Although most of these alleles are common, we also identified two rare alleles (MAF < 0.05) that belong to two different genes, Gigyf2 and Hectd4. Both genes are high confidence autism associated genes and both have an extension of one amino acid (Q and A, respectively) in five difference strains (129S1, BTBR, FVB, RHJ and WSB). Here, HECTD4 is linked to autism.