Battleship Captain
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...Okay. There are several elements here which are getting mixed up.
The Pariah Gene (A.K.A. 'Blank' or 'Null' humans)
The potential to be a blank exists within the human genome, just like the potential to be a psyker. One need not be a descendent of a Silent Sister to be a pariah, and yes, they can be male or female (see Wystan Frauka and Culexus Assassins). Blanks are born continuously across the imperium - albeit that they are supposed to be a million times rarer than a psyker, so actually finding them - especially since (unlike psykers) there's no betraying psychic phenomena, rage-induced fires, warp activities, etc for a hunter to home in on - is nigh impossible.
How common are they? Well, Gregor Eisenhorn meets Elisabeth Bequin by chance, which prompts his interest in Pariahs, and is able to put together the Distaff out of his own resources. It's never made clear how many members the Distaff has, but it's clearly a significant enough number to require Bequin to dedicate her time to running it, and to loan out members to Gregor's allies. This is one inquisitor, operating (broadly) in a single sector.
As a counter-example, to give an upper limit to how common they are, Inqusitor Amberly Vail encounters one (Gunner Jurgen) and pointedly keeps him secret from the rest of her ordos as an 'ace in the hole' because he's such a valuable asset, considering him more important (professionally speaking, anyway) than a multiply-honoured Hero Of The Imperium.
Also note that whilst it may be (partially) forgotten, it is possible to genetically grow a Pariah to order. 'Beta Bequin' in Pariah - along with her peers - is essentially a cloned pariah. Equally, in the Horus Heresy series, in Nemesis, the Culexus Assassin forming part of the Execution Force, Iota, is a 'protiphage' - a clone, or replicae, bred for her unique genetic gift.
The Sisters Of Silence
The Silent Sisterhood was an organisation during the great crusade and the horus heresy. This organisation was large, and consisted entirely of females with the pariah gene. It is not known for definite if any or all were protiphage replicae, but given that the artwork of them (In Collected Visions) and their descriptions (in various stories) gives them a wide variety of skin tones and ethnic appearances, it seems unlikely that a significant proportion were clones.
The Silent Sisterhood were based on Luna. They weren't based on Terra itself as the presence of large numbers of pariahs would cause complications for the psyker-based arms of the Imperium, like the Astra Telepathica. It should be noted that the guards in the City of Sight, the Telepathica's academy/headquarters, the Black Sentinals, were not pariahs, despite the advantages this might have provided when confronting psychic phenomena.
Their primary functions were as witch-hunters, hunting down rogue psykers, and crewing the black ships which carried psykers to Terra across the imperium, and have been seen in both roles in Horus Heresy stories. They also acted as a military force in special circumstances where their null abilities were of significant value - such as the boarding of the Jorgall Worldship (Flight Of The Eisenstein), the assault on Prospero (various), or the War in the Webway. They were well trained and equipped but lacked legion genetic enhancements.
As noted by Laurie Goulding, they do not exist anymore in a 41st millenium setting. We've seen on board the black ships in 3rd-party narrator omniscient in RPG sourcebooks and several black library novels. The Silent Sisterhood's old role is now filled by Inquisitorial Stormtroopers and Adepta Sororitas Battle Sisters.
Were they wiped out in the Heresy? Well, we know a lot of them went to Prospero - and would have suffered heavy casualties. We know a lot more were sent into the webway to fight the daemonic incursions, and presumably suffered even heavier casualties before the gate was sealed. But the thing to bear in mind is that you can't "wipe them out". You can wipe out a space marine chapter or legion, because it's a specific genetic inheritance possessed by only a few thousand individuals. Kill them and there are no more. But there are always pariahs, just like there are always psykers or redheads or tall people. Even if the Sisterhood had been wiped out to the last woman, it could have been rebuilt if the desire was there to do so, and given their inherent suitability for their role, it's wierd that they weren't.
They do not exist in the 41st millenium. The Culexus Temple does, but then Clade Culexus existed back in the Great Crusade, too, so it's not like the one superseded the other. But they're also not unknown to informed individuals in the 41st millenium. Inquisitor Czevak in Atlas Infernal encounters a relic from the Silent Sisterhood, and is able to recognise what it is and who it was made from.
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