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NM_000441.2(SLC26A4):c.2145G>T (p.Lys715Asn)

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Interpretation:
Uncertain significance​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
5 (Most recent: Aug 17, 2021)
Last evaluated:
Nov 26, 2019
Accession:
VCV000043541.12
Variation ID:
43541
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.2145G>T (p.Lys715Asn)

Allele ID
52710
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107710109 (GRCh38) GRCh38 UCSC
7: 107350554 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000441.2(SLC26A4):c.2145G>T MANE Select
NC_000007.13:g.107350554G>T
NC_000007.14:g.107710109G>T
... more HGVS
Protein change
K715N
Other names
-
Canonical SPDI
NC_000007.14:107710108:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00012
Exome Aggregation Consortium (ExAC) 0.00013
Links
ClinGen: CA261425
dbSNP: rs397516427
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 Nov 26, 2019 RCV000675123.3
Likely pathogenic 1 criteria provided, single submitter Mar 22, 2012 RCV000036476.2
Likely pathogenic 1 criteria provided, single submitter Oct 1, 2017 RCV000585409.3
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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
748 824

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 26, 2019)
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: SCV001245156.1
Submitted: (Feb 07, 2020)
Evidence details
Publications
PubMed (2)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.2145G>T (p.Lys715Asn) variant in SLC26A4 has been identified in 0.06777% (95% CI of 29/30610) of South Asian chromosomes in gnomAD. The p.Lys715Asn variant has … (more)
Likely pathogenic
(Apr 12, 2021)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: germline
Department of Otolaryngology – Head & Neck Surgery,Cochlear Implant Center
Accession: SCV001571754.2
Submitted: (Aug 17, 2021)
Evidence details
Comment:
PS1_Strong, PM2_Supporting, BP4_Supporting
Likely pathogenic
(Oct 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000693248.10
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Apr 10, 2018)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: unknown
Counsyl
Accession: SCV000800691.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (5)
Likely pathogenic
(Mar 22, 2012)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000060131.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (2)
Comment:
The Lys715Asn variant in SLC26A4 has been reported in a heterozygous state in th ree probands with hearing loss and was absent from 100 control … (more)

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
Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Sloan-Heggen CM Human genetics 2016 PMID: 26969326
Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran. Sloan-Heggen CM Journal of medical genetics 2015 PMID: 26445815
Spectrum and frequency of GJB2, GJB6 and SLC26A4 gene mutations among nonsyndromic hearing loss patients in eastern part of India. Adhikary B Gene 2015 PMID: 26188157
Distinct and novel SLC26A4/Pendrin mutations in Chinese and U.S. patients with nonsyndromic hearing loss. Dai P Physiological genomics 2009 PMID: 19509082
SLC26A4 mutation spectrum associated with DFNB4 deafness and Pendred's syndrome in Pakistanis. Anwar S Journal of human genetics 2009 PMID: 19287372
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/b6f4c008-3e27-485a-bddb-183a7f974693 - - - -

Text-mined citations for rs397516427...

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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 Oct 07, 2021