The server certificate is sent by the server, to be validated by the client. The client certificate is sent by the client, to be validated by the server. They live in different worlds and have no need whatsoever to relate to the same certificate authority.
For client certificate validation with Apache, see this documentation. The server will need to validate the client certificate with regards to some trusted CA; you use
SSLCACertificatePath to configure these CA. It is possible to put a specific client certificate there directly, too (that's called "direct trust"). You will probably want to add a
SSLRequire clause: validating a certificate is well and jolly, but often you want to grant access to a specific client, as in "human user", not just to anybody who could obtain a certificate from a given CA. The certificate, once validated, gives you some strong guarantee that the client's identity is really the one specified in the certificate, but it is still up to you to device whether a specific identity is to be accepted or not; and
SSLRequire is the main tool for configure that.