicate the silver to the Lord from my hand for my son, to make a carved image and a metal image. Now therefore I will restore it to you.” So when he restored the money to his mother, his mother took 200 pieces of silver and gave it to the silversmith, who made it into a carved image and a metal image. And it was in the house of Micah. And the man Micah had a shrine, and he made an ephod and household gods, and ordained one of his sons, who became his priest. In those days there was no king in Israel. Everyone did what was right in his own eyes. …]
But the people of Dan took what Micah had made, and the priest who belonged to him, and they came to Laish, to a people quiet and unsuspecting, and struck them with the edge of the sword and burned the city with fire. And there was no deliverer because it was far from Sidon, and they had no dealings with anyone. It was in the valley that belongs to Beth-rehob. Then they rebuilt the city and lived in it. And they named the city Dan, after the name of Dan their ancestor, who was born to Israel; but the name of the city was Laish at the first.
This is a rather compelling idea, but on the other hand we have no direct evidence that this was the case - Dan could have simply been arbitrarily omitted to make the list twelve. (For the record, Ezekiel 48 names Dan among the tribes who will receive a portion of the land in the eschatological future - that list follows the standard practice of omitting Levi and including Ephraim and Manasseh.)
There’s a possibility that John’s list was inspired by the census in Numbers 1:20-43. In that list Ephraim is named in association with Joseph (v. 32 “Of the children of Joseph, namely, of the children of Ephraim…”) in departure from the usual formula (the other eleven tribes read “Of the children of…”), just prior to 1:34, which reads “Of the children of Manasseh.” If this was the case, John probably simply chose ‘Joseph’ over ‘Ephraim’.