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One of the main characters in my story has an intersex mother (dead by the time of the plot). She was assigned male at birth due to her prominent penis that led a physician to conclude that she may have a male reproductive capacity. However, she developed a female gender identity in addition to going through basically a female puberty. Although she had unfeminine facial features and a deep voice and could get an erection, she naturally grew breasts and menstruated and, obviously, could get pregnant at some point. She was also exclusively attracted to men if that matters.

Is there any particular natal condition in the real world that could cause something like this, you know, a syndrome or something like that? What would be her chromosomes?

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Yes - Ovotesticular disorder

Including a single documented case of someone with xy chromosomes getting pregnant, and cases of people being able to produce either ova in Male appearing bodies or sperm in Female appearing bodies. Theoretically both are possible simultaneously, giving self fertilisation potential, but hasnt been observed.

External genatalia appearance for this is subject to testosterone levels during gestation. Its typically ambiguous, however heavy testosterone levels while in the womb (perhaps mother was on hormone patches?) and genatalia will be very Male at first glance, with erections, but smaller testes. And if shes one of the 50% of those with this condition, she'll start ovulating during puberty.

Theres also a 12% chance she could be able to "father" a child. Attracted to Male bodies will mean this is unlikely to come up, but she could find an equivalent person with the same condition who identifies as male and she could theoretically impregnate him.

From the wikipedia link:

There are extremely rare cases of fertility in "truly hermaphroditic" humans. These individuals typically have functional ovarian tissue, but underdeveloped testes that are unable to engage in spermatogenesis. As a result, these individuals are fertile, but not auto-fertile.

There is evidence that 50% of individuals with ovotestes can go through ovulation but spermatogenesis is rare.

Spermatogenesis has been documented in 12% of cases.

...

As of 2010, there have been at least 11 reported cases of fertility in true hermaphrodite humans in the scientific literature, with one case of a person with XY-predominant (96%) mosaic giving birth.

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    $\begingroup$ There was a case found with a bird recently who was half/half split left/right. Source $\endgroup$
    – IT Alex
    Oct 21 '20 at 15:27
  • $\begingroup$ Thank you, this has been very helpful :-) $\endgroup$
    – 1995inHUN
    Oct 21 '20 at 16:15
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    $\begingroup$ These cases (both the answer and the comment) seem to be chimera. This results when two ova are fertilized and then stick together to produce one individual with two sets of genetics, each distributed in a patchwork around their body. It is fairly rare, and mixed sex cases even more rare. But, as the answer indicates, it has been observed. It won't "breed true" in any sense, since it results from processes at and just after conception rather than genetics. $\endgroup$
    – puppetsock
    Oct 22 '20 at 1:00
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You describe congenital adrenal hyperplasia

In extreme virilization a elongated clitoris with a phallic like structure.[8][9][10] Ambiguous genitalia, in some infants, such that it can be initially difficult to identify external genitalia as "male" or "female" Early pubic hair and rapid growth in childhood Precocious puberty or failure of puberty to occur (sexual infantilism: absent or delayed puberty) Excessive facial hair, virilization, and/or menstrual irregularity in adolescence Infertility due to anovulation Clitoromegaly, enlarged clitoris and shallow vagina[11]

This metabolic mutation leads to excess male hormone. That causes genital ambiguity at birth and bigger muscles / more body hair etc later in life. These are masculine looking females but they are female and can conceive and give birth. Persons with this condition are not vanishingly rare and have been recognized since antiquity.

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  • $\begingroup$ This is interesting but I intended this person to have an actual penis and testicles that produce even potentially fertile sperm. She's more like what used to be called a "true hermaphrodite". Yes, she was female because she could give birth and identified as such but she had actual male genitalia $\endgroup$
    – 1995inHUN
    Oct 21 '20 at 16:20
  • $\begingroup$ That is much trickier than the virilized female described in your question! $\endgroup$
    – Willk
    Oct 21 '20 at 18:51
  • $\begingroup$ "She was assigned male at birth due to her prominent penis" I don't think there's ambiguity here. A penis is not a clitoris. I also said that she had erections. Yes, I heard that a clitoris could visibly inflate like in the case of hyenas or trans men on hormone therapy but that's not what we usually mean by that word. So I don't think I described a virilized female, I described a sexually ambiguous person. $\endgroup$
    – 1995inHUN
    Oct 22 '20 at 16:41
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    $\begingroup$ The penis and the clitoris are the same exact organ. The development of that organ is a continuum influenced by hormone levels. Males with androgen insensitivity syndrome have normal external female genitalia. Females with an extreme excess of androgens (as in the syndrome that is my answer) have penises and no vaginal opening whichmakes trouble when they menstruate because they have uteri.. What is not dependent on hormones are the gonads: males have testes and females have ovaries (and uteri). $\endgroup$
    – Willk
    Oct 24 '20 at 1:35
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    $\begingroup$ Sorry for the late reply. I actually didn't know this, although it makes a lot of sense in retrospect. I knew that the penis wasn't a gonad but I still didn't realize that structurally it was the same thing as a clitoris. Thank you for the answer. $\endgroup$
    – 1995inHUN
    Dec 11 '20 at 15:52

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