Query early, query often

Is there any point to asking an agent if they're open to considering a particular subject? Should you just go ahead and put in the effort to meet their submission requirements?

My novel is about a teenager who was born with a genetic condition resulting in short stature and a sexually ambiguous body. It's written from a Christian perspective and based on ten years of answering inquiries on behalf of a support group for the parents of such children.

I've written to several agents who represent Christian authors and the replies have been fairly consistent: They don't know of any Christian publishing houses that will handle the subject material. A few of the smaller Christian publishers I've contacted directly have asked to read the manuscript, but even one of them said they wouldn't ordinarily consider the subject. They were offering to give feedback on the manuscript, not consider it.

I'm assuming that, because most of the novel is written from the teen's perspective, I should be approaching agents who represent YA. Is it a waste of time to ask them if they'll consider a book that is explicitly Christian in outlook? Should I look for agents who represent Christian fiction as well as YA?

For the reader's benefit I'll state that this question came from a writer in the USA, a land of many and varied publishing houses and agents; this variation in turn facilitates the allocation of very specific genres for fiction. Also, Christian fiction is not a big genre here in the land of widespread godless-convict ancestry and declared-atheist prime minister; accordingly, I'm answering this question without knowing much about the genre at all. First things first, however ...

I can understand why it's tempting to ask a question about subject matter/genre without doing a full submission, but here's why agents don't like it: first, everyone would do it and we'd spend most of the day answering these questions; second, it's a question asked out of context, because we really need to see your writing before we can say definitively whether or not we like a subject or genre. I could, in abstract, say I don't want to see stories about this or that, but if the manuscript was amazing, I'd change my mind. So for a writer to give him- or herself the best chance of getting an agent or publisher, you need to show us your writing.

Also, going through the submission-writing process can be very useful for your writing. It forces you to think about whether or not you have a clear storyline; whether or not there's a readership for your story. If you don't ask yourself these questions before you send off a submission, you can't expect an agent/publisher to answer them for you.

When it comes to [Kevin '07 reference there for those feeling nostalgic] who you should query: query as many people as possible. If you think your book could have three different genre labels attached to it, query agents who look after books in those genres. Let them work out if it's exactly right for them or not - by reading what you've written. Yes, it's a lot of work, but you've spent all that time writing the novel - don't you want to give it the best chance of finding the right agent?