There are a lot of bases, theories and techniques in proof assistants. Let me show you how deep the rabbit hole is (in suggested order of implementation):
(Fibrational) Dependent Type Theories
- CoC (Calculus of Constructions, PTS, Coquand)
- CiC (Calculus of Inductive Constructions, Paulin-Mohring)
- MLTT (Martin-Löf)
- HoTT-I (Isaev)
- Cubical (Cubical Type System, CCHM)
- HTS (Homotopy Type System with Two Equalities, 2LTT, Voevodsky, ACKS)
- de Rham (Infinitesimal Shape Modality, Cherubini, Groupoid)
- Cartesian Cubical (ABCFHL)
- Guarded Cubical (BBCGSV)
- Rezk (Synthetic Theory of $\infty$-categories, Riehl, Shulman, Kudasov)
- Equivariant Super HoTT (Schreiber)
These are what we basically call Type Theories in Martin-Löf sense with 5 inference rules, some of them are monadic modalities. But on the market there are present proof assistants based on different theories, like custom model checkers or direct term rewriting systems. They internalize upper MLTT type systems into itself, like Dedukti. So the full answer to this question could be a good survey type PhD! Systems 1-7 are implemented as examples and included as parts of cubical.systems.
Embeddable DSL in host language
Before fibrational provers, the logic of computable functions was built upon relying on STLC flavours. In that sense you can write a needed type-checking rules in ML language as in meta theory and embed programs as strings instead of direct internalizations in the style of synthetic dependent type theories. This technique is not unique to HOL series, but is known as embeddable DSL in host-language technique. In that sense ACL2 is embeddable DSL in ANSI Common Lisp.
Ad-hoc dedicated model checkers and other LF
Everything that is big enough or impractical to run in the main Proof Assistant environment usually is being rewritten into separate ad-hoc model checker for the sake of speed, simplicity, etc. This category could include all known models checking cores: Reference SMT solver Z3 by Leonardo de Moura, TLA+ by Leslie Lamport, even Metamath-like systems or set-theoretical systems like Mizar. I think if you built the basis only for Set theory but not all mathematics it is called ad-hoc. Logical Frameworks like Twelf or system with separate language for automation of inference rules like Andromeda are also could be treated as separate ad-hoc logical systems. Modern powerful ad-hoc term rewriting systems like Dedukti could eat 2LTT with less effort than HoTT in HOL by Josh Chen.