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NM_000441.2(SLC26A4):c.416-1G>A

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
3 (Most recent: Sep 24, 2021)
Last evaluated:
May 19, 2021
Accession:
VCV000371079.5
Variation ID:
371079
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.416-1G>A

Allele ID
357530
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107674163 (GRCh38) GRCh38 UCSC
7: 107314608 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107314608G>A
NC_000007.14:g.107674163G>A
NG_008489.1:g.18529G>A
NM_000441.2:c.416-1G>A MANE Select splice acceptor
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:107674162:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Links
ClinGen: CA16041102
dbSNP: rs1057516988
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 May 19, 2021 RCV000579267.2
Pathogenic 2 no assertion criteria provided Sep 16, 2020 RCV000410577.2
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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
748 824

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 19, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000680758.1
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed … (more)
Pathogenic
(Jun 22, 2016)
no assertion criteria provided
Method: clinical testing
Pendred syndrome
Allele origin: unknown
Counsyl
Accession: SCV000486551.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (4)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Pendred syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001455797.1
Submitted: (Dec 28, 2020)
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
Mono-allelic mutations of SLC26A4 is over-presented in deaf patients with non-syndromic enlarged vestibular aqueduct. Pang X International journal of pediatric otorhinolaryngology 2015 PMID: 26100058
Mutation spectrum and genotype-phenotype correlation of hearing loss patients caused by SLC26A4 mutations in the Japanese: a large cohort study. Miyagawa M Journal of human genetics 2014 PMID: 24599119
Pendred syndrome in two Galician families: insights into clinical phenotypes through cellular, genetic, and molecular studies. Palos F The Journal of clinical endocrinology and metabolism 2008 PMID: 17940114
Two common and three novel PDS mutations in Thai patients with Pendred syndrome. Snabboon T Journal of endocrinological investigation 2007 PMID: 18250610

Text-mined citations for rs1057516988...

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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