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What happens when you have a homozygous mutation on a gene (eg. a swapped base), that is considered pathogenic, but without developing the disease?

It it were a heterozygous mutation I would get it, because we still have at least one healthy/wild-type copy of the gene, so at most the disease will just manifest in a more mild form, but with a homozygous I have no idea how is it possible to NOT develop the disease.

Also, what happens when heterozygous mutations develop the disease? In these cases why does the healthy version of the gene goes "quiet"?

One example is HH caused by HFE gene mutation (mostly C282Y and H63D), and not everyone develops the disease, doesn't matter if they are heterozygous or homozygous.

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What happens when you have a homozygous mutation on a gene (eg. a swapped base), that is considered pathogenic, but without developing the disease?

It may be an example of incomplete penetrance of variable expressivity. Simply, you are probably dealing with a complex trait in which either more than one gene is involved, or there is interaction between genetics and envronmental factors.

Also, what happens when heterozygous mutations develop the disease? In these cases why does the healthy version of the gene goes "quiet"?

I assume you are still talking about a putatively recessive disease. One possible explanation is haploinsufficiency, i.e. the WT allele alone doesn't produce enough transcript and the heterozygous individuals has "problems"

One example is HH caused by HFE gene mutation (mostly C282Y and H63D), and not everyone develops the disease, doesn't matter if they are heterozygous or homozygous.

And indeed HH is an excellent example of complex disease, in which genetics is involved, but the inheritance is not purely Mendelian.

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