ClinVar Miner

Submissions for variant NM_012434.5(SLC17A5):c.291G>A (p.Thr97=)

gnomAD frequency: 0.00002  dbSNP: rs386833990
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000426686 SCV000517211 likely pathogenic not provided 2020-05-28 criteria provided, single submitter clinical testing In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 20101035, 25085675, 15172001, 28662915, 28771251)
Counsyl RCV000049967 SCV000794171 likely pathogenic Salla disease 2017-09-18 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000049967 SCV001588446 pathogenic Salla disease 2023-12-26 criteria provided, single submitter clinical testing This sequence change affects codon 97 of the SLC17A5 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SLC17A5 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs386833990, gnomAD 0.004%). This variant has been observed in individual(s) with free sialic acid storage disease (PMID: 28662915, 28771251). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56554). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in deletion of the 197 bases of exon 2 and introduces a premature termination codon (PMID: 15172001). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab RCV000049967 SCV002027581 likely pathogenic Salla disease 2021-09-05 criteria provided, single submitter clinical testing
Baylor Genetics RCV000049967 SCV004201212 pathogenic Salla disease 2024-03-21 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000426686 SCV004226560 likely pathogenic not provided 2022-08-24 criteria provided, single submitter clinical testing PP4, PM2, PM3_strong
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049967 SCV000082376 probable-pathogenic Salla disease no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Natera, Inc. RCV000049967 SCV001453516 pathogenic Salla disease 2020-09-16 no assertion criteria provided clinical testing

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