ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.1561G>A (p.Val521Met)

gnomAD frequency: 0.00003  dbSNP: rs139902461
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001563571 SCV001786541 uncertain significance not provided 2021-02-02 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV002405249 SCV002708724 uncertain significance Inborn genetic diseases 2014-07-25 criteria provided, single submitter clinical testing The p.V521M variant (also known as c.1561G>A), located in coding exon 5 of the ATP7A gene, results from a G to A substitution at nucleotide position 1561. The valine at codon 521 is replaced by methionine, an amino acid with highly similar properties. This variant was previously reported in the SNPDatabase as rs139902461. Based on data from the 1000 Genomes Project, the A allele has an overall frequency of approximately 0% (0/503) total male alleles studied.. Based on data from the NHLBI Exome Sequencing Project (ESP), the A allele was absent out of 2440 total male alleles studied. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
Invitae RCV002569018 SCV003302853 likely benign Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2023-11-17 criteria provided, single submitter clinical testing
Natera, Inc. RCV001836449 SCV002089055 uncertain significance Menkes kinky-hair syndrome 2020-09-24 no assertion criteria provided clinical testing

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