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NM_000441.2(SLC26A4):c.1615-2A>G

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Aug 12, 2021)
Last evaluated:
Jun 3, 2021
Accession:
VCV001033029.6
Variation ID:
1033029
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.1615-2A>G

Allele ID
1020324
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107700081 (GRCh38) GRCh38 UCSC
7: 107340526 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107340526A>G
NC_000007.14:g.107700081A>G
NG_008489.1:g.44447A>G
NM_000441.2:c.1615-2A>G MANE Select splice acceptor
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:107700080:A:G
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/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jan 18, 2018 RCV001335321.2
Pathogenic 2 criteria provided, multiple submitters, no conflicts Jun 3, 2021 RCV001389807.3
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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
Pathogenic
(Jan 18, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Allele origin: maternal
Baylor Genetics
Accession: SCV001528448.1
Submitted: (Mar 05, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported in patients with Pendred syndrome [PMID … (more)
Pathogenic
(Aug 14, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001591288.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change affects an acceptor splice site in intron 14 of the SLC26A4 gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Jun 03, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001780309.1
Submitted: (Aug 10, 2021)
Evidence details
Comment:
Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Not observed at a significant frequency in large population cohorts … (more)
Likely pathogenic
(-)
criteria provided, single submitter
Method: research
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
(Autosomal recessive inheritance)
Allele origin: germline
Otorhinolaryngology Lab - LIM32, University of Sao Paulo School of Medicine Clinics Hospital
Accession: SCV001792215.1
Submitted: (Aug 12, 2021)
Evidence details
Publications
PubMed (1)
Comment:
in compound heterozygosis with the c.481T>A variant in a subject with bilateral non-syndromic sensorineural prelingual hearing loss (familial)

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
Molecular and genetic characterization of a large Brazilian cohort presenting hearing loss. Batissoco AC Human genetics 2021 PMID: 34599368
Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran. Sloan-Heggen CM Journal of medical genetics 2015 PMID: 26445815
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
Evaluation of genotype-phenotype relationships in patients referred for endocrine assessment in suspected Pendred syndrome. Soh LM European journal of endocrinology 2015 PMID: 25394566
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
Novel splice-site mutation c.1615-2A>G (IVS14-2A>G) in the SLC26A4 gene causing Pendred syndrome in a consanguineous Portuguese family. Simões-Teixeira H American journal of medical genetics. Part A 2011 PMID: 21416585
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
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Record last updated Oct 16, 2021