NM_000441.2(SLC26A4):c.2089+1G>A AND Rare genetic deafness

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 11, 2014
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000151908.4

Allele description [Variation Report for NM_000441.2(SLC26A4):c.2089+1G>A]

NM_000441.2(SLC26A4):c.2089+1G>A

Gene:

SLC26A4:solute carrier family 26 member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q22.3

Genomic location:

Preferred name:

NM_000441.2(SLC26A4):c.2089+1G>A

HGVS:

NC_000007.14:g.107704386G>A
NG_008489.1:g.48752G>A
NM_000441.2:c.2089+1G>AMANE SELECT
NC_000007.13:g.107344831G>A
NM_000441.1:c.2089+1G>A

Links:

dbSNP: rs727503430

NCBI 1000 Genomes Browser:

rs727503430

Molecular consequence:

NM_000441.2:c.2089+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

Name:: Rare genetic deafness
Identifiers:: MedGen: C5680250; Orphanet: 96210

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000200416	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Pathogenic (Apr 11, 2014)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17876604, 15355436, 24033266

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000200416

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Pathogenic
(Apr 11, 2014)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Pendred syndrome among patients with congenital hypothyroidism detected by neonatal screening: identification of two novel PDS/SLC26A4 mutations.

Banghova K, Al Taji E, Cinek O, Novotna D, Pourova R, Zapletalova J, Hnikova O, Lebl J.

Eur J Pediatr. 2008 Jul;167(7):777-83. Epub 2007 Sep 18.

PubMed [citation]

PMID:: 17876604

Screening of SLC26A4 (PDS) gene in Pendred's syndrome: a large spectrum of mutations in France and phenotypic heterogeneity.

Blons H, Feldmann D, Duval V, Messaz O, Denoyelle F, Loundon N, Sergout-Allaoui A, Houang M, Duriez F, Lacombe D, Delobel B, Leman J, Catros H, Journel H, Drouin-Garraud V, Obstoy MF, Toutain A, Oden S, Toublanc JE, Couderc R, Petit C, Garabédian EN, et al.

Clin Genet. 2004 Oct;66(4):333-40.

PubMed [citation]

PMID:: 15355436

See all PubMed Citations (3)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000200416.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (3)

Description

The 2089+1G>A variant in SLC26A4 has been previously identified in two individua ls with Pendred syndrome and segregated with disease in an affected sibling of one of these individuals (Blons 2004, Banghova 2008). This variant was absent fr om large population studies. The variant occurs in the invariant region (+1/2) o f the 5? splice consensus sequence and is predicted to cause altered splicing le ading to an abnormal or absent protein. In summary, this variant meets our crite ria to be classified as pathogenic (http://pcpgm.partners.org/LMM).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

Last Updated: Jun 29, 2025

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