Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans

PLoS Genet. 2020 Apr 15;16(4):e1008643. doi: 10.1371/journal.pgen.1008643. eCollection 2020 Apr.


Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss. Furthermore, we detected another de novo missense variant of SLC12A2 in a sporadic case. SLC12A2 encodes Na+, K+, 2Cl- cotransporter (NKCC) 1 and plays critical roles in the homeostasis of K+-enriched endolymph. Slc12a2-deficient mice have congenital, profound deafness; however, no human variant of SLC12A2 has been reported as associated with hearing loss. All identified SLC12A2 variants mapped to exon 21 or its 3'-splice site. In vitro analysis indicated that the splice-site variant generates an exon 21-skipped SLC12A2 mRNA transcript expressed at much lower levels than the exon 21-included transcript in the cochlea, suggesting a tissue-specific role for the exon 21-encoded region in the carboy-terminal domain. In vitro functional analysis demonstrated that Cl- influx was significantly decreased in all SLC12A2 variants studied. Immunohistochemistry revealed that SLC12A2 is located on the plasma membrane of several types of cells in the cochlea, including the strial marginal cells, which are critical for endolymph homeostasis. Overall, this study suggests that variants affecting exon 21 of the SLC12A2 transcript are responsible for hereditary hearing loss in humans.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Chlorides / metabolism
  • Cochlea / metabolism
  • Cochlea / pathology
  • Deafness / congenital
  • Deafness / genetics
  • Exons / genetics
  • Female
  • Gene Expression
  • HEK293 Cells
  • Hearing Loss, Sensorineural / congenital*
  • Hearing Loss, Sensorineural / genetics*
  • Humans
  • Infant
  • Macaca fascicularis
  • Male
  • Mutation*
  • Pedigree
  • Protein Domains / genetics*
  • RNA Splicing
  • RNA, Messenger / analysis
  • RNA, Messenger / genetics
  • Solute Carrier Family 12, Member 2 / chemistry*
  • Solute Carrier Family 12, Member 2 / genetics*
  • Solute Carrier Family 12, Member 2 / metabolism


  • Chlorides
  • RNA, Messenger
  • SLC12A2 protein, human
  • Solute Carrier Family 12, Member 2

Grant support

This work was supported by the Japan Society for the Promotion of Science KAKENHI (15K10773 and 18K09336) to HM, NIH grants (DC014553 and DC017482) to KH, and a Grant-in-Aid for Clinical Research from the National Hospital Organization (H27-NHO (kankaku)-02) and Project for Development of Made-to-Order Medicine from Japan Agency for Medical Research and Development (Yokohama H17-16(27)) to TM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.