ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.1399G>A (p.Val467Met)

gnomAD frequency: 0.00002  dbSNP: rs760443267
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002315380 SCV000849225 uncertain significance Inborn genetic diseases 2023-05-03 criteria provided, single submitter clinical testing The c.1399G>A (p.V467M) alteration is located in exon 15 (coding exon 15) of the ATP13A2 gene. This alteration results from a G to A substitution at nucleotide position 1399, causing the valine (V) at amino acid position 467 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV000805500 SCV000945458 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2022-08-09 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. ClinVar contains an entry for this variant (Variation ID: 588886). This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. This variant is present in population databases (rs760443267, gnomAD 0.006%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 467 of the ATP13A2 protein (p.Val467Met).

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