Submissions for variant NM_000441.2(SLC26A4):c.1003T>C (p.Phe335Leu)

gnomAD frequency: 0.00077  dbSNP: rs111033212

Total submissions: 24

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Hearing Loss Variant Curation Expert Panel	RCV000576732	SCV001438398	likely pathogenic	Pendred syndrome	2020-08-19	reviewed by expert panel	curation	The c.1003T>C (p.Phe335Leu) variant has been identified in over 20 probands with Hearing loss, 6 of whom had a second pathogenic or suspected pathogenic variant in trans (PM3_VeryStrong; PMIDs: 19509082, 29293505, 25394566, 20668687, 20597900, 19426954, 19204907, 18285825, 17503324, 17357124, 17309986, 15689455, 14679580, 11317356, Laboratory for Molecular Medicine internal data). The variant has been reported to segregate with disease in one affected family member (PP1; PMID: 18285825). Multiple probands presented with hearing loss and enlarged vestibular aqueducts (EVA) which are highly specific to Pendred syndrome (PP4; PMIDs: 14679580, 18285825, 19509082, 25394566, Laboratory for Molecular Medicine internal data). Evidence has been published indicating that the p.Phe335Leu variant may be pathogenic when in trans with a functionally-null or severely hypomorphic variant but not as a mono-allelic variant or in the homozygous state (PMIDs: 19204907, 24051746). The c.1003T>C (p.Phe335Leu) variant was present in 0.203% (76/30612 CI 95%) of South Asian alleles in gnomAD v2.1.1, which is a high enough frequency apply BS1_Supporting. Additionally it was present in 2.1% (27/910 CI 95%) of Amish alleles in gnomAD v3.1 (BA1). The ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for Pendred syndrome outweighs the high allele frequency of the variant in population databases. Therefore, neither BS1_Supporting nor BA1 will contribute to the overall classification. A functional study demonstrates that the p.Phe335Leu variant may impact protein function (PS3_Supporting; PMID: 19204907). Finally, the REVEL computational prediction analysis tool produced a score of 0.828, which is above the threshold necessary to apply PP3. In summary, this variant has been classified as likely pathogenic for autosomal recessive Pendred syndrome based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM3_VeryStrong, PS3_Supporting, PP1, PP3, PP4.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000824769	SCV000060075	pathogenic	Rare genetic deafness	2022-06-23	criteria provided, single submitter	clinical testing	The p.Phe335Leu variant in SLC26A4 has been reported in more than 25 probands with hearing loss, at least 19 of whom had temporal bone abnormalities, and at least 6 of whom had a second pathogenic variant in SLC26A4 (Campbell 2001 PMID 11317356, Prasad 2004 PMID 14679580, Pryor 2005 PMID 15689455, Madden 2007 PMID 17309986, Samanich 2007 PMID 17357124, Yang 2007 PMID 17503324, Pera 2008 PMID 18285825, Choi 2009 PMID 19204907, Dai 2009 PMID 19509082, Yang 2009 PMID 19426954, Pourova 2010 PMID 20597900, Rodriguez 2010 PMID 20668687, Chattaraj 2013 PMID 24051746, Landa 2013 PMID 23965030, Soh 2015 PMID 25394566, Likar 2018 PMID 29293505, LMM data). The variant also segregated with hearing loss and EVA in at least 1 affected family member (Pera 2008 PMID 18285825). Other variants at this position, p.Phe335Ser and p.Phe335Val, have been detected in individuals with hearing loss (Madden 2007 PMID 17309986, Nanose 2018 PMID 29739340), suggesting that changes to this position may not be tolerated. Furthermore, in vitro functional studies provide some evidence that the p.Phe335Leu variant may impact protein function (Choi 2009 PMID 19204907). This variant has also been identified in 0.25% (77/30778) of South Asian chromosomes, including 1 homozygote, by the Genome Aggregation Database (http://gnomAD.broadinstitute.org). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency and it is not known if individuals with hearing loss were excluded from the population studies included in gnomAD. In addition, a case-control comparison using Chi-squared analysis revealed a statistically significantly difference between the number of cases with the variant versus controls (p-value of <0.0001). In summary, despite its high frequency in the general population, this variant meets criteria to be classified as pathogenic for autosomal recessive hearing loss. ACMG/AMP criteria applied: PM3_Very Strong, PP1, PS3_P, PP3, BS1_Supporting.
