ClinVar Miner

Submissions for variant NM_000441.2(SLC26A4):c.1437+2T>G

dbSNP: rs397516418
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000036442 SCV000060097 pathogenic Rare genetic deafness 2012-07-25 criteria provided, single submitter clinical testing The 1437+2T>G variant in SLC26A4 has not been reported in the literature nor pre viously identified by our laboratory. This variant occurs in the invariant regio n (+/- 1/2) of the splice consensus sequence and is predicted to cause altered s plicing leading to an abnormal or absent protein. In summary, this variant meets our criteria to be classified as pathogenic (http://pcpgm.partners.org/LMM).
Counsyl RCV000410548 SCV000486196 likely pathogenic Pendred syndrome 2016-04-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001056726 SCV001221188 likely pathogenic not provided 2023-07-08 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 12 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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC26A4-related conditions. ClinVar contains an entry for this variant (Variation ID: 43508). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Genome-Nilou Lab RCV001785460 SCV002026932 likely pathogenic Autosomal recessive nonsyndromic hearing loss 4 2021-09-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000410548 SCV002026933 likely pathogenic Pendred syndrome 2021-09-05 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004528182 SCV004112657 likely pathogenic SLC26A4-related disorder 2023-08-22 criteria provided, single submitter clinical testing The SLC26A4 c.1437+2T>G variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature or a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Variants that disrupt the consensus splice donor site in SLC26A4 are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Baylor Genetics RCV001785460 SCV004201930 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2023-05-25 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005031471 SCV005673633 likely pathogenic Autosomal recessive nonsyndromic hearing loss 4; Pendred syndrome 2024-02-07 criteria provided, single submitter clinical testing

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