Functional evaluation of autism-associated mutations in NHE9

Nat Commun. 2013;4:2510. doi: 10.1038/ncomms3510.


NHE9 (SLC9A9) is an endosomal cation/proton antiporter with orthologues in yeast and bacteria. Rare, missense substitutions in NHE9 are genetically linked with autism but have not been functionally evaluated. Here we use evolutionary conservation analysis to build a model structure of NHE9 based on the crystal structure of bacterial NhaA and use it to screen autism-associated variants in the human population first by phenotype complementation in yeast, followed by functional analysis in primary cortical astrocytes from mouse. NHE9-GFP localizes to recycling endosomes, where it significantly alkalinizes luminal pH, elevates uptake of transferrin and the neurotransmitter glutamate, and stabilizes surface expression of transferrin receptor and GLAST transporter. In contrast, autism-associated variants L236S, S438P and V176I lack function in astrocytes. Thus, we establish a neurobiological cell model of a candidate gene in autism. Loss-of-function mutations in NHE9 may contribute to autistic phenotype by modulating synaptic membrane protein expression and neurotransmitter clearance.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Astrocytes / metabolism*
  • Astrocytes / pathology
  • Autistic Disorder / genetics*
  • Autistic Disorder / metabolism
  • Autistic Disorder / pathology
  • Cerebral Cortex / metabolism*
  • Cerebral Cortex / pathology
  • Conserved Sequence
  • Endosomes / metabolism*
  • Endosomes / pathology
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Excitatory Amino Acid Transporter 1 / genetics
  • Excitatory Amino Acid Transporter 1 / metabolism
  • Gene Expression Regulation
  • Genetic Complementation Test
  • Glutamic Acid / metabolism
  • Humans
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Primary Cell Culture
  • Receptors, Transferrin / genetics
  • Receptors, Transferrin / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Sodium-Hydrogen Exchangers / chemistry
  • Sodium-Hydrogen Exchangers / genetics
  • Sodium-Hydrogen Exchangers / metabolism*
  • Structural Homology, Protein


  • Escherichia coli Proteins
  • Excitatory Amino Acid Transporter 1
  • NHE9 protein, mouse
  • NhaA protein, E coli
  • Receptors, Transferrin
  • SLC9A9 protein, human
  • Slc1a3 protein, mouse
  • Sodium-Hydrogen Exchangers
  • Glutamic Acid