ClinVar Genomic variation as it relates to human health

The c.1061T>C variant in SLC26A4 is a missense variant predicted to cause substitution of phenylalanine by serine at amino acid 354 (p.Phe354Ser). The filtering allele frequency (95% CI) in gnomAD v.2.1.1 was 0.1102% (153/251206 alleles, 6 homozygotes) in Latino/Admixed American population which meets the AR threshold (>=0.07%) for BS1_P. Although the REVEL computational prediction analysis tool produced a score of 0.955, PP3 was not applied. It was observed in 3 probands with sensorineural hearing loss, however they were not scored due to the high FAF in gnomAD (PMID: 26226137, 32747562, 27861301). Functional studies have shown that this variant does not affect the ability of the protein to mediate iodide and chloride transport (PMID:22116359, 31599023) meeting BS3. In summary, this variant is likely benign for autosomal recessive nonsyndromic hearing loss based on the ACMG/AMP criteria applied as specified by the ClinGen Hearing Loss Expert Panel: BS3, BS1_P (ClinGen Hearing Loss VCEP specifications version 2; 11/28/2023)

This variant is associated with the following publications: (PMID: 32747562, 28444304, 27861301, 26764160, 26226137, 33152970, 33199029, 21045265, 25262649, 31599023, 30245029, 15355436, 26894580, 28941661, 27771369, 23280318, 16570074, 23965030, 19017801, 19509082, 22116359)

This sequence change replaces phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 354 of the SLC26A4 protein (p.Phe354Ser). This variant is present in population databases (rs111033243, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with non-syndromic deafness and/or Pendred syndrome (PMID: 15355436, 26894580, 32747562). This variant is also known as F355S. ClinVar contains an entry for this variant (Variation ID: 43492). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC26A4 protein function. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on SLC26A4 function (PMID: 19509082, 22116359). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Variant summary: SLC26A4 c.1061T>C (p.Phe354Ser) results in a non-conservative amino acid change located in the SLC26A/SulP transporter domain (IPR011547) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00055 in 1614856 control chromosomes, including 6 homozygotes, predominantly at a frequency of 0.0024 within the Latino subpopulation in the gnomAD v4 database. This frequency is not significantly higher than estimated for a pathogenic variant in SLC26A4 causing Pendred Syndrome (0.00055 vs 0.0035), allowing no conclusion about variant significance, although the presence of 6 homozygotes is not suggestive of a highly penetrant variant associated with an autosomal recessive disorder. c.1061T>C has been reported in the literature in several compound heterozgyous and homozygous individuals with SLC26A4-related disorders (e.g. Blons_2004, Franze_2016, Wolf_2017, Bademci_2016), however no co-segregation data was reported. The variant has also been reported in multiple heterozygous individuals affected with non-syndromic hearing loss without other features of Pendred Syndrome (e.g. Albert_2006, Dai_2009, Landa_2013, Chouchen_2021), and in individuals with autoimmune thyroid diseases (Graves' Disease and Hashimoto's Thyroiditis) (e.g. Kallel_2013); however no second SLC26A4 variant was identified in these cases. These data do not allow any conclusion about variant significance. Multiple publications report experimental evidence evaluating an impact on protein function (e.g. Dai_2009, Dossena_2011, Wasano_2020). These studies found that the variant had similar Cl-/OH- and I-/Cl- transport activity to the WT protein, but had conflicting results with respect to HCO3-/Cl- exchange, with at least one study reporting an approximately 70% reduction in transport activity and another identifying no impairment. The following publications have been ascertained in the context of this evaluation (PMID: 32747562, 16570074, 30245029, 26226137, 15355436, 33199029, 19509082, 22116359, 26894580, 23280318, 23965030, 31599023, 27861301). Multiple submitters have reported clinical-significance assessments for this variant to ClinVar after 2014 with conflicting interpretations (VUS, n = 7; likely benign, n = 5; likely pathogenic, n = 1; other, n = 1). Based on the evidence outlined above, the variant was classified as uncertain significance.

SLC26A4: PP3, BS1

The p.Phe354Ser variant (rs111033243) has been studied extensively due to a possible role in Pendred syndrome (PS) and deafness with enlarged vestibular aqueduct (EVA); conflicting evidence has emerged. Firstly, the p.Phe354Ser variant has been observed as a homozygote in a patient included in a cohort of autosomal recessive nonsyndromic deafness (ARNSD) patients (Bademci 2016), and was observed in trans with a pathogenic SLC26A4 variant in a patient included in a PS cohort (Blons 2004; reported as p.Phe355Ser). However, it has also been found at a similar frequency in patient and control populations (Hadj-Kacem 2010), and has even been found in controls while being absent from absent from a hearing impaired population (Pera 2008). This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.05 percent (identified on 159 out of 276,944 chromosomes). Data concerning the effect of the p.Phe354Ser variant on SLC26A4 protein function are also mixed, with some studies suggesting no effect on solute transport (Dossena 2011), while others suggesting a decrease in Cl-/HC03- exchange activity (Dai 2009). Moreover, the phenylalanyl at codon 354 is highly conserved considering 11 species up to chicken and there is a large physiochemical difference with the substituted serine (Alamut software v2.9.0). Thus, based on the available information, the clinical significance of the p.Phe354Ser variant cannot be determined with certainty.

p.Phe354Ser in exon 9 of SLC26A4: This variant is not expected to have clinical significance due to equal frequencies in probands with hearing loss and controls and the fact that none of the probands had a variant affecting the other allele (Albert 2006, Dai 2009, Pera 2008, LMM data). This variant was also identified in equal frequency among patients with Graves' and/or Hashimoto's thyroiditis bu t no history of hearing loss (4/237) and in matched controls (5/206) (Hadj-Kacem 2010). In vitro functional studies have shown that this variant did not impact protein function (Dossena 2011). In addition, this variant has been identified i n 0.15% (51/34394) of Latino chromosomes and 78/126480 European chromosomes by t he Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs111033243).

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Benign effect in vitro experiment

SLC26A4 c.1061T>C, p.F354S alters a highly conserved residue of SLC26A4 that is predicted to weaken a transmembrane domain. The variant is homozygous in 4 Palestinian children with pre-lingual severe to profound hearing loss (Abu Rayyan 2020). It is present in 5 of 1300 Palestinian controls, as a heterozygote, and present in 164/282612 alleles on gnomAD, all heterozygotes.