ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.1933C>T (p.Arg645Ter) (rs72554640)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000193235 SCV000246657 pathogenic Menkes kinky-hair syndrome 2013-02-08 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000757017 SCV000885042 pathogenic not provided 2017-08-16 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000193235 SCV001338560 pathogenic Menkes kinky-hair syndrome 2020-04-03 criteria provided, single submitter clinical testing Variant summary: ATP7A c.1933C>T (p.Arg645X) 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. The variant was absent in 183238 control chromosomes (gnomAD). c.1933C>T has been reported in the literature in multiple individuals affected with Menkes kinky-hair syndrome (e.g. Das_1994, Hahn_2001, Mohamed_2015, Tumer_1997). These data indicate that the variant is very likely to be associated with disease. Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000193235 SCV000844970 pathogenic Menkes kinky-hair syndrome 2018-09-18 no assertion criteria provided clinical testing The observed variant c.1933C>T has not been reported in 1000 Genomes and ExAC databases. The in silico prediction of the given variant is damaging by MutationTaster2 and LRT.

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