ClinVar Genomic variation as it relates to human health
NM_000441.2(SLC26A4):c.2219G>T (p.Gly740Val)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Likely pathogenic(2); Uncertain significance(8)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000441.2(SLC26A4):c.2219G>T (p.Gly740Val)
Variation ID: 43545 Accession: VCV000043545.49
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7q22.3 7: 107350628 (GRCh37) [ NCBI UCSC ] 7: 107710183 (GRCh38) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jan 31, 2015 Oct 20, 2024 Mar 26, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000441.2:c.2219G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000432.1:p.Gly740Val missense NC_000007.14:g.107710183G>T NC_000007.13:g.107350628G>T NG_008489.1:g.54549G>T - Protein change
- G740V
- Other names
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- Canonical SPDI
- NC_000007.14:107710182:G:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00020 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00025
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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SLC26A4 | - | - |
GRCh38 GRCh37 |
1383 | 1582 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (3) |
criteria provided, multiple submitters, no conflicts
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Feb 13, 2024 | RCV000584878.25 | |
Conflicting interpretations of pathogenicity (4) |
criteria provided, conflicting classifications
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Mar 13, 2024 | RCV001164905.10 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Mar 26, 2024 | RCV001164904.10 | |
no classifications from unflagged records (1) |
no classifications from unflagged records
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Dec 5, 2023 | RCV001375368.5 | |
Uncertain significance (1) |
criteria provided, single submitter
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Feb 2, 2023 | RCV004017307.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive nonsyndromic hearing loss 4
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001327065.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
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, … (more)
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. (less)
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Uncertain significance
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Pendred syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001327066.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
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, … (more)
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. (less)
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Uncertain significance
(Sep 05, 2021)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive nonsyndromic hearing loss 4
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV002027506.1
First in ClinVar: Nov 29, 2021 Last updated: Nov 29, 2021 |
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Uncertain significance
(Sep 05, 2021)
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criteria provided, single submitter
Method: clinical testing
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Pendred syndrome
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV002027517.1
First in ClinVar: Nov 29, 2021 Last updated: Nov 29, 2021 |
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Uncertain significance
(Oct 17, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003278564.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 740 of the SLC26A4 protein (p.Gly740Val). … (more)
This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 740 of the SLC26A4 protein (p.Gly740Val). This variant is present in population databases (rs111033310, gnomAD 0.1%). This missense change has been observed in individual(s) with deafness and/or clinical features of Pendred syndrome (PMID: 20597900, 23804846, 25788563, 25991456). ClinVar contains an entry for this variant (Variation ID: 43545). 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. 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. (less)
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Uncertain Significance
(Feb 02, 2023)
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criteria provided, single submitter
Method: clinical testing
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Rare genetic deafness
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000060136.7
First in ClinVar: May 03, 2013 Last updated: Apr 20, 2024 |
Comment:
Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Albert 2006 PMID: 16570074 1 proband (HL+EVA) with T307M (VUS) in cis, … (more)
Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Albert 2006 PMID: 16570074 1 proband (HL+EVA) with T307M (VUS) in cis, and Y530H (LP) in trans; 1 sib-pair (HL+EVA) with FS in trans, Landa 2013 PMID 23965030 2 probands with HL +EVA or goiter, 1 carries a splice variant (phase unknown), the second only het Makretskaya (2018) PMID: 30240412 Het in 1 pt with congenital hypothyroidism ACMG/AMP codes: PM3, PM2_Supporting (AJ high- however bottleneck pop). (less)
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Likely pathogenic
(Mar 26, 2024)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive nonsyndromic hearing loss 4
