Submissions for variant NM_000052.7(ATP7A):c.1000G>A (p.Ala334Thr) (rs368622356)

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Total submissions: 3

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000445022	SCV000531041	uncertain significance	not provided	2018-02-26	criteria provided, single submitter	clinical testing	The A334T variant of uncertain significance in the ATP7A gene has not been published as pathogenic or been reported as benign to our knowledge. This variant is also observed in 0.01%-0.02% alleles, including nine hemizygous individuals, across ethnic groups in large population cohorts (Lek et al., 2016), indicating it may be a rare benign variant. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Nevertheless, the A334T 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.Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign.
Invitae	RCV001085591	SCV001092198	benign	Menkes kinky-hair syndrome; Cutis laxa, X-linked; Distal spinal muscular atrophy, X-linked 3	2019-12-31	criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics,University Medical Centre Ljubljana	RCV001196180	SCV001366715	uncertain significance	Plagiocephaly; Focal seizures with impairment of consciousness or awareness; Muscular hypotonia of the trunk; Febrile seizures; Delayed speech and language development; Generalized tonic-clonic seizures; Enlarged cisterna magna; Complex febrile seizures	2019-08-17	criteria provided, single submitter	clinical testing	This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2. This variant was detected in heterozygous state.

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