ClinVar Miner

Submissions for variant NM_006517.5(SLC16A2):c.576-1G>A

dbSNP: rs886042238
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000331950 SCV000332809 pathogenic not provided 2015-07-09 criteria provided, single submitter clinical testing
Invitae RCV001378271 SCV001575808 likely pathogenic Spastic paraplegia 2020-06-26 criteria provided, single submitter clinical testing 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. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SLC16A2 are known to be pathogenic (PMID: 20083155, 25527620). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Disruption of this splice site (also known as EX3-1G>C) has been observed in individual(s) with clinical features of X-linked SLC16A2-specific thyroid hormone cell transporter deficiency (PMID: 16957765). ClinVar contains an entry for this variant (Variation ID: 281817). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 2 of the SLC16A2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

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