ClinVar Miner

Submissions for variant NM_000052.7(ATP7A):c.278C>T (p.Thr93Met)

gnomAD frequency: 0.00012  dbSNP: rs539177302
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000414022 SCV000491101 uncertain significance not specified 2016-12-15 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the ATP7A gene. The T93M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. This variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, and it was not observed with any significant frequency in the 1000 Genomes Project and Exome Aggregation Consortium, indicating it is not a common benign variant in these populations. The T93M 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. However, this substitution occurs at a position that is not conserved across species and in silico analysis predicts this variant likely does not alter the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign.
Invitae RCV000530559 SCV000639978 benign Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 2023-12-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV002436234 SCV002751732 uncertain significance Inborn genetic diseases 2018-07-19 criteria provided, single submitter clinical testing The p.T93M variant (also known as c.278C>T), located in coding exon 2 of the ATP7A gene, results from a C to T substitution at nucleotide position 278. The threonine at codon 93 is replaced by methionine, an amino acid with 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.
Revvity Omics, Revvity Omics RCV003144246 SCV003834472 uncertain significance not provided 2021-07-08 criteria provided, single submitter clinical testing
Natera, Inc. RCV001828381 SCV002089030 uncertain significance Menkes kinky-hair syndrome 2020-02-12 no assertion criteria provided clinical testing

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