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

gnomAD frequency: 0.00004  dbSNP: rs121908362

Total submissions: 24

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	2022-12-28	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); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 20842945, 19786220, 20583162, 23705809, 25266519, 22884721, 20826203, 23469187, 23755160, 24224479, 9618166, 27176802, 28583500, 27082237, 30693673, 32477112, 31599023, 34943631, 34943614, 11405873, 24007330, 22975760, 11502831, 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, 32877901, 34170635, 32447495, 15905611, 32459320, 32645618, 32536503, 33597575, 33724713, 34006472, 35204885, 35276235, 35114279, 34801268, 35249537, 34545167, 18310264)
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	2024-01-05	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 with a positive predictive value of 95%. 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 Genetics, 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	RCV000005095	SCV001244768	pathogenic	Pendred syndrome	2021-05-06	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Pendred syndrome (MIM#274600). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 20301640). (I) 0200 - Variant is predicted to result in a missense amino acid change from histidine to arginine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 32 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated STAS domain (DECIPHER, Uniprot). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. It is prevalent in individuals with Asian descent with Pendred syndrome or deafness 4 with enlarged vestibular aqueduct (ClinVar, PMID: 20301640). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
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.
Fulgent Genetics, Fulgent Genetics	RCV002476929	SCV002800066	pathogenic	Autosomal recessive nonsyndromic hearing loss 4; Pendred syndrome	2021-11-08	criteria provided, single submitter	clinical testing
Molecular Diagnostics Lab, Nemours Children's Health, Delaware	RCV000005095	SCV003935252	pathogenic	Pendred syndrome	2020-05-07	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000005094	SCV004201811	pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2023-10-30	criteria provided, single submitter	clinical testing
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	not provided	Pendred syndrome		no assertion 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