ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.1618C>G (p.Pro540Ala)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002401012 SCV002708002 uncertain significance Inborn genetic diseases 2019-09-26 criteria provided, single submitter clinical testing The p.P540A variant (also known as c.1618C>G), located in coding exon 5 of the ATP7A gene, results from a C to G substitution at nucleotide position 1618. The proline at codon 540 is replaced by alanine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV003097014 SCV003487982 likely benign Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2023-05-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003988006 SCV004804219 uncertain significance not specified 2024-01-08 criteria provided, single submitter clinical testing Variant summary: ATP7A c.1618C>G (p.Pro540Ala) results in a non-conservative amino acid change located in the Heavy metal-associated domain, HMA (IPR006121) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 1.1e-05 in 183475 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1618C>G in individuals affected with Menkes Kinky-Hair Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1776536). Based on the evidence outlined above, the variant was classified as uncertain significance.

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