NM_000441.2(SLC26A4):c.1281TGC[1] (p.Ala429del) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Jul 29, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000441.2(SLC26A4):c.1281TGC[1] (p.Ala429del)]

NM_000441.2(SLC26A4):c.1281TGC[1] (p.Ala429del)

SLC26A4:solute carrier family 26 member 4 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_000441.2(SLC26A4):c.1281TGC[1] (p.Ala429del)
  • NC_000007.13:g.107334864_107334866del
  • NC_000007.14:g.107694420TGC[1]
  • NG_008489.1:g.38786TGC[1]
  • NM_000441.2:c.1281TGC[1]MANE SELECT
  • NP_000432.1:p.Ala429del
  • NC_000007.13:g.107334864_107334866del
  • NC_000007.13:g.107334865TGC[1]
  • NC_000007.13:g.107334868_107334870delTGC
  • NM_000441.1:c.1284_1286del
  • NM_000441.1:c.1284_1286delTGC
  • NM_000441.2:c.1284_1286delTGCMANE SELECT
  • c.1284_1286delTGC
Protein change:
dbSNP: rs111033306
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000441.2:c.1281TGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001381002Invitaecriteria provided, single submitter
Likely pathogenic
(Oct 14, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV001874248GeneDxcriteria provided, single submitter
Likely pathogenic
(Jul 29, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss.

Sloan-Heggen CM, Bierer AO, Shearer AE, Kolbe DL, Nishimura CJ, Frees KL, Ephraim SS, Shibata SB, Booth KT, Campbell CA, Ranum PT, Weaver AE, Black-Ziegelbein EA, Wang D, Azaiez H, Smith RJH.

Hum Genet. 2016 Apr;135(4):441-450. doi: 10.1007/s00439-016-1648-8. Epub 2016 Mar 11.

PubMed [citation]

Identification of SLC26A4 mutations in patients with hearing loss and enlarged vestibular aqueduct using high-resolution melting curve analysis.

Mercer S, Mutton P, Dahl HH.

Genet Test Mol Biomarkers. 2011 May;15(5):365-8. doi: 10.1089/gtmb.2010.0177. Epub 2011 Mar 2.

PubMed [citation]
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001381002.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)


This variant, c.1284_1286del, results in the deletion of 1 amino acid(s) of the SLC26A4 protein (p.Ala429del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs775837019, ExAC 0.01%). This variant has been observed in individuals affected with Pendred syndrome (PMID: 26969326, 21366435, 25394566, 23336812). ClinVar contains an entry for this variant (Variation ID: 43501). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001874248.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


In-frame deletion of one amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 21366435, 25394566, 33199029, 20668687, 23336812, 9618167, 23555729, 26969326, 21704276, 14679580)

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 23, 2021

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