The goal of this study was two-fold: to assess the function of genetic variations in NHE9/SLC9A9 associated with autism and to evaluate NHE9 as a candidate gene for autism spectrum disorders in a neurobiological model. To this end, we exploited studies done with cation/proton antiporter orthologs from bacteria and yeast model organisms. Phylogenetic clustering of human NHE9 with yeast Nhx1 supports a common structural fold that relates back to the more distant bacterial ortholog, NhaA. Pairwise alignment allowed some autism-associated variants found in human NHE9 to be directly modeled on the yeast protein. In support of this, we found that conserved differences between NHE9 and Nhx1 could be swapped out without loss of function. Therefore, yeast Nhx1 serves as a convenient NHE9 surrogate for analyzing a subset of variants with a conservation score of >5 (Figure 1A) that may be mapped by homology with relatively high confidence. Given the rapidly increasing availability of genomic information and the prevalence of a large number of rare variants differing between individual genotypes, it will be important to have in place facile, inexpensive and
