tldr biology is dice rolls and humans are intersex for no reason sometimes
on a side note one of my friends had this and she only found out when she started transitioning. she is now a trans woman with XX chromosomes. i can only imagine how fucking vindicating it must have felt
De La Chappell syndrome, congenital adrenal hyperplasia, androgen exposure in utero, ovotesticular disorder of of sex development all result in a person with cis male characteristics and in some cases cis male typical genitalia despite having xx chromosomes
This is the best resource I've seen to show things relatively simply.
The TL;DR is that a whole "Y" chromosome isn't exactly responsible for "maleness", the SRY gene is. It's normally on the Y chromosome, but mutations can occur placing that gene onto the X chromosome. Inversely, someone could inherit a Y chromosome without that gene, in which case they would develop with female traits.
It's not considered trans because someone with 46XX plus the SRY gene would develop male genitalia, be identified as male at birth, and likely identify themselves as male. For some types of these conditions, there are plenty of people walking around with no clue that their chromosomes don't match their gender.
Disclaimer: I'm not a geneticist, so i could have explained something a little off.
I'm also not a geneticist but I did study genetics for a while and that's pretty much what I remember learning, so you're good.
The books Mutants: On Genetic Variety and the Human Body by Armand Marie Leroi explains it all very well and touches on many other related genetic conditions like the Klinefelter syndrome (XXY). It's an incredible read all around that really opened my eyes to how malleable biology is.
Exceptions: While XX and XY are the most common sex chromosome combinations, there are exceptions, such as individuals with variations in their sex chromosomes, such as XXY (Klinefelter syndrome) or XYY.
cis just means your current gender identity is the same that was assigned to you at birth. there are cases where someone has XX chromosomes, but the body develops as male.
I can try. The cis part means the person's naughty bits are aligned with their gender identity. The male is their gender identity. So post-bottom surgery it's perfectly possible. If you use different definitions for concepts though you will have difficulty making it work.
None of this has anything to do with the claimed PhD in genomics though. These are socio-cultural concepts. So they should stick their PhD where it belongs and address the arguments head on instead of trying to argue from authority.
I don't have a PhD, but my understanding of the basics is this:
All people start out developing as female in the womb before a certain point where a large dose of testosterone caused (usually) by the Y chromosome activating (basically the only time in life that it does apart from starting puberty AFAIK) causes the proto-labia and vagina to push outwards and form the ball sack and enlarging the clitoris and urethra into what we know of as the penis. This is why you can see that line down the middle of your ball sack; that's where your labia fused together. It's also why the tissue that makes up your ball sack is biologically identical to the tissue that makes up the inside of the vagina. It's an outie vs. an innie.
There are many reasons why this wouldn't happen "correctly" since biology is more a wonder of things somehow working at all after evolution is done with them rather than a perfectly designed, well-oiled machine. Sometimes the Y chromosome simply doesn't activate, or it does, but the person has androgen insensitivity and so the testosterone doesn't do anything, or they develop as female but have testicles where their ovaries should be, rendering them infertile but otherwise a perfectly normal woman. Sometimes a person is XX, but they experienced a higher than normal amount of testosterone during development and developed male instead of female.
And that's before you get into the issue of intersex people, who are often surgically altered as babies when they're born by the doctor to match with the genitalia that the doctor thinks should be the "correct" one. In a number of places, the doctors don't have to ask permission or even tell the parents after.
Also, your definition of cis male is slightly off. "Cis" is the opposite Latin prefix of "trans," meaning a non-changing/stable state of being, and in this case it's used to mean that one's gender identity matches up with the one that you were given at birth. It ultimately has nothing to do with what genitalia you have, and it's simply an identification saying that your sense of gender matches up with the sex that the doctor declared and that you therefore aren't trans. It's an after the fact solution to the question of what to call people who aren't trans and comes from the use of trans to identify somebody who transitions from one gender to another.
Chemists have moved away from cis and trans partly because of all of this. We use zusammen-together or entgegen-opposite now. I can attest to how politically charged a class about organic molecules can become.
I am not deeply versed on the socio-cultural side of it all, and there is clearly space to learn. I am reluctant to let cis hinge on a doctor's proclamation but I'll let it sit there for the moment.
As somebody with a bit of learning on the matter (it's amazing the hats you have to wear to prove you deserve to live - from anthropologist to biologist to archeologist), it's interesting to see how the language of the community has evolved as our scientific understanding of sex vs gender has.
The term started as transsexual, and there are older people who refer to themselves by that term, but by the 2000s the term had shifted in favor of transgender, noting the recognition that sex doesn't equate to gender that happened around that time.
Then came the use of cis as well as AMAB and AFAB (assigned male/female at birth) in order to better describe the complexity involved around the fact that a doctor has to declare you one gender or another when you're born, and the easiest way to do that with the highest likelihood of being correct is based on sexual characteristics - namely, what genitalia you have. So cis is used to describe people who have no reason to disagree with the doctor's assessment, and there's a lot of discussion around where intersex people fall in the community (do they fit in the trans umbrella term?).
People like Dunning-Kruger up there are basically arguing that isotopes don't exist.