Are there any spells that aren't on any class's spell list?

Question

Chapter 11 of the 5e Player's Handbook has a list of spells each spellcasting class can learn, followed by a description of all the spells in the game.

I am wondering: are there any spells that are described in the second part of the chapter that aren't in any class spell list in the first part of the chapter?

I am thinking those could be spells only learned by certain class or race features, or spells added to the spell list by sub classes. They could also just be spells described but not mentioned anywhere else in the book, for whatever reason.

My questions regards the PHB primarily. But I would also by interested in knowing if this is the case for any of the supplementary books, that add new spells, like XGtE.

Answer 1

There is the Ravnica spell encode thoughts

While not the PHB, the Guildmasters' Guide to Ravnica includes character options for use in that particular setting (Ravnica). Among these the encode thoughts cantrip which is only obtainable through the Dimir Guild Background option (pages 45-50). That feature adds it to the class list for you, much in the same way the Fiend Patron adds fireball to the list of that particular Warlock, even though it is not on that class list in general.

D&D Beyond incorrectly lists it as a Wizard spell, which is probably because Wizard is the only spellcaster class suggested for a Dimir character.

Dunamancy spells from Explorer's Guide to Wildemount

The dunamancy spells don't start on any classes spell list, but become availible to one or both of the wizard subclasses also in that book or by DM opt-in to other spellcasters. (Thanks to @raithyn for pointing these out.)

Answer 2

No. There are no secret spells. But:

Trap the Soul does not exist in 5e but appears in the Wizard's spell list in the original printing of the PHB. Details here.

Destructive Wave is in the Paladin's spell list, but it's listed as Destructive Smite in the original printing of the PHB. There is no entry for Destructive Smite under the spell descriptions.

It's listed correctly in the D&D Beyond Compendium and in the official Errata. Details here.

From the PHB errata:

Paladin Spells (p. 209). Under 5th Level, “destructive smite” has been changed to “destructive wave.”

Wizard Spells (p. 211). Under 8th Level, “Trap the Soul” has been removed.

Answer 3

There used to be the spell Wall of Water that was exclusive to the Triton race from VGtM, but when XGtE came out it was added to the Druid, Sorcerer, and Wizard spell lists.