Appaloosa is famously known by its spots and many varied expressions of those spots. Appaloosa is not the result of just one mutation, but of a group. The Leopard Complex (LP) is what creates the ability for appaloosa to exist. Pattern genes change the leopard complex into the many other versions of appaloosa. The varnish roan appaloosa pattern is the leopard complex without any other patterning mutations. Pattern 1 (PATN1) is what creates the well known leopard appaloosa patterns. A homozygous appaloosa will have more white than a heterozygous. Horses that are homozygous for LP have Congenital Stationary Night-blindness (CSNB). Understanding how the appaloosa pattern works is a complicated mix and is still being researched. The Appaloosa Project is leading the research into understanding appaloosa. There are tests available for LP and PATN1.
PATN1 has been found via testing in breeds with no appaloosa marked individuals. It can be carried unseen because without the Leopard Complex there isn't anything to create the spotting. It's possible that PATN1 may eventually be found in a Chincoteague Pony.
A photo exists of an appaloosa mare and foal at the 1981 Pony Penning. This is the only known example and they did not breed on. The foal was born the night after the auction and since she missed the auction the pair was turned back out on Assateague. They were likely part of a group of Mustangs introduced that year most of which did not survive the winter. The presence of appaloosa that year was also mentioned newspaper article.