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NM_000441.2(SLC26A4):c.2291C>T (p.Thr764Met)

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Interpretation:
Uncertain significance​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 28, 2018
Accession:
VCV000043546.5
Variation ID:
43546
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.2291C>T (p.Thr764Met)

Allele ID
52715
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107712594 (GRCh38) GRCh38 UCSC
7: 107353039 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107353039C>T
NC_000007.14:g.107712594C>T
NM_000441.2:c.2291C>T MANE Select NP_000432.1:p.Thr764Met missense
NG_008489.1:g.56960C>T
Protein change
T764M
Other names
NM_000441.1(SLC26A4):c.2291C>T(p.Thr764Met)
NM_000441.1(SLC26A4):c.2291C>T
Canonical SPDI
NC_000007.14:107712593:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00006
Exome Aggregation Consortium (ExAC) 0.00010
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00014
Links
dbSNP: rs150597240
ClinGen: CA132713
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 reviewed by expert panel Sep 28, 2018 RCV000346954.3
Uncertain significance 1 criteria provided, single submitter Jul 25, 2012 RCV000036482.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000289695.2
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000764681.1
Likely benign 1 criteria provided, single submitter Dec 7, 2020 RCV001460836.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC26A4 - - GRCh38
GRCh37
749 825

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Sep 28, 2018)
reviewed by expert panel
Method: curation
Pendred syndrome
(Autosomal recessive inheritance)
Allele origin: germline
ClinGen Hearing Loss Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000840520.3
Submitted: (Feb 27, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The allele frequency of the p.Thr764Met variant in SLC26A4 is 0.01% (3/24024) of African alleles and 0.007% (9/126592) of European (Non-Finnish) alleles by the Genome … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000466110.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000466109.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000895812.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Jul 25, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000060137.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Variant classified as Uncertain Significance - Favor Benign. The Thr764Met varia nt in SLC26A4 has not been reported in the literature nor previously identified by … (more)
Likely benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001664718.1
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Pendred syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001459945.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/edaf7951-7b12-42e2-855d-4a2dc61b69c8 - - - -

Text-mined citations for rs150597240...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021