ClinVar Miner

Submissions for variant NM_012434.5(SLC17A5):c.1016G>A (p.Trp339Ter)

gnomAD frequency: 0.00001  dbSNP: rs1057516910
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410279 SCV000486419 likely pathogenic Salla disease 2016-05-26 criteria provided, single submitter clinical testing
Baylor Genetics RCV000410279 SCV001525424 pathogenic Salla disease 2024-03-24 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000410279 SCV002027571 likely pathogenic Salla disease 2021-09-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000410279 SCV002230080 pathogenic Salla disease 2022-11-06 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 370976). This premature translational stop signal has been observed in individual(s) with sialic acid storage disease (PMID: 15805149). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Trp339*) in the SLC17A5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC17A5 are known to be pathogenic (PMID: 10581036, 10947946, 15172001).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000410279 SCV003845172 pathogenic Salla disease 2023-02-24 criteria provided, single submitter clinical testing Variant summary: SLC17A5 c.1016G>A (p.Trp339X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 4e-06 in 251350 control chromosomes (gnomAD). c.1016G>A has been reported in the literature in individuals affected with Sialic Acid Storage Disorder (example: Froissart_2005). These data indicate that the variant is very likely to be associated with disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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