Functionally important genes underlying microcephaly, neuron dendrite and axon growth, synapse formation, and ion channels are found to contain intronic SVAs (Supplementary Figs. 4–7), with the SVA sequences frequently being human-specific, and sometimes displaying species-specific expansions (e.g., ATRX, KDM6A), tandem insertions (CDK5RAP2, KDM6A, RAB2A, IL1RAPL1, KCNH1) or even repeated integrations at multiple sites in the same gene (KDM6A, ATP8A2, GRID1, NRXN1). Here, ATRX is linked to microcephaly.