NM_000441.2(SLC26A4):c.1195T>C (p.Ser399Pro) AND Deafness, autosomal recessive 4, with enlarged vestibular aqueduct

Clinical significance:Uncertain significance (Last evaluated: Jul 22, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV001004635.4

Allele description [Variation Report for NM_000441.2(SLC26A4):c.1195T>C (p.Ser399Pro)]

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

Gene:
SLC26A4:solute carrier family 26 member 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q22.3
Genomic location:
Preferred name:
NM_000441.2(SLC26A4):c.1195T>C (p.Ser399Pro)
HGVS:
  • NC_000007.14:g.107690169T>C
  • NG_008489.1:g.34535T>C
  • NM_000441.2:c.1195T>CMANE SELECT
  • NP_000432.1:p.Ser399Pro
  • NC_000007.13:g.107330614T>C
  • NM_000441.1:c.1195T>C
  • p.Ser399Pro
Protein change:
S399P
Links:
dbSNP: rs747431002
NCBI 1000 Genomes Browser:
rs747431002
Molecular consequence:
  • NM_000441.2:c.1195T>C - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
loss_of_function_variant [Sequence Ontology: SO:0002054]

Condition(s)

Name:
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct (DFNB4)
Synonyms:
NEUROSENSORY NONSYNDROMIC RECESSIVE DEAFNESS 4; DEAFNESS, AUTOSOMAL RECESSIVE 4, WITH ENLARGED VESTIBULAR AQUEDUCT, DIGENIC; Nonsyndromic enlarged vestibular aqueduct (NSEVA); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010933; MedGen: C3538946; Orphanet: 90636; OMIM: 600791

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000994883National Institute of Sensory Organs,National Hospital Organization Tokyo Medical Center

See additional submitters

no assertion criteria providedAffects
(Aug 20, 2019)
germlineliterature only, in vitro

PubMed (3)
[See all records that cite these PMIDs]

SCV001323033Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001806725Nilou-Genome Labcriteria provided, single submitter
Uncertain significance
(Jul 22, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedin vitro
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only, clinical testing

Citations

PubMed

Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain.

Bassot C, Minervini G, Leonardi E, Tosatto SC.

Biochimie. 2017 Jan;132:109-120. doi: 10.1016/j.biochi.2016.10.002. Epub 2016 Oct 19.

PubMed [citation]
PMID:
27771369

Systematic quantification of the anion transport function of pendrin (SLC26A4) and its disease-associated variants.

Wasano K, Takahashi S, Rosenberg SK, Kojima T, Mutai H, Matsunaga T, Ogawa K, Homma K.

Hum Mutat. 2020 Jan;41(1):316-331. doi: 10.1002/humu.23930. Epub 2019 Oct 26.

PubMed [citation]
PMID:
31599023
PMCID:
PMC6930342
See all PubMed Citations (4)

Details of each submission

From National Institute of Sensory Organs,National Hospital Organization Tokyo Medical Center, SCV000994883.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)
2not providednot providednot providednot providedin vitro PubMed (3)

Description

in vitro experiment

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided
2germlineyesnot providednot providedassert pathogenicitynot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001323033.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Nilou-Genome Lab, SCV001806725.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2021

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