GeneDx	RCV000656976	SCV000565574	likely pathogenic	not provided	2024-06-17	criteria provided, single submitter	clinical testing	Published functional studies have shown normal plasma membrane localization but lower exchange rate constant for p.(F335L) compared to wild-type constructs (PMID: 19204907); the significance of this residual activity for overall protein function is currently unclear; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Classified as likely pathogenic by the ClinGen Hearing Loss Variant Curation Expert Panel (SCV001438398.2; PMID: 30311386); This variant is associated with the following publications: (PMID: 20668687, 21704276, 36499699, 19426954, 27771369, 23965030, 14679580, 26485571, 17503324, 19998422, 23336812, 11317356, 29372807, 32165640, 31589614, 28444304, 24222258, 29293505, 16950989, 17357124, 30275481, 17309986, 16570074, 28984810, 18285825, 29739340, 30609409, 20597900, 19509082, 25394566, 15689455, 31980526, 34426522, 33138774, 34416374, Liu[article]2022, 36833263, 36362242, 34545167, 19204907, 30311386, 34405919, 37853563)
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000656976	SCV000605152	likely pathogenic	not provided	2020-11-18	criteria provided, single submitter	clinical testing	The c.1003T>C; p.Phe335Leu variant (rs111033212) has been reported extensively in the literature in individuals with hearing loss, and many of these patients also had dilated vestibular aqueduct (DVA) or other abnormalities of the temporal bone without goiter (Campbell 2001, Choi 2009, Madden 2007, Pera 2008, Pourova 2010, Prasad 2004). Multiple probands also had a second pathogenic variant in trans (Choi 2009 and Pera 2008). This variant segregated with bilateral hearing loss in one affected family member (Pera 2008), and functional studies indicate that the p.Phe335Leu variant causes a mild but significant reduction in transporter activity compared to wild-type (Choi 2009). This variant is found in the South Asian population with an allele frequency of 0.25% (76/30,612 alleles, including 1 homozygotes) in the Genome Aggregation Database. The phenylalanine at codon 335 is moderately conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.858). Based on available information, this variant is considered to be likely pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000036420	SCV000893729	pathogenic	Autosomal recessive nonsyndromic hearing loss 4; Pendred syndrome	2018-10-31	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV002291265	SCV000916170	likely pathogenic	SLC26A4-related disorder	2018-12-13	criteria provided, single submitter	clinical testing	The SLC26A4 c.1003T>C (p.Phe335Leu) missense variant has been identified in a compound heterozygous state in two siblings with SLC26A4-related disorders, and in a heterozygous state in at least 17 individuals in whom a second variant was not identified (Campbell et al. 2001; Albert et al. 2006; Madden et al. 2007; Yang et al. 2007; Pera et al. 2008; Choi et al. 2009; Pourová et al. 2010; Landa et al. 2013; Rendtorff et al. 2013). The compound heterozygous siblings were described with clinical features of hearing loss and enlarged vestibular aqueduct (EVA), where one of the siblings had bilateral EVAs and the other sibling had unilateral EVA. Most of the heterozygous probands presented with hearing loss with EVA, and the p.Phe335Leu variant was first identified in these probands through single-gene analyses of SLC26A4. In many probands with SLC26A4-related disorders, a second disease-causing variant is not identified (Yang et al. 2009). Digenic inheritance of heterozygous variants in SLC26A4 and KCNJ10 in association with hearing loss has been reported, and the p.Phe335Leu variant has been reported in a heterozygous state in two probands who also carried a KCNJ10 variant in a heterozygous state (Yang et al. 2009; Landa et al. 2013). The p.Phe335Leu variant is reported at a frequency of 0.00307 in the South Asian population of 1000 Genomes. Functional studies showed that the SLC26A4 protein carrying the p.Phe335Leu variant traffics to the plasma membrane in a manner indistinguishable from wild type protein and has substantial residual activity, but has a reduced Cl−/I− exchange rate constant (Choi et al. 2009). Based on the collective evidence, the p.Phe335Leu variant is classified as likely pathogenic for SLC26A4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	RCV000576732	SCV000993594	likely pathogenic	Pendred syndrome	2018-10-22	criteria provided, single submitter	research
Labcorp Genetics (formerly Invitae), Labcorp	RCV000656976	SCV001045245	pathogenic	not provided	2024-01-31	criteria provided, single submitter	clinical testing	This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 335 of the SLC26A4 protein (p.Phe335Leu). This variant is present in population databases (rs111033212, gnomAD 0.3%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with deafness (PMID: 19509082, 20128824, 24051746, 25394566, 26485571). 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. This variant has been shown to cause SLC26A4-related conditions when it occurs in trans with a functionally null variant; however the effect of this variant on homozygous individuals has not been well documented in the literature. (PMID: 19578036, 19204907). ClinVar contains an entry for this variant (Variation ID: 4842). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SLC26A4 protein function. Experimental studies have shown that this missense change affects SLC26A4 function (PMID: 19204907). For these reasons, this variant has been classified as Pathogenic.
