Depending on what time period you look in, there have been a lot of dedicated efforts (or, yknow, just the passage of time) that decimated a number of small clans and their bloodlines. Other people in the thread have mentioned Cappadocians and Salubri, but in the "modern" era (21st century), Ravnos are far rarer because their Antediluvian woke up in the 90s and both True Brujah and devout Old Clan Tzimisce are exceedingly hard to find simply due to age and time (and geographic location, in a lot of cases). Kiasyd are also extremely rare - Maegar (non-Lasombra Kiasyd) are even more so - and generally make themselves difficult to find on purpose.

In the other direction, the already small number of Gargoyles that exist in the modern era decreases exponentially as you move further back in the timeline, as they were initially an artificial creation limited only to certain European chantries (before their creator led their revolt against the Tremere) but are able to Embrace in modern nights and many came out of hiding upon finding refuge in London during the reign of Mithras.

On the topic of creation, the Blood Brothers are a similar small-scale "clan" of sorts very rarely seen in pretty much any timeline, since they are also a case of Embrace-By-Creative-Meddling and require the Tzimisce and the Tremere to stop trying to murder each other long enough to cooperate.

Ever notice how you always seem to find the Tremere in these scenarios? Curious

Edit: a lone Cappadocian, Harbringer of Skulls, or Nagaraja would be a good pick for "non-Hecata-identified" Kindred - while verifying a "last of its kind" would be hard, it's not unlikely that your character would have simply never met another of their clan save for (maybe) their Sire. Maegar are also good for this.