ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.2172+5G>A

dbSNP: rs797045347
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002049796 SCV002111194 likely pathogenic Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2022-08-08 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 9 of the ATP7A gene. It does not directly change the encoded amino acid sequence of the ATP7A protein. It affects a nucleotide within the consensus splice site. 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. This variant disrupts the c.2172+5G nucleotide in the ATP7A gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 10319589, 21494555). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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: 1345204). This variant has been observed in individuals with clinical features of Menkes disease (Invitae).

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