Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000441.2(SLC26A4):c.1225C>T (p.Arg409Cys)

Help
Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Jul 10, 2019
Accession:
VCV000371421.5
Variation ID:
371421
Description:
single nucleotide variant
Help

NM_000441.2(SLC26A4):c.1225C>T (p.Arg409Cys)

Allele ID
357540
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107690199 (GRCh38) GRCh38 UCSC
7: 107330644 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107330644C>T
NC_000007.14:g.107690199C>T
NG_008489.1:g.34565C>T
NM_000441.2:c.1225C>T MANE Select NP_000432.1:p.Arg409Cys missense
Protein change
R409C
Other names
-
Canonical SPDI
NC_000007.14:107690198:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA4432722
dbSNP: rs147952620
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Sep 22, 2016 RCV000411132.1
Pathogenic 1 criteria provided, single submitter Jul 10, 2019 RCV000811142.3
Likely pathogenic 1 no assertion criteria provided Feb 26, 2019 RCV000770861.1
Help
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

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Sep 22, 2016)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: unknown
Counsyl
Accession: SCV000486998.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (5)
Pathogenic
(Jul 10, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000951393.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change replaces arginine with cysteine at codon 409 of the SLC26A4 protein (p.Arg409Cys). The arginine residue is highly conserved and there is a … (more)
Likely pathogenic
(Feb 26, 2019)
no assertion criteria provided
Method: case-control
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: inherited
Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery,Institute of Otolaryngology, Chinese PLA General Hospital
Accession: SCV000902369.1
Submitted: (Apr 29, 2019)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
KCNJ10 may not be a contributor to nonsyndromic enlargement of vestibular aqueduct (NSEVA) in Chinese subjects. Zhao J PloS one 2014 PMID: 25372295
Analysis of the thyroid phenotype in 42 patients with Pendred syndrome and nonsyndromic enlargement of the vestibular aqueduct. Ladsous M Thyroid : official journal of the American Thyroid Association 2014 PMID: 24224479
Molecular etiology of hearing impairment associated with nonsyndromic enlarged vestibular aqueduct in East China. Chai Y American journal of medical genetics. Part A 2013 PMID: 23918157
Molecular epidemiology and functional assessment of novel allelic variants of SLC26A4 in non-syndromic hearing loss patients with enlarged vestibular aqueduct in China. Yuan Y PloS one 2012 PMID: 23185506
Extremely discrepant mutation spectrum of SLC26A4 between Chinese patients with isolated Mondini deformity and enlarged vestibular aqueduct. Huang S Journal of translational medicine 2011 PMID: 21961810
Phenotypic analyses and mutation screening of the SLC26A4 and FOXI1 genes in 101 Taiwanese families with bilateral nonsyndromic enlarged vestibular aqueduct (DFNB4) or Pendred syndrome. Wu CC Audiology & neuro-otology 2010 PMID: 19648736
Mutation analysis of SLC26A4 in mainland Chinese patients with enlarged vestibular aqueduct. Reyes S Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery 2009 PMID: 19786220
[Screening of SLC26A4 (PDS) gene mutation in cochlear implant recipients with inner ear malformation]. Chen DY Zhonghua yi xue za zhi 2007 PMID: 18167283
Two frequent missense mutations in Pendred syndrome. Van Hauwe P Human molecular genetics 1998 PMID: 9618166

Text-mined citations for rs147952620...

Help
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 08, 2021