ClinVar Miner

Submissions for variant NM_014270.5(SLC7A9):c.1399+2dup (rs755715459)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001054684 SCV001219032 uncertain significance not provided 2019-01-28 criteria provided, single submitter clinical testing This sequence change falls in intron 12 of the SLC7A9 gene. It does not directly change the encoded amino acid sequence of the SLC7A9 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs755715459, ExAC 0.01%). This variant has been reported in combination with another SLC7A9 variant in an individual affected with cystinuria (PMID: 16374432). This variant has also been observed as heterozygous in a family and an individual with cystinuria, in whom the second allele was not identified (PMID: 16374432, Invitae). This variant is also known as IVS12+3insT in the literature. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
The Laboratory of Genetics and Metabolism, Hunan Children’s Hospital RCV000991119 SCV001142196 pathogenic Cystine urolithiasis no assertion criteria provided research

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