You can’t combine three Thul runes in the cube.
Clicking Transmute does nothing.
It’s three thul runes and a chipped topaz to upgrade to amn.
Oh, thank you! Weird that it’d just change like that, guess I’ll look at the documentation for what’s up.
I’d suggest you look up Arreat Summit’s Horadric Cube recipes. I’d link you, but apparently you’re not allowed to link to anything, not even Blizzard’s own websites. 
Thul used to be the highest you could upgrade runes to. They added more recipes that required gems to upgrade that were previously ladder only.
Be glad that got changed 
You can still post a link as long as it’s not clickable. Highlight the url then press the “preformatted text” button. It will turn the url into a grey text box:
http://classic.battle.net/diablo2exp/items/cube.shtml
You can post some links but it requires a higher forum “trust” level.
You have to have been posting in and reading a certain number of threads.
Even then you can only post links to a few sites they determined to be fine, mostly blizzard owned stuff and youtube.