title: High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.
abstract: BACKGROUND
  Cochlear outer hair cells change their length in response to variations in membrane potential. This capability, called electromotility, is believed to enable the sensitivity and frequency selectivity of the mammalian cochlea. Prestin is a transmembrane protein required for electromotility. Homozygous prestin knockout mice are profoundly hearing impaired. In humans, a single nucleotide change in SLC26A5, encoding prestin, has been reported in association with hearing loss. This DNA sequence variation, IVS2-2A>G, occurs in the exon 3 splice acceptor site and is expected to abolish splicing of exon 3.
  
  
  METHODS
  To further explore the relationship between hearing loss and the IVS2-2A>G transition, and assess allele frequency, genomic DNA from hearing impaired and control subjects was analyzed by DNA sequencing. SLC26A5 genomic DNA sequences from human, chimp, rat, mouse, zebrafish and fruit fly were aligned and compared for evolutionary conservation of the exon 3 splice acceptor site. Alternative splice acceptor sites within intron 2 of human SLC26A5 were sought using a splice site prediction program from the Berkeley Drosophila Genome Project.
  
  
  RESULTS
  The IVS2-2A>G variant was found in a heterozygous state in 4 of 74 hearing impaired subjects of Hispanic, Caucasian or uncertain ethnicity and 4 of 150 Hispanic or Caucasian controls (p = 0.45). The IVS2-2A>G variant was not found in 106 subjects of Asian or African American descent. No homozygous subjects were identified (n = 330). Sequence alignment of SLC26A5 orthologs demonstrated that the A nucleotide at position IVS2-2 is invariant among several eukaryotic species. Sequence analysis also revealed five potential alternative splice acceptor sites in intron 2 of human SLC26A5.
  
  
  CONCLUSIONS
  These data suggest that the IVS2-2A>G variant may not occur more frequently in hearing impaired subjects than in controls. The identification of five potential alternative splice acceptor sites in intron 2 of human SLC26A5 suggests a potential mechanism by which expression of prestin might be maintained in cells carrying the SLC26A5 IVS2-2A>G DNA sequence variation. Additional studies are needed to evaluate the effect of the IVS2-2A>G transition on splicing of SLC26A5 transcripts and characterize the hearing status of individuals homozygous for the IVS2-2A>G variant.
authors.affiliation: The Bobby R. Alford Department of Otorhinolaryngology and Communicative Sciences, Baylor College of Medicine, One Baylor Plaza, NA102, Houston, TX 77030, USA. tang@bmc.tmc.edu
authors.forename: Hsiao-Yuan
authors.initials: HY
authors.lastname: Tang
authors.forename: Anping
authors.initials: A
authors.lastname: Xia
authors.forename: John S
authors.initials: JS
authors.lastname: Oghalai
authors.forename: Fred A
authors.initials: FA
authors.lastname: Pereira
authors.forename: Raye L
authors.initials: RL
authors.lastname: Alford
mesh_terms: D000225:Adenine / Q000378:metabolism*; D000483:Alleles; D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D027321:Anion Transport Proteins; D003051:Cochlea / Q000737:chemistry / Q000378:metabolism; D004272:DNA, Mitochondrial / Q000235:genetics; D005091:Exons / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D006147:Guanine / Q000378:metabolism*; D018069:Hair Cells, Vestibular / Q000737:chemistry / Q000378:metabolism; D034381:Hearing Loss / Q000235:genetics*; D006801:Humans; D007438:Introns / Q000235:genetics; D051379:Mice; D020409:Molecular Motor Proteins; D002679:Pan troglodytes / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D051381:Rats; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D000076988:Sulfate Transporters; D015027:Zebrafish / Q000235:genetics; D029961:Zebrafish Proteins / Q000235:genetics
chemical_list: D027321:Anion Transport Proteins; D004272:DNA, Mitochondrial; D020409:Molecular Motor Proteins; C498720:Pres protein, mouse; D011506:Proteins; D022821:RNA Splice Sites; D012335:RNA, Ribosomal; C075526:RNA, ribosomal, 12S; C498719:SLC26A5 protein, human; C409207:Slc26a5 protein, rat; D000076988:Sulfate Transporters; D029961:Zebrafish Proteins; D006147:Guanine; D000225:Adenine