ClinVar Miner

Submissions for variant NM_030777.4(SLC2A10):c.1411+2T>A

gnomAD frequency: 0.00011  dbSNP: rs761721442
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000197685 SCV000250742 likely pathogenic not provided 2017-12-12 criteria provided, single submitter clinical testing The c.1411+2T>A variant in the SLC2A10 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This splice site variant destroys the canonical splice donor site in intron 3, which is predicted to cause abnormal gene splicing. The c.1411+2T>A variant is observed in 10/24,038 (0.04%) alleles from individuals of African background in large population cohorts (Lek et al., 2016). We interpret c.1411+2T>A as a likely pathogenic variant.
Revvity Omics, Revvity RCV001781572 SCV002023548 likely pathogenic Arterial tortuosity syndrome 2020-06-12 criteria provided, single submitter clinical testing
AiLife Diagnostics, AiLife Diagnostics RCV000197685 SCV002503049 likely pathogenic not provided 2021-12-27 criteria provided, single submitter clinical testing
Invitae RCV001781572 SCV002965261 likely pathogenic Arterial tortuosity syndrome 2024-01-18 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 3 of the SLC2A10 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 SLC2A10 are known to be pathogenic (PMID: 17935213, 22488877, 23494979). This variant is present in population databases (rs761721442, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SLC2A10-related conditions. ClinVar contains an entry for this variant (Variation ID: 213751). 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.

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