ClinVar Miner

Submissions for variant NM_003982.4(SLC7A7):c.149T>A (p.Met50Lys)

dbSNP: rs386833811
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000049776 SCV000746726 likely pathogenic Lysinuric protein intolerance 2020-05-03 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000049776 SCV002500800 likely pathogenic Lysinuric protein intolerance 2022-03-31 criteria provided, single submitter clinical testing Variant summary: SLC7A7 c.149T>A (p.Met50Lys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251180 control chromosomes (gnomAD). The variant, c.149T>A, has been reported in the literature in at least one patient affected with Lysinuric Protein Intolerance as a paternally inherited variant, where the variant in trans was not identified (Palacin_2001, Sperandeo_2005, Sperandeo_2008, Barilli_2010, Barilli_2012). Publications also reported experimental evidence evaluating an impact on protein function, and demonstrated that the variant abolished the transport activities (Sperandeo_2005), in addition, transport defects and other functional disturbances were also demonstrated in patient derived cells (Barilli_2010, Barilli_2012). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049776 SCV000082183 probable-pathogenic Lysinuric protein intolerance no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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