ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.3490C>T (p.Arg1164Ter)

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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 RCV002459020 SCV002617222 uncertain significance Inborn genetic diseases 2018-01-31 criteria provided, single submitter clinical testing The p.R1164* variant (also known as c.3490C>T), located in coding exon 29 of the ATP13A2 gene, results from a C to T substitution at nucleotide position 3490. This changes the amino acid from an arginine to a stop codon within coding exon 29. Premature stop codons are typically deleterious in nature, however, this stop codon occurs at the 3' terminus of ATP13A2, is not expected to trigger nonsense-mediated mRNA decay, and impacts only the last 17 amino acids of the protein. The exact functional impact of these removed amino acids is unknown at this time. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV003099519 SCV003264051 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2022-06-21 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1164*) in the ATP13A2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 17 amino acid(s) of the ATP13A2 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

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