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NM_000441.2(SLC26A4):c.1149+3A>G AND Autosomal recessive nonsyndromic hearing loss 4

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Apr 19, 2023
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:
RCV003152674.2

Allele description [Variation Report for NM_000441.2(SLC26A4):c.1149+3A>G]

NM_000441.2(SLC26A4):c.1149+3A>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.1149+3A>G
HGVS:
  • NC_000007.14:g.107689203A>G
  • NG_008489.1:g.33569A>G
  • NM_000441.2:c.1149+3A>GMANE SELECT
  • NC_000007.13:g.107329648A>G
  • NM_000441.1:c.1149+3A>G
  • c.1149+3A>G
Links:
dbSNP: rs111033314
NCBI 1000 Genomes Browser:
rs111033314
Molecular consequence:
  • NM_000441.2:c.1149+3A>G - intron variant - [Sequence Ontology: SO:0001627]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV0038417663billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 23, 2023)
unknownclinical testing

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

SCV004201943Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 19, 2023)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic basis of hearing loss associated with enlarged vestibular aqueducts in Koreans.

Park HJ, Lee SJ, Jin HS, Lee JO, Go SH, Jang HS, Moon SK, Lee SC, Chun YM, Lee HK, Choi JY, Jung SC, Griffith AJ, Koo SK.

Clin Genet. 2005 Feb;67(2):160-5.

PubMed [citation]
PMID:
15679828

Next generation sequencing study in a cohort of Italian patients with syndromic hearing loss.

Lenarduzzi S, Morgan A, Faletra F, Cappellani S, Morgutti M, Mezzavilla M, Peruzzi A, Ghiselli S, Ambrosetti U, Graziano C, Seri M, Gasparini P, Girotto G.

Hear Res. 2019 Sep 15;381:107769. doi: 10.1016/j.heares.2019.07.006. Epub 2019 Jul 13.

PubMed [citation]
PMID:
31387071
See all PubMed Citations (3)

Details of each submission

From 3billion, SCV003841766.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 15679828, 31387071). The variant has been reported to be associated with SLC26A4 related disorder (ClinVar ID: VCV000043493). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004201943.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024