While a new genetic anomaly is fairly convenient, it does work. Perhaps it is a passive gene, which allows her to still be "normal," but there will be the issue of how it was discovered.
Out of curiosity, are Gambit/Beast/Colossus/Xavier required for any reason? I know they are popular characters, but is there something about their specific abilities/skills/backstories you need, or just iconic spots you think will add to the setting? I ask because I play a pretty mean Banshee, and he is the type that would make a pretty good leader (he's effectively had his own school of mutants twice, after all). Also, he spent quite a bit of time working with Moira on genetics, so might be able to help with that angle.
As far as points go, I am thinking of a simple point assignment moderated by all the players with GMs having final say. While some mutants are just more powerful than others, usually weaker characters have something else to make up for it (usually scientific expertise). My go-to for a custom system is usually Song of Ice and Fire, as it is very easy to customize. Here's a rough draft of what it would look like.
*Agility - Measures dexterity, nimbleness, reflexes, and flexibility
*Athletics - Physical fitness, coordination, training, raw muscle
*Awareness - A measure of how accurate your senses and perception are and how quickly you respond to changes in your environment
*Cunning - Encapsulates intelligence, intellect, and the application of collected knowledge
*Deception - The ability to lie or deceive
*Endurance - a measure of your physical well being, health and hardiness
*Fighting - Ability fight unarmed or with hand held weapons
*Knowledge - general understanding and the world about you
*Marksmanship - Skill with ranged weapons and to use them accurately in combat
*Mechanics - Your ability to understand and interact with technology, to repair or improve upon it
*Medical - Your understanding of accumulated medical knowledge, from applying a band-aid to open heart surgery
*Persuasion - Ability to manipulate emotions and beliefs in others
*Projection - Raw power of projection
*Stealth - The ability to move about unseen or unheard
*Survival - The ability to get by in hostile or unforgiving environments
*Thievery - Pick pocketing, casing a place, picking a lick, escaping from the brig
*Warfare - The ability to manage a battlefield, from tactical commands, to long term strategy, and the ability to issue commands for subordinate units to follow
*Will - Your mental fortitude
*Other - Could be luck, wealth, status in the homo sapien and/or homo superior community
These numbers would mainly be used for character creation, as well as a quick "who is better at what" if it comes up. Let me know what you think.