ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.1721C>T (p.Thr574Met)

gnomAD frequency: 0.00005  dbSNP: rs782076879
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000444044 SCV000532003 uncertain significance not specified 2016-09-28 criteria provided, single submitter clinical testing The T574M variant in the ATP7A gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The T574M variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret T574M as a variant of uncertain significance.
Mayo Clinic Laboratories, Mayo Clinic RCV001508048 SCV001713949 uncertain significance not provided 2021-03-16 criteria provided, single submitter clinical testing
Invitae RCV001861618 SCV002148686 likely benign Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2023-12-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV002402192 SCV002714192 uncertain significance Inborn genetic diseases 2021-01-25 criteria provided, single submitter clinical testing The p.T574M variant (also known as c.1721C>T), located in coding exon 6 of the ATP7A gene, results from a C to T substitution at nucleotide position 1721. The threonine at codon 574 is replaced by methionine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on data from gnomAD, this allele has an overall frequency of 0.002% (4/204728) total alleles studied, with 0 hemizygote(s) observed. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001833557 SCV002089059 uncertain significance Menkes kinky-hair syndrome 2019-10-28 no assertion criteria provided clinical testing

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