Molecular Pathogenesis
Loss of the endocochlear potential is the cause of deafness in Pendred syndrome / nonsyndromic enlarged vestibular aqueduct (PDS/NSEVA) [Wangemann et al 2004]. Normal endolymphatic K+ concentrations suggest that absent or dysfunctional pendrin results in a secondary loss of KCNJ10 protein expression and the endocochlear potential.
The thyroid phenotype (PDS and NSEVA) depends on the degree of residual iodide transport function in pendrin, the protein encoded by SLC26A4 [Pryor et al 2005, Pera et al 2008].Biallelic loss-of-function variants in SLC26A4 are invariably associated with thyroid dysfunction resulting from impaired iodide organification and reduced iodide efflux into the thyroid follicle. In the absence of pendrin, expression of the chloride channel-5 (ClC-5) will also be increased and will transiently compensate for apical iodide efflux. In more affected follicles, dual oxidase (Duox) and thyroid peroxidase (TPO) are relocated in the cytosol, leading to abnormal intracellular thyroid hormone synthesis, which results in cell destruction [Senou et al 2010].
However, the correlation between variant type (missense vs nonsense) and the development of thyroid enlargement is not robust and individuals who are biallelic for pathogenic/likely pathogenic variants in SLC26A4 are at increased risk of developing thyroid-related manifestations regardless of variant type.
In persons with PDS/NSEVA the identification of double heterozygosity for a single pathogenic variant in both SLC26A4 and KCNJ10 provides additional proof for the involvement of KCNJ10 in the pathogenesis of PDS/NSEVA [Yang et al 2009]. Data from Yang et al [2007] are also consistent with a dosage-dependent model for the molecular pathogenesis of PDS/NSEVA that involves not only SLC26A4 but also FOXI1, which regulates its transcriptional regulatory machinery.
Digenic inheritance. Rare reports of apparent digenic inheritance, in which an affected individual is a double heterozygote (heterozygous in each of two of the involved genes), include:
In two families, persons with enlarged vestibular aqueduct (EVA) demonstrated double heterozygosity with a pathogenic variant in
SLC26A4 and a pathogenic variant in
FOXI1. In support of the pathogenic nature of this genotype, the investigators showed that
FOXI1 activates transcription of
SLC26A4 by binding to a 5'-conserved
cis-acting promoter element [
Yang et al 2007]. In other families with PDS/NSEVA,
Yang et al [2007] found pathogenic variants in the promoter site of
SLC26A4 that abolished
FOXI1-mediated activation of gene transcription.
In two other families, affected persons had double heterozygosity with a pathogenic variant in
SLC26A4 and a pathogenic variant in
KCNJ10. The identified
SLC26A4 pathogenic variants have been previously implicated in PDS/NSEVA. The
KCNJ10 pathogenic variants reduce K(+) conductance activity, which is critical for generating and maintaining the endocochlear potential [
Yang et al 2009].
Pathogenic variants in FOXI1 or KCNJ10 are a rare cause of EVA [Jonard et al 2010, Wu et al 2010].
FOXI1
Gene structure.
FOXI1, the forkhead box L1 gene, encodes a single exon with a coding region of 1038 nucleotides (NM_005250.2). Its two transcript variants encode different isoforms (isoform "a" has 378 and isoform "b" has 283 amino acids). For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. To date, biallelic pathogenic variants in FOXI1 have not been identified. However, five nonsynonymous putative pathogenic variants have been identified, one of which was a single amino acid deletion in the forkhead DNA-binding domain [Yang et al 2007]. The transcriptional regulatory element in the SLC26A4 promoter that binds FOXI1 comprises two adjacent FOXI1 binding sites in a head-to-head orientation. Termed FBS1 and FBS2, both binding sites – in this specific orientation – are required for FOXI1-mediated transcriptional activation of SLC26A4. Pathogenic variants in FBS1 or FBS2 in trans with pathogenic variants in the coding sequence of SLC26A4 are a rare cause of PDS/NSEVA [Yang et al 2007] (see Molecular Pathogenesis, Digenic inheritance).
Normal gene product.
FOXI1, which encodes the 345 amino acid protein FOXI1 (NP_005241.1), is an early otic vesicle-specific gene necessary for the development of the cochlea and vestibule and upstream regulator of SLC26A4. One function of FOXI1 protein is as a transcription factor that controls expression of SLC26A4 [Yang et al 2007].
Abnormal gene product. In vitro studies demonstrated that FOXI1 isoform constructs encoded by FOXI1 transcripts with one of the five putative pathogenic variants had compromised FOXI1 transactivation-mediated SLC26A4 expression. These data support the causal relationship between FOXI1 defects and PDS/NSEVA [Yang et al 2007]. Mice homozygous for the targeted deletion of Foxi1 have sensorineural deafness and dilated vestibular aqueduct [Hulander et al 2003].
KCNJ10
Gene structure.
