NM_000441.2(SLC26A4):c.2089+1G>A AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 5, 2024
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:: RCV000492847.9

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]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000582142	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (May 3, 2017)	germline	clinical testing	Citation Link,
SCV000944137	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 5, 2024)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 16199547, 16283880, 25394566, 26252218, 26445815, 2422447, 15355436, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000582142

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(May 3, 2017)

germline

clinical testing

Citation Link,

SCV000944137

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 5, 2024)

germline

clinical testing

PubMed (8)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Assessment of the genetic causes of recessive childhood non-syndromic deafness in the UK - implications for genetic testing.

Hutchin T, Coy NN, Conlon H, Telford E, Bromelow K, Blaydon D, Taylor G, Coghill E, Brown S, Trembath R, Liu XZ, Bitner-Glindzicz M, Mueller R.

Clin Genet. 2005 Dec;68(6):506-12.

PubMed [citation]

PMID:: 16283880

See all PubMed Citations (8)

Details of each submission

From GeneDx, SCV000582142.3

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

Description

The c.2089+1G>A variant in the SLC26A4 gene has been reported previously in the presence of another SLC26A4 variant, in individuals with Pendred syndrome, exhibiting sensorineural hearing loss, vestibular aqueductal enlargement and both with and without thyroid involvement (Blons et al., 2004; Banghova et al., 2008; Ladsous et al., 2014). This splice site variant destroys the canonical splice donor site in intron 18. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.2089+1G>A variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.2089+1G>A as a pathogenic variant.

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

From Invitae, SCV000944137.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

This sequence change affects a donor splice site in intron 18 of the SLC26A4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SLC26A4 are known to be pathogenic (PMID: 16283880, 25394566, 26252218, 26445815). This variant is present in population databases (rs727503430, gnomAD 0.02%). Disruption of this splice site has been observed in individuals with Pendred syndrome (PMID: 2422447, 15355436). ClinVar contains an entry for this variant (Variation ID: 165263). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Apr 6, 2024

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