ClinVar Miner

Submissions for variant NM_000441.2(SLC26A4):c.2168A>G (p.His723Arg)

gnomAD frequency: 0.00006  dbSNP: rs121908362
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Total submissions: 21
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Mass General Brigham Personalized Medicine RCV000036477 SCV000060132 pathogenic Rare genetic deafness 2011-07-28 criteria provided, single submitter clinical testing The His723Arg variant in SLC26A4 has been reported in 37 probands with hearing l oss and enlarged vestibular aqueducts (EVA) or Pendred syndrome (Wu 2005, Van Ha uwe 1998, Lee 2008, Asakura 2010, Cho 2006, Dai 2008, Hu 2007, Ishihara 2010, Ki m 2009, Park 2003, Reyes 2009, Tsukamoto 2003, Usami 1999, Yoon 2008). Many of t hese probands were homozygous or compound heterozygous and the variant has segre gated with disease in several families. Furthermore, functional studies revealed that the His723Arg variant disrupts the normal cellular localization and ion tr ansport activity of the protein (Yoon 2008, Ishihara 2010). In summary, this var iant meets our criteria to be classified as pathogenic.
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center RCV000005095 SCV000267506 likely pathogenic Pendred syndrome 2016-03-18 criteria provided, single submitter reference population
GeneDx RCV000480319 SCV000568753 pathogenic not provided 2020-04-24 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect with intracellular retention and decreased protein activity in comparison to wild type (Yoon et al., 2008); This variant is associated with the following publications: (PMID: 20842945, 19786220, 20583162, 23705809, 25266519, 22884721, 20826203, 23469187, 23755160, 24224479, 9618166, 27176802, 28583500, 27082237, 30693673, 31599023, 11405873, 24007330, 22975760, 11502831, 18310264, 21961810, 24338212, 26035154, 26100058, 26346818, 27384033, 26763877, 28990112, 28981942, 28786104, 28964290, 27374754, 28802383, 29234782, 28093008, 28052261, 17322586, 30282152, 29447821, 30589569, 30036422, 30733538, 31347505, 30842343, 31564438, 29650690, 31541171, 31827275, 32203226, 30896630, 32425884, 30275481, 32447495, 15905611, 32459320)
Division of Hearing and Balance Research,National Hospital Organization Tokyo Medical Center RCV000005094 SCV000611824 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2017-07-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000480319 SCV000886131 pathogenic not provided 2017-09-22 criteria provided, single submitter clinical testing The c.2168A>G; p.His723Arg (rs121908362) is one of commonly observed variants reported in patients with Pendred Syndrome and hearing loss across the Asian population (Van Hauwe, 1998; Ishihara, 2010; Sagong, 2013; Asakura, 2010; Li, 2016). Lee (2014) noted that patients with two copies of the p.His723Arg variant had poorer hearing and higher proportion of incomplete cochlear turns (Mondini structures) compared to compound heterozygotes with a single copy and a different SLC26A4 variant. Cell-based and biochemical experiments further demonstrated that p.His723Arg polypeptides are impaired at reaching the plasma membrane and exhibit abnormal ion exchange activity that can be rescued at low temperature (Yoon, 2008). This variant is listed in the Genome Aggregation Database (gnomAD) in the East Asian population at a frequency of 0.16 percent (identified on 31 out of 18,868 chromosomes with 0 homozygotes) and is reported to the ClinVar database as a pathogenic/likely pathogenic variant (Variation ID: 4825). The histidine at position 723 is highly conserved across 12 species (Alamut v2.9.0), and computational analyses of the effects of the p.His723Arg variant on protein structure and function indicate a deleterious effect (SIFT: damaging, MutationTaster: disease causing, PolyPhen-2: probably damaging). Altogether the p.His723Arg variant is pathogenic.
Illumina Laboratory Services,Illumina RCV000778813 SCV000915193 pathogenic SLC26A4-Related Disorders 2017-04-28 criteria provided, single submitter clinical testing The SLC26A4 c.2168A>G (p.His723Arg) missense variant is a common founder variant in both the Japanese and Korean populations (Park et al. 2003). Across a selection of the available literature, it has been identified in a homozygous state in 26 patients, in a compound heterozygous state in 67 patients, and in a heterozygous state in 19 patients, including those with Pendred syndrome and autosomal recessive nonsyndromic hearing loss with enlarged vestibular aqueduct (Tsukamoto et al. 2003; Park et al. 2005; Cho et al. 2006; Kim et al. 2009; Reyes et al. 2009; Miyagawa et al. 2014; Lu et al. 2015; Tsukada et al. 2015). Family studies have demonstrated inheritance of the variant from unaffected heterozygous parents. The p.His723Arg variant was identified in a heterozygous state in three of 1024 Asian control alleles (Park et al. 2003; Yuan et al. 2012; Miyagawa et al. 2014) and is reported at a frequency of 0.00174 in the East Asian population of the Exome Aggregation Consortium. Functional studies in HEK 293 and HeLa cells showed the variant causes the protein to be retained in the endoplasmic reticulum rather than localized to the cell membrane and significantly reduces chloride bicarbonate ion exchange function, consistent with the proposed disease mechanism. The defects were rescued by incubation at low temperature, suggesting they may be due to protein misfolding (Yoon et al. 2008). Based on the collective evidence, the p.His723Arg variant is classified as pathogenic for SLC26A4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000480319 SCV000939369 pathogenic not provided 2021-12-09 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 723 of the SLC26A4 protein (p.His723Arg). This variant is present in population databases (rs121908362, gnomAD 0.2%). This missense change has been observed in individual(s) with Pendred syndrome (PMID: 11405873, 17322586, 20583162, 22884721, 23705809, 24338212). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 4825). 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: 20583162). For these reasons, this variant has been classified as Pathogenic.
