NM_000441.2(SLC26A4):c.1615-2A>G AND Autosomal recessive nonsyndromic hearing loss 4

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Sep 5, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001335321.4

Allele description [Variation Report for NM_000441.2(SLC26A4):c.1615-2A>G]

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

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.1615-2A>G

HGVS:

NC_000007.14:g.107700081A>G
NG_008489.1:g.44447A>G
NM_000441.2:c.1615-2A>GMANE SELECT
NC_000007.13:g.107340526A>G
NM_000441.1:c.1615-2A>G

Links:

dbSNP: rs758823761

NCBI 1000 Genomes Browser:

rs758823761

Molecular consequence:

NM_000441.2:c.1615-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Autosomal recessive nonsyndromic hearing loss 4 (DFNB4)
Synonyms:: NEUROSENSORY NONSYNDROMIC RECESSIVE DEAFNESS 4; DEAFNESS, AUTOSOMAL RECESSIVE 4, WITH ENLARGED VESTIBULAR AQUEDUCT, DIGENIC; Nonsyndromic enlarged vestibular aqueduct (NSEVA); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010933; MedGen: C3538946; Orphanet: 90636; OMIM: 600791

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Gene Links for GEO Profiles (Select 132290864) (1)
Gene
GRM7 glutamate metabotropic receptor 7 [Homo sapiens]
GRM7 glutamate metabotropic receptor 7 [Homo sapiens]
Gene ID:2917

Gene
txid83485[Organism:noexp] (296)
SRA
Gene Links for Nucleotide (Select 158258101) (1)
Gene
CLCNKB chloride voltage-gated channel Kb [Homo sapiens]
CLCNKB chloride voltage-gated channel Kb [Homo sapiens]
Gene ID:1188

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001528448	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 18, 2018)	maternal	clinical testing	PubMed (3) [See all records that cite these PMIDs] 21416585, 24224479, 25741868
SCV001792215	Otorhinolaryngology Lab - LIM32, University of Sao Paulo School of Medicine Clinics Hospital	criteria provided, single submitter (ClinGen HL ACMG Specifications v1)	Likely pathogenic	germline	research	PubMed (2) [See all records that cite these PMIDs] 30311386, 34599368
SCV002026953	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001528448

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 18, 2018)

maternal

clinical testing

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

SCV001792215

Otorhinolaryngology Lab - LIM32, University of Sao Paulo School of Medicine Clinics Hospital

criteria provided, single submitter

(ClinGen HL ACMG Specifications v1)

Likely pathogenic

germline

research

PubMed (2)
[See all records that cite these PMIDs]

SCV002026953

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 5, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	yes	research

Citations

PubMed

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, Matos TD, Marques MC, Dias O, Andrea M, Barreiros E, Barreiros L, Moreno F, Fialho G, Caria H, Del Castillo I.

Am J Med Genet A. 2011 Apr;155A(4):924-7. doi: 10.1002/ajmg.a.33740. Epub 2011 Mar 17. No abstract available.

PubMed [citation]

PMID:: 21416585

Analysis of the thyroid phenotype in 42 patients with Pendred syndrome and nonsyndromic enlargement of the vestibular aqueduct.

Ladsous M, Vlaeminck-Guillem V, Dumur V, Vincent C, Dubrulle F, Dhaenens CM, Wémeau JL.

Thyroid. 2014 Apr;24(4):639-48. doi: 10.1089/thy.2013.0164. Epub 2014 Jan 20.

PubMed [citation]

PMID:: 24224479

See all PubMed Citations (5)

Details of each submission

From Baylor Genetics, SCV001528448.1

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

Description

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 21416585, 24224479]

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

From Otorhinolaryngology Lab - LIM32, University of Sao Paulo School of Medicine Clinics Hospital, SCV001792215.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	yes	research	PubMed (2)

Description

in compound heterozygosis with the c.481T>A variant in a subject with bilateral non-syndromic sensorineural prelingual hearing loss (familial)

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

From Genome-Nilou Lab, SCV002026953.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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