KCNJ10 comprises two exons (NM_002241.4), the first of which is noncoding. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. To date, biallelic pathogenic variants in KCNJ10 have not been identified in persons with PDS/NSEVA. However, digenic inheritance of one KCNJ10 pathogenic variant and one SLC26A4 pathogenic variant has been reported as causally related to PDS/NSEVA in two affected individuals (see Molecular Pathogenesis) [Yang et al 2009].
See Genetically Related Disorders for other phenotypes resulting from pathogenic variants in KCNJ10.
Normal gene product.
KCNJ10 encodes a 379-amino-acid residue protein (NP_002232.2) that is a member of the inward rectifier-type potassium channel family, characterized by an increased tendency to allow potassium to flow into (rather than out of) a cell (provided by RefSeq; 7/2008). It is expressed in the stria vascularis of the cochlea, in the distal convoluted tubule of the kidney, and in glial cells in the brain.
Abnormal gene product. In vitro functional assays demonstrated that the two KCNJ10 pathogenic variants identified in families with PDS/NSEVA encode proteins that are detrimental to channel activity and reduce K+ conductance by about 50% [Yang et al 2009].
SLC26A4
Gene structure.
SLC26A4 comprises 21 exons; exon 1 is noncoding and partially overlaps SLC26A4-AS1 (SLC26A4 antisense RNA 1), located on the "–" strand. The mRNA product is approximately 5 kb long, with an open reading frame of 2343 bases, producing the 780-amino-acid protein pendrin. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. Hundreds of pathogenic variants have been reported in SLC26A4 in association with PDS/NSEVA (Deafness Variation Database).
Three pathogenic variants – p.Leu236Pro (26%), p.Thr416Pro (15%), and c.1001+1G>A (14%) – are seen more frequently than other pathogenic variants in persons of northern European descent and account for 50% of the PDS/NSEVA-causing alleles in individuals with a molecularly confirmed diagnosis in this population group [Coyle et al 1998, Campbell et al 2001]. Each of these recurrent variants occurs on distinct but common haplotypes, suggesting common founders in these independently ascertained families [Coyle et al 1998, Van Hauwe et al 1998, Park et al 2003].
Other population groups also have unique diverse pathogenic variants reflecting a few prevalent founder variants:
Single- and multiexon deletions have been reported in SLC26A4 [Pera et al 2008].
The frequency of episodes of vertigo and the rate of progression of hearing loss may be pathogenic variant dependent [Sugiura et al 2005b].
Haplotype reconstruction based on SLC26A4-linked short tandem repeat markers that segregate with the EVA phenotype in multiplex families with PDS/NSEVA in which only one SLC26A4 pathogenic variant is found suggests the presence of pathogenic variants in regulatory regions [Choi et al 2009a].
The "Caucasian EVA" (CEVA) haplotype comprising 12 variants upstream of SLC26A4 is frequently found in persons with NSEVA in trans with a coding or splice site variant. The heterozygous carrier frequency of the CEVA haplotype is greater than 5% in Caucasian controls, potentially making this haplotype the most common pathogenic allele of any gene implicated in hereditary hearing loss [Chattaraj et al 2017]. This haplotype is not observed in East Asian populations (e.g., Koreans and Japanese), perhaps explaining the ethnic variability in the frequency with which biallelic SLC26A4 variants are identified in different population groups.
For evidence of non-SLC26A4 haplotypes influencing clinical outcome, see FOXI1, Pathogenic variants.
Table 2.
SLC26A4 Pathogenic Variants Discussed in This GeneReview
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Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
- 1.
Variant designation that does not conform to current naming conventions
Normal gene product.
SLC26A4 encodes the 780-amino acid (86-kd) transmemberane encoding protein, pendrin, which functions as a chloride, iodide, bicarbonate, and formate transporter.
SLC26A4 belongs to the solute carrier 26 gene family and has significant homology to 13 other SLC26 proteins. Human SLC26 family members are involved in a range of key anion transport activities including Cl-/HCO3-, I-/HCO3-, and SO42-/HCO3- exchange, and are associated with debilitating disorders including PDS/NSEVA, chondrodysplasias, and congenital chloride diarrhea [Dawson & Markovich 2005, Kere 2006].
Abnormal gene product. Pathogenic variants in SLC26A4 may result in partial or complete loss of pendrin activity. Functional studies suggest that missense SLC26A4 pathogenic variants that retain residual iodide transport function are more likely to be associated with PDS/NSEVA than with PDS [Scott et al 2000]. All truncating variants eliminate pendrin function.
Using mouse models, it has been shown that pendrin is required between embryonic day 16.5 and postnatal day two for normal hearing but not for maintenance of hearing [Choi et al 2011a]. Endolymph volume in homozygous null mice (Slc26a4-/-) is increased and tissue mass in areas occupied by type I and II fibrocytes is reduced. Slc26a4-/- mice lack an endocochlear potential, which is normally generated across the basal cell barrier of the stria vascularis by the potassium channel KCNJ10 and localizes to the intermediate cells.