ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.490C>T (p.Arg164Trp)

gnomAD frequency: 0.00002  dbSNP: rs199624796
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001857477 SCV002284121 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2022-03-16 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 143196). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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"). This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. 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 sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 164 of the ATP13A2 protein (p.Arg164Trp).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003114286 SCV003801172 uncertain significance not specified 2023-01-07 criteria provided, single submitter clinical testing Variant summary: ATP13A2 c.490C>T (p.Arg164Trp) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.1e-05 in 282388 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.490C>T in individuals affected with Neurodegeneration With Brain Iron Accumulation and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter has assessed the variant since 2014: the variant was classified as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
Undiagnosed Diseases Program Translational Research Laboratory, National Institutes of Health RCV000132730 SCV000187659 pathogenic Kufor-Rakeb syndrome no assertion criteria provided not provided Converted during submission to Pathogenic.

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