ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.1870-1G>C

dbSNP: rs797045338
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000195126 SCV000246653 pathogenic Menkes kinky-hair syndrome 2013-02-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003765212 SCV004571516 pathogenic Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2023-03-12 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 210401). Disruption of this splice site has been observed in individuals with Menkes disease (MD) (PMID: 8981948, 21494555). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 7 of the ATP7A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ATP7A are known to be pathogenic (PMID: 11241493, 20652413).
Clinical Genetics Laboratory, Skane University Hospital Lund RCV004696867 SCV005199646 pathogenic not provided 2023-09-15 criteria provided, single submitter clinical testing
GeneDx RCV004696867 SCV005201694 pathogenic not provided 2023-07-28 criteria provided, single submitter clinical testing Reported previously in a patient with classic Menkes disease; parental testing not performed (Tumer et al., 1997); Published functional studies in vivo demonstrated that the variant created a cryptic splice site resulting in a frameshift; wildtype transcript was not identified (Skjorringe et al., 2011); Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 8981948, 21494555)
Inherited Neuropathy Consortium Ii, University Of Miami RCV000195126 SCV004011890 uncertain significance Menkes kinky-hair syndrome 2016-01-06 no assertion criteria provided literature only

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.