ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.2828C>T (p.Thr943Ile)

gnomAD frequency: 0.00004  dbSNP: rs1401431520
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000799158 SCV000938810 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2023-03-09 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 645131). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ATP13A2 protein function. This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 943 of the ATP13A2 protein (p.Thr943Ile).
Ambry Genetics RCV002440664 SCV002750405 uncertain significance Inborn genetic diseases 2017-11-27 criteria provided, single submitter clinical testing The p.T943I variant (also known as c.2828C>T), located in coding exon 25 of the ATP13A2 gene, results from a C to T substitution at nucleotide position 2828. The threonine at codon 943 is replaced by isoleucine, 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.
Fulgent Genetics, Fulgent Genetics RCV000799158 SCV002792173 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2021-07-11 criteria provided, single submitter clinical testing

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