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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003841766	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 23, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15679828, 31387071, 25741868
SCV004201943	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 19, 2023)	unknown	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

SCV003841766

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 23, 2023)

unknown

clinical testing

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

SCV004201943

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 19, 2023)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

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

From Baylor Genetics, SCV004201943.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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