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NM_000441.2(SLC26A4):c.1437+2T>G

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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:
Nov 19, 2019
Accession:
VCV000043508.4
Variation ID:
43508
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.1437+2T>G

Allele ID
52678
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107694718 (GRCh38) GRCh38 UCSC
7: 107335163 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107335163T>G
NC_000007.14:g.107694718T>G
NM_000441.2:c.1437+2T>G MANE Select splice donor
NG_008489.1:g.39084T>G
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:107694717:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA261412
dbSNP: rs397516418
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 Jul 25, 2012 RCV000036442.2
Likely pathogenic 1 criteria provided, single submitter Apr 13, 2016 RCV000410548.1
Likely pathogenic 1 criteria provided, single submitter Nov 19, 2019 RCV001056726.2
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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
(Apr 13, 2016)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: unknown
Counsyl
Accession: SCV000486196.1
Submitted: (Nov 23, 2016)
Evidence details
Pathogenic
(Jul 25, 2012)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000060097.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
The 1437+2T>G variant in SLC26A4 has not been reported in the literature nor pre viously identified by our laboratory. This variant occurs in the invariant … (more)
Likely pathogenic
(Nov 19, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001221188.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change affects a donor splice site in intron 12 of the SLC26A4 gene. It is expected to disrupt RNA splicing and likely results … (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
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
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

Text-mined citations for rs397516418...

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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 Jul 07, 2021