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004201822.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Likely pathogenic
(Mar 13, 2024)
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criteria provided, single submitter
Method: clinical testing
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Pendred syndrome
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002555750.3
First in ClinVar: Aug 03, 2022 Last updated: Jun 29, 2024 |
Comment:
Variant summary: SLC26A4 c.2219G>T (p.Gly740Val) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Variant summary: SLC26A4 c.2219G>T (p.Gly740Val) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0003 in 251252 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in SLC26A4 causing Pendred Syndrome (0.0003 vs 0.0035), allowing no conclusion about variant significance. c.2219G>T has been reported in the literature in individuals affected with Hearing loss (Albert_2006, Tang_2015, Baldyga_2023). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25788563, 25991456, 30240412, 30245029, 23804846, 18285825, 16570074, 23401162, 23965030, 20597900, 36833263).ClinVar contains an entry for this variant (Variation ID: 43545). Based on the evidence outlined above, the variant was classified as likely pathogenic. (less)
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Uncertain significance
(Feb 13, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV005324856.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
Comment:
Identified with an SLC26A4 variant of unknown significance in additional patients with hearing loss with or without enlarged vestibular aqueduct in published literature (PMID: 18285825, … (more)
Identified with an SLC26A4 variant of unknown significance in additional patients with hearing loss with or without enlarged vestibular aqueduct in published literature (PMID: 18285825, 16570074, 23965030); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 20597900, 30240412, 30245029, 23401162, 34426522, 25991456, 23965030, 16570074, 18285825, 35249537, 36147510, 25788563, 36833263, 23804846) (less)
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Uncertain significance
(Jul 01, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV000693249.30
First in ClinVar: Mar 03, 2018 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 2
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Uncertain significance
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Pendred syndrome
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001459943.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Likely pathogenic
(Apr 12, 2021)
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Flagged submission
flagged submission
Method: clinical testing
Reason: Outlier claim with insufficient supporting evidence
Source: ClinGen
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Hearing impairment
Affected status: yes
Allele origin:
germline
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Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center
Accession: SCV001571751.2
First in ClinVar: May 01, 2021 Last updated: May 01, 2021 |
Comment:
PM2_Supporting, PM3_Moderate, PP4_Supporting
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Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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The Genetic Background of Hearing Loss in Patients with EVA and Cochlear Malformation. | Bałdyga N | Genes | 2023 | PMID: 36833263 |
Genomic Landscape and Mutational Signatures of Deafness-Associated Genes. | Azaiez H | American journal of human genetics | 2018 | PMID: 30245029 |
High frequency of mutations in 'dyshormonogenesis genes' in severe congenital hypothyroidism. | Makretskaya N | PloS one | 2018 | PMID: 30240412 |
DNA sequence analysis and genotype-phenotype assessment in 71 patients with syndromic hearing loss or auditory neuropathy. | Tang HY | BMJ open | 2015 | PMID: 25991456 |
Deafness gene variations in a 1120 nonsyndromic hearing loss cohort: molecular epidemiology and deafness mutation spectrum of patients in Japan. | Nishio SY | The Annals of otology, rhinology, and laryngology | 2015 | PMID: 25788563 |
Lack of significant association between mutations of KCNJ10 or FOXI1 and SLC26A4 mutations in Pendred syndrome/enlarged vestibular aqueducts. | Landa P | BMC medical genetics | 2013 | PMID: 23965030 |
Advancing genetic testing for deafness with genomic technology. | Shearer AE | Journal of medical genetics | 2013 | PMID: 23804846 |
Significance of unilateral enlarged vestibular aqueduct. | Greinwald J | The Laryngoscope | 2013 | PMID: 23401162 |
Spectrum and frequency of SLC26A4 mutations among Czech patients with early hearing loss with and without Enlarged Vestibular Aqueduct (EVA). | Pourová R | Annals of human genetics | 2010 | PMID: 20597900 |
A mutational analysis of the SLC26A4 gene in Spanish hearing-impaired families provides new insights into the genetic causes of Pendred syndrome and DFNB4 hearing loss. | Pera A | European journal of human genetics : EJHG | 2008 | PMID: 18285825 |
SLC26A4 gene is frequently involved in nonsyndromic hearing impairment with enlarged vestibular aqueduct in Caucasian populations. | Albert S | European journal of human genetics : EJHG | 2006 | PMID: 16570074 |
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Text-mined citations for rs111033310 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.