ClinVar Miner

Submissions for variant NM_006996.3(SLC19A2):c.807+2T>G

dbSNP: rs1234256852
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000498583 SCV000589788 likely pathogenic not provided 2017-11-01 criteria provided, single submitter clinical testing The c.807+2 T>G splice site variant in the SLC19A2 gene destroys the canonical splice donor site in intron 2. 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. Although this variant has not been previously reported to our knowledge, it is predicted to be a likely pathogenic variant.
Fulgent Genetics, Fulgent Genetics RCV000762862 SCV000893232 likely pathogenic Megaloblastic anemia, thiamine-responsive, with diabetes mellitus and sensorineural deafness 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000498583 SCV004323093 likely pathogenic not provided 2023-12-23 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 of the SLC19A2 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 SLC19A2 are known to be pathogenic (PMID: 10391221, 10391223, 10874303). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SLC19A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 432105). 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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