ClinVar Miner

Submissions for variant NM_012434.5(SLC17A5):c.507del (p.Ala169_Leu170insTer)

gnomAD frequency: 0.00002  dbSNP: rs386833992
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000049969 SCV000699339 likely pathogenic Salla disease 2021-01-04 criteria provided, single submitter clinical testing Variant summary: SLC17A5 c.507delA (p.Leu170X) 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 1.6e-05 in 250998 control chromosomes. c.507delA has been reported in the literature in at least one individual affected with Sialic Acid Storage Disorder (Aula_2006). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae RCV000049969 SCV001581161 pathogenic Salla disease 2023-09-04 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu170*) 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). This variant is present in population databases (rs386833992, gnomAD 0.003%). This premature translational stop signal has been observed in individuals with SLC17A5-related conditions (PMID: 12592494, 16715535, 28662915). ClinVar contains an entry for this variant (Variation ID: 56556). For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab RCV000049969 SCV002027578 pathogenic Salla disease 2021-09-05 criteria provided, single submitter clinical testing
Baylor Genetics RCV000049969 SCV004201230 pathogenic Salla disease 2023-06-08 criteria provided, single submitter clinical testing
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049969 SCV000082378 probable-pathogenic Salla disease no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Counsyl RCV000049969 SCV000220348 pathogenic Salla disease 2018-02-27 no assertion criteria provided clinical testing

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