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I have just installed a new shower flange in a second story subfloor. There are a few small spaces/gaps around the flange that are open due to the hole in the subfloor being cut a little asymmetrical and a little too large in certain spots. However 90+ percent of the underside of the flange sits on solid subflooring. Should I silicon seal these gaps? A prefab shower pan will be installed over the subfloor and over the top of the flange (adhered to the subfloor with modified polymer thinset) and silicon sealed to the top of the shower flange around the bolts--so in theory moisture should never get to the subfloor and leak through the small gaps around the outside of the flange. My gut tells me to seal the gaps around the outside of the flange, but my concern is that in the event the seal between the top of the flange and the underside of the prefab shower pan ever leaks (not likely but you never know), the water would just get trapped and spread along the subfloor (if I seal those gaps) as opposed to draining through those holes, dropping down, and staining the drywall ceiling below. So should I fill in those gaps around the outside of the flange?

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It probably doesn't matter much one way or the other since it's unlikely for water to get that far. I personally would not bother. Consider this: If water were to get that far, you would want to know about this and take action. If it's sealed, water could just sit there unnoticed, rotting out anything it touches.

If it leaked down and stained the ceiling, you would notice fairly soon and take measures to stop it. Stained drywall ceiling is way more easier to repair than a rotted subfloor.

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+1, you don't need that area sealed, and the shower pan will hold it in place. Also, if you add a bunch of sealant before attaching the drain to the shower pan, you're reducing your ability to adjust it into place once attached to the shower. –  Shimon Rura Nov 19 '13 at 2:29
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You make a good case for an early warning system saving major money if it does leak. If you are truly 90% supported, silicone sealing won't add any support.

The pan-to-drain seal and your drain pipe connections are more important.

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