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NM_000441.2(SLC26A4):c.754T>C (p.Ser252Pro)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Apr 28, 2021)
Last evaluated:
Mar 26, 2020
Accession:
VCV001065210.2
Variation ID:
1065210
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.754T>C (p.Ser252Pro)

Allele ID
1053520
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107675098 (GRCh38) GRCh38 UCSC
7: 107315543 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107315543T>C
NC_000007.14:g.107675098T>C
NG_008489.1:g.19464T>C
NM_000441.2:c.754T>C MANE Select NP_000432.1:p.Ser252Pro missense
Protein change
S252P
Other names
-
Canonical SPDI
NC_000007.14:107675097:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Mar 26, 2020 RCV001381508.1
Pathogenic 1 no assertion criteria provided - RCV001375686.1
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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
748 824

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Mar 26, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001579940.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (8)
Comment:
This sequence change replaces serine with proline at codon 252 of the SLC26A4 protein (p.Ser252Pro). The serine residue is highly conserved and there is a … (more)
Pathogenic
(-)
no assertion criteria provided
Method: research
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: germline
Precision Medicine Center,Zhengzhou University
Accession: SCV001572607.1
Submitted: (Apr 28, 2021)
Evidence details
Comment:
PM2: gnomAD genomes East Asian allele frequency =0.00005437<0.00007 PM3_VeryStrong: Pathogenic mutation confirmed in trans in five patients PP3: REVEL score >0.7 PP4: Patient's phenotype highly … (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
Mutation Spectrum of Common Deafness-Causing Genes in Patients with Non-Syndromic Deafness in the Xiamen Area, China. Jiang Y PloS one 2015 PMID: 26252218
Developing regional genetic counseling for southern Chinese with nonsyndromic hearing impairment: a unique mutational spectrum. Chen K Journal of translational medicine 2014 PMID: 24612839
Genetic mutations in nonsyndromic deafness patients of Chinese minority and Han ethnicities in Yunnan, China. Xin F Journal of translational medicine 2013 PMID: 24341454
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
Mutational analysis of the SLC26A4 gene in Chinese sporadic nonsyndromic hearing-impaired children. Hu X International journal of pediatric otorhinolaryngology 2012 PMID: 22796198
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
[An investigation of SLC26A4 gene mutation in nonsydromic hearing impairment in Hunan province of China]. Jiang L Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology, head, and neck surgery 2010 PMID: 20842945
Origins and frequencies of SLC26A4 (PDS) mutations in east and south Asians: global implications for the epidemiology of deafness. Park HJ Journal of medical genetics 2003 PMID: 12676893

Record last updated Oct 08, 2021