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NM_000441.2(SLC26A4):c.1262A>C (p.Gln421Pro)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 20, 2020
Accession:
VCV000556159.3
Variation ID:
556159
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.1262A>C (p.Gln421Pro)

Allele ID
544382
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107690236 (GRCh38) GRCh38 UCSC
7: 107330681 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107330681A>C
NC_000007.14:g.107690236A>C
NG_008489.1:g.34602A>C
NM_000441.2:c.1262A>C MANE Select NP_000432.1:p.Gln421Pro missense
Protein change
Q421P
Other names
-
Canonical SPDI
NC_000007.14:107690235:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
dbSNP: rs201660407
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Jan 22, 2018 RCV000672119.1
Pathogenic 1 criteria provided, single submitter Sep 20, 2020 RCV001386692.1
Likely pathogenic 1 no assertion criteria provided Feb 26, 2019 RCV000770862.1
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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
Likely pathogenic
(Jan 22, 2018)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: unknown
Counsyl
Accession: SCV000797186.1
Submitted: (Jul 10, 2018)
Evidence details
Pathogenic
(Sep 20, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001587029.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces glutamine with proline at codon 421 of the SLC26A4 protein (p.Gln421Pro). The glutamine 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: SCV000902371.1
Submitted: (Apr 29, 2019)
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
Novel pathogenic variants underlie SLC26A4-related hearing loss in a multiethnic cohort. Cengiz FB International journal of pediatric otorhinolaryngology 2017 PMID: 28964290
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
A distinct spectrum of SLC26A4 mutations in patients with enlarged vestibular aqueduct in China. Wang QJ Clinical genetics 2007 PMID: 17718863

Text-mined citations for rs201660407...

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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 08, 2021