There are many things that can go wrong with a protein. The simplest is misregulation, like a regulatoy motif being disrupted, gene architecture (TAD) being cha

There are many things that can go wrong with a protein. The simplest is misregulation, like a regulatoy motif being disrupted, gene architecture (TAD) being changed, splicing changes (somehow linked to missequence proteins but only via changed ration of different splice isoforms) or mRNA being degraded faster or slower (UTR mutations), all leading to different protein concentrations (if its a protein being affected, might as well be some RNA molecule). There is not that much known about these diseases so its hard to give typical examples. Here is an example of a tool that tries to predict such variants via ML, they curated a few hundered variants via literature search: https://www.ncbi.nlm.nih.gov/pubmed/27569544 https://www.ncbi.nlm.nih.gov/pubmed/27569544