ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3007G>A (p.Ala1003Thr) (rs201497300)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169133 SCV000220347 likely pathogenic Wilson disease 2014-05-23 criteria provided, single submitter literature only
Invitae RCV000169133 SCV000626849 pathogenic Wilson disease 2019-04-16 criteria provided, single submitter clinical testing This sequence change replaces alanine with threonine at codon 1003 of the ATP7B protein (p.Ala1003Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs201497300, ExAC 0.02%). This variant has been described as a common Wilson disease mutation in different populations (PMID: 23789284, 26799313, 16791614). It has been reported as homozygous or in combination with other ATP7B variants in multiple individuals affected with Wilson disease (PMID: 21610751, 12885331, 2679931, Invitae) and observed to segregate with the disease in a Lebanese family (PMID: 25390358). ClinVar contains an entry for this variant (Variation ID: 188802). A structural modeling analysis specifically for the ATP7B gene (PMID: 22692182), suggests that this amino acid position is likely to be sensitive to change, although this analysis has not been confirmed by functional studies. For these reasons, this variant has been classified as Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000169133 SCV001362724 pathogenic Wilson disease 2019-11-22 criteria provided, single submitter clinical testing Variant summary: ATP7B c.3007G>A (p.Ala1003Thr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.6e-05 in 240334 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in ATP7B causing Wilson Disease (4.6e-05 vs 0.0054). c.3007G>A has been reported in the literature in multiple homozygous- and compound heterozygous individuals affected with Wilson Disease (e.g. Ljubic_2016). These data indicate that the variant is very likely to be associated with disease. Two ClinVar submissions (evaluation after 2014) cite the variant likely pathogenic (1x) and pathogenic (1x). Based on the evidence outlined above, the variant was classified as pathogenic.
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV000415237 SCV000492605 likely pathogenic Epileptic encephalopathy 2016-03-15 no assertion criteria provided clinical testing

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