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NM_000441.2(SLC26A4):c.1195T>C (p.Ser399Pro)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Aug 23, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000554065.7
Variation ID:
554065
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.1195T>C (p.Ser399Pro)

Allele ID
544380
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107690169 (GRCh38) GRCh38 UCSC
7: 107330614 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107330614T>C
NC_000007.14:g.107690169T>C
NG_008489.1:g.34535T>C
NM_000441.2:c.1195T>C MANE Select NP_000432.1:p.Ser399Pro missense
Protein change
S399P
Other names
-
Canonical SPDI
NC_000007.14:107690168:T:C
Functional consequence
loss_of_function_variant [Sequence Ontology SO:0002054]
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00012
The Genome Aggregation Database (gnomAD), exomes 0.00013
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
dbSNP: rs747431002
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 criteria provided, multiple submitters, no conflicts Jul 22, 2021 RCV000669625.3
Uncertain significance 3 criteria provided, multiple submitters, no conflicts Jul 22, 2021 RCV001004635.4
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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 25, 2017)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: unknown
Counsyl
Accession: SCV000794397.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001323032.1
Submitted: (Feb 20, 2020)
Evidence details
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)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001323033.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
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)
Uncertain significance
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806725.1
Submitted: (Aug 23, 2021)
Evidence details
Uncertain significance
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806726.1
Submitted: (Aug 23, 2021)
Evidence details
Affects
(Aug 20, 2019)
no assertion criteria provided
Method: literature only, in vitro
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
(Autosomal recessive inheritance)
Allele origin: germline
National Institute of Sensory Organs,National Hospital Organization Tokyo Medical Center
Additional submitter:
The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders,Northwestern University
Accession: SCV000994883.2
Submitted: (Oct 30, 2019)
Evidence details
Publications
PubMed (3)
Comment:
in vitro experiment

Functional evidence

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Functional consequence Method Result Submitter Supporting information
loss_of_function_variant
  1. Method not provided
  1. HCO3-/Cl- exchange_normal; I-/Cl- exchange_impaired; signal at cell membrane_positive; intracellular puncta_positive; splicing_unaffected
National Institute of Sensory Organs,National Hospital Organization Tokyo Medical Center
Additional submitter:
The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders,Northwestern University
Accession: SCV000994883.2
Submitted: (Oct 30, 2019)
Evidence details
Publications
PubMed (3)

Citations for this variant

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Title Author Journal Year Link
Systematic quantification of the anion transport function of pendrin (SLC26A4) and its disease-associated variants. Wasano K Human mutation 2020 PMID: 31599023
Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain. Bassot C Biochimie 2017 PMID: 27771369
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
Assessment of the genetic causes of recessive childhood non-syndromic deafness in the UK - implications for genetic testing. Hutchin T Clinical genetics 2005 PMID: 16283880

Text-mined citations for rs747431002...

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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 Sep 29, 2021