ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.4005+1G>T

dbSNP: rs797045391
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000193560 SCV000246726 pathogenic Menkes kinky-hair syndrome 2013-02-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001852548 SCV002307899 likely pathogenic Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2022-10-31 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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: 210468). Disruption of this splice site has been observed in individual(s) with Menkes disease (PMID: 21494555). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 20 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).
Inherited Neuropathy Consortium Ii, University Of Miami RCV000193560 SCV004011847 uncertain significance Menkes kinky-hair syndrome 2016-01-06 no assertion criteria provided literature only

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