Myriad Genetics, Inc.	RCV000576732	SCV001194145	likely pathogenic	Pendred syndrome	2019-12-17	criteria provided, single submitter	clinical testing	NM_000441.1(SLC26A4):c.1003T>C(F335L) is classified as likely pathogenic in the context of Pendred syndrome. Sources cited for classification include the following: PMID 29372807, 25394566, 26485571, 27771369, 29293505, 28444304 and 28984810. Classification of NM_000441.1(SLC26A4):c.1003T>C(F335L) is based on the following criteria: This variant 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.
Genome-Nilou Lab	RCV000576732	SCV001652762	likely pathogenic	Pendred syndrome	2021-05-18	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000656976	SCV002023542	likely pathogenic	not provided	2023-06-15	criteria provided, single submitter	clinical testing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	RCV000005114	SCV002569371	uncertain significance	Autosomal recessive nonsyndromic hearing loss 4	2022-05-02	criteria provided, single submitter	clinical testing	A heterozygous missense variation in exon 9 of the SLC26A4 gene that results in the amino acid substitution of Leucine for Phenalalanine at codon 335 was detected. The observed variant c.1003 T>C (p.Phe335Leu) the variant has a minor allele Frequency of 0.08% 1000 genomes, gnomAD databases. The in silico prediction of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by LRT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as uncertain significance
MGZ Medical Genetics Center	RCV000005114	SCV002581825	pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2022-08-29	criteria provided, single submitter	clinical testing
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	RCV002291265	SCV002583769	likely pathogenic	SLC26A4-related disorder	2022-07-25	criteria provided, single submitter	clinical testing	PS3_Supporting, PM3_Strong, PP1, PP3, PP4
Lifecell International Pvt. Ltd	RCV000576732	SCV003842260	likely pathogenic	Pendred syndrome		criteria provided, single submitter	clinical testing	A Heterozygous Missense, Splice site region variant c.1003T>C in Exon 9 of the SLC26A4 gene that results in the amino acid substitution p.Phe335Leu was identified. The observed variant has a minor allele frequency of 0.086%, in gnomAD exomes and 0.045% in genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as LikelyPathogenic. For these reasons, this variant has been classified as Likely Pathogenic
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000576732	SCV003844306	pathogenic	Pendred syndrome	2024-07-11	criteria provided, single submitter	clinical testing	Variant summary: SLC26A4 c.1003T>C (p.Phe335Leu) results in a non-conservative amino acid change located in the SLC26A/SulP transporter domain (IPR002645) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00086 in 251190 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not significantly higher than estimated for a pathogenic variant in SLC26A4 causing Pendred Syndrome (0.00086 vs 0.0035), allowing no conclusion about variant significance. c.1003T>C has been reported in the literature in multiple individuals affected with Pendred Syndrome (Teek_2013, Rendtorff_2013, etc.) and EVA (Hearing loss and enlargement of the vestibular aqueduct) (Pera_2008, Choi_2009, Muskett_2016, etc.). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating showing the variant effect results in reduced protein activity (Choi_2009). The following publications have been ascertained in the context of this evaluation (PMID: 19578036, 33502066, 26485571, 18285825, 23336812, 24222258). ClinVar contains an entry for this variant (Variation ID: 4842). Based on the evidence outlined above, the variant was classified as pathogenic.
Duke University Health System Sequencing Clinic, Duke University Health System	RCV000005114	SCV003918981	pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2023-04-20	criteria provided, single submitter	research
Neuberg Centre For Genomic Medicine, NCGM	RCV000005114	SCV004175768	pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2023-03-01	criteria provided, single submitter	clinical testing	The missense/ splice region variant c.1003T>C (p.Phe335Leu) in the SLC26A4 gene has been reported previously in a compound heterozygous and heterozygous state in individuals affected with Nonsyndromic hearing loss and enlargement of the vestibular aqueduct. Published functional studies have shown normal plasma membrane localization but a lower exchange rate constant for p.(F335L) compared to wild-type constructs (Nonose et al., 2018; Choi et al., 2009). This variant is reported with the allele frequency (0.08%) in the gnomAD and novel in the 1000 genome database. It is submitted to ClinVar with varying interpretations as Pathogenic/ Likely Pathogenic. The amino acid Phenylalanine at position 335 is changed to a Leucine changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Phe335Leu in SLC26A4 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics	RCV000005114	SCV004201803	likely pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2024-03-30	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	RCV000005114	SCV004810358	likely pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2024-04-04	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000656976	SCV004810836	likely pathogenic	not provided	2024-06-01	criteria provided, single submitter	clinical testing	SLC26A4: PM3:Strong, PM2:Supporting, PS3:Supporting
OMIM	RCV000005114	SCV000025291	pathogenic	Autosomal recessive nonsyndromic hearing loss 4	2009-05-01	no assertion criteria provided	literature only
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000656976	SCV001809021	uncertain significance	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000656976	SCV001972971	uncertain significance	not provided		no assertion criteria provided	clinical testing