The GWAS studies found that a mutation near the CA10 gene is associated with risk of these conditions, but that doesn't itself provide much detail on what the mutation does, such as whether it upregulates or downregulates CA10 in the brain.
The mutation that increases risk of ME/CFS seems to be associated with increased CA10 in the prostate, based on a different dataset (GTEx), but I would guess the prostate itself is not relevant in these conditions.
We'll need further study to see if we can find out what is actually different about CA10 in ME/CFS (assuming CA10 is even the relevant protein associated with the mutation, which isn't a guarantee).