How do all I'm about to start a new game, one of the first time DH players want's to run a Mutie Assassin the proposal is as follows

It has no sex organs at all. Indeed it has no identifiable gender,
though it is human (base-line genetics). It excretes all its waste
through a cloaca where normally human anus is found. It is in its early
twenties now but the total lack of sexual characteristics, neither male
body hair and musculature or female breasts and hips it looks like a
pre-pubescent child, albeit a tall one. It does have rather startling
yellow eyes and white hair.

Because it is a filthy mutie it was "recruited" by the inquisition at a
very early age.It has known a life of servitude and self-hate. It has
been trained as an assassin. Who would suspect an innocent early teen as
a highly trained assassin? It is disturbingly good at disguise and
makeup. It only seems to have a personality when it is pretending to be
someone else. It has been known to masquerade as a xeno when required.

It is treated as a tool and it knows its place. It kills when commanded
too and never at any other time. It is a follower, as it has had all
ideas of rebellion beaten out of it over nearly 20 years. It doesn't
truly believe in the God-Emperor but it knows to keep its big trap shut.

Radicals Handbook isn't out in my part of the world yet, how would I doi it with every book (in print) but the Radicals Handbook?

Um, I'd make a background package as per the IH which reflect the mechanics of the character and then charge xp for it as a background package, based on the balance of benefits and penalties imposed by the modifications (keeping in mind that being a mutant in the first place is a penalty). You can also add insanity, talents, skills, and modify attributes as needed to bring the xp cost in line with a background package or reflect the character at hand.

For example, I'd say you're looking at:

XP Cost: 400.

Stats: Strength -5, Toughness +5. Fellowship is set at 10 and cannot be increased.

Talents: Chem Geld, Dark Soul, Peer (Mutants), Talented (Disguise, Decieve, Charm).

Skills: Charm, Decieve, Disguise.

Mutation: The mutant is almost supernaturally able to mimic emotions, mannerisms, and other elements of disguise. When making Interaction tests involving deception, or when disguised as a child, the mutant gains a +30 bonus and counts as having Unnatural Fellowship (x2) for the purpose of making opposed tests to maintain the deception. While the mutant may pass for a human child, or on closer inspection, a eunuch, purity tests or skilled examination will reveal its true nature.

Reminds me kinda of androgynus warrior gang in Lord of Night

Just out of curiosity, Hodgepodge, why those stat changes?

I understand the -5 strength, t=but the +5 toughness seems out of place.

For some reason, the term "cloaca" really grosses me out.

Be careful your first time player doesn't get too bored playing a minimal personality character. I can imagine it'd get a little dull after a while when not disguised.

The toughness was to represent years of being beaten. Perception or Willpower might also work.

Also yes to the above. It might be simpler to give him the Chem Geld trait and the Wyrd package with the Shape Flesh (with a potential +20 Disguise) power and just have him be an escapee from some Magos Biologis' experiments with creating genetically engineered psykers. That gives a somewhat wider range of powers to keep things interesting. Also, the complete lack of personality might be better off as simply dampened and traumatized emotions, represented (along with his background as an experiment) by the Mind Cleansed origin.

If someone presented that character consept to me I would be tempted to say no for the following reasons:

1) It looks like player is trying to set himself up to become a Callidus assassin or similar, mutant version of it...

2) Does the player know how huge disadvantages he is taking here? We are talking about obvious mutant with no personality to speak of... Thats both hard to play and even harder for GM to run comfortably.

However, if you confident in your players abilities and (more importantly) you are, as a GM, comfortable with the idea in your campaign then the background package Hodgepodge built up is pretty good to go with. I'd personally modify the build as:

XP Cost: 400.

Stats: Strength -5, Willpower +5, Fellowship +5

Talents: Chem Geld, Dark Soul, Talented (Disguise, Deceive, Charm).

Skills: Charm, Deceive, Disguise.

Mutation: The mutant is almost supernaturally able to mimic emotions, mannerisms, and other elements of disguise, but when not disguised it has very withdrawn, almost lacking of any personality. All Fellowship tests made when not disguised use a basic Fellowship score of 10. While the mutant may pass for a human child, or on closer inspection, a eunuch, purity tests or skilled examination will reveal its true nature.

The change I've made make the Fellowship mechanics a bit easier to handle and also leave the character with room for improvement in its disguise, charm and deceive skills by raising Fellowship with XP. I removed the Peer (Mutant) because in my opinion the characters history and lack of personality prevent it from having such a bond.