National Institute of Sensory Organs,National Hospital Organization Tokyo Medical Center RCV000005094 SCV000994909 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2019-08-20 criteria provided, single submitter clinical testing in vitro experiment
Baylor Genetics RCV000005095 SCV001163099 pathogenic Pendred syndrome criteria provided, single submitter clinical testing
Myriad Women's Health, Inc. RCV000005095 SCV001194173 pathogenic Pendred syndrome 2019-12-04 criteria provided, single submitter clinical testing NM_000441.1(SLC26A4):c.2168A>G(H723R) is classified as pathogenic in the context of Pendred syndrome. Sources cited for classification include the following: PMID 18310264, 24007330, 20826203 and 17718863. Classification of NM_000441.1(SLC26A4):c.2168A>G(H723R) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute RCV000005094 SCV001244768 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2018-01-03 criteria provided, single submitter clinical testing A homozygous missense variant was identified, NM_000441.1(SLC26A4):c.2168A>G in exon 19 of 21 of the SLC26A4 gene. This substitution is predicted to create a minor amino acid change from histidine to arginine at position 723, NP_000432.1(SLC26A4):p.(His723Arg).The histidine at this position has very high conservation (100 vertebrates, UCSC). In silico software predicts this variant to be disease causing (Polyphen, SIFT, CADD, Mutation Taster).It is situated in a STAS domain (predicted binding function). This variant is present in the gnomAD population database at a frequency of 0.01% (31 heterozygotes, 0 homozygotes). It has been previously reported as a pathogenic variant in numerous patients with hearing loss, enlarged vestibular aqueducts or Pendred syndrome (OMIM, ClinVar). In addition, functional studies show that this variant disrupts the normal cellular localisation and ion transport activity of the protein (Yoon JS. et al., (2008)). Parental testing has confirmed homozygosity. Based on current information, this variant has been classified as PATHOGENIC.
Genome-Nilou Lab RCV000005094 SCV002026974 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2021-09-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000005095 SCV002026975 pathogenic Pendred syndrome 2021-09-05 criteria provided, single submitter clinical testing
3billion RCV000005094 SCV002058697 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2022-01-03 criteria provided, single submitter clinical testing Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000004825, PMID:9618166, PS1_S).A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000949741, PMID:19040761,24599119, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.933, 3CNET: 0.958, PP3_P). A missense variant is a common mechanism associated with Deafness (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000113, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000005095 SCV002074332 pathogenic Pendred syndrome 2022-01-19 criteria provided, single submitter clinical testing Variant summary: SLC26A4 c.2168A>G (p.His723Arg) results in a non-conservative amino acid change located in the STAS domain 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 0.00012 in 251294 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in SLC26A4 causing Pendred Syndrome (0.00012 vs 0.0035), allowing no conclusion about variant significance. c.2168A>G has been reported in the literature in multiple individuals affected with Pendred Syndrome or hearing loss (e.g. Sagong_2012, Jung_2016). These data indicate that the variant is very likely to be associated with disease. Fifteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
OMIM RCV000005094 SCV000025270 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2008-07-01 no assertion criteria provided literature only
OMIM RCV000005095 SCV000025271 pathogenic Pendred syndrome 2008-07-01 no assertion criteria provided literature only
GeneReviews RCV000005095 SCV000086786 pathogenic Pendred syndrome 2017-10-19 no assertion criteria provided literature only
Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery,Institute of Otolaryngology, Chinese PLA General Hospital RCV000005094 SCV000902362 likely pathogenic Autosomal recessive nonsyndromic hearing loss 4 2019-02-26 no assertion criteria provided case-control
The Core Laboratory in Medical Center of Clinical Research,Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine RCV000005095 SCV001438729 pathogenic Pendred syndrome 2020-05-12 no assertion criteria provided clinical testing
Natera, Inc. RCV000005095 SCV001459941 pathogenic Pendred syndrome 2020-09-16 no assertion criteria provided clinical testing

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