ClinVar Miner

Submissions for variant NM_001257180.2(SLC20A2):c.1703C>T (p.Pro568Leu)

gnomAD frequency: 0.00001  dbSNP: rs763252801
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Inherited Metabolic Diseases, Karolinska University Hospital RCV001374416 SCV001571375 likely pathogenic Idiopathic basal ganglia calcification 1 2021-04-13 criteria provided, single submitter clinical testing
GeneDx RCV001751740 SCV001986321 uncertain significance not provided 2019-08-05 criteria provided, single submitter clinical testing Identified a patient with a diagnosis of idiopathic basal ganglia calcification (Hsu et al., 2013) and in siblings with brain calcifications and tonic-clonic seizures (Fjaer et al., 2015) in published literature. However, the siblings were also found to have a variant in another gene that may be contributing to the phenotype (Fjaer et al., 2015).; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 23334463, 26475232, 30609140, 25212438, 25726928, 31618668)
Invitae RCV001751740 SCV002240262 pathogenic not provided 2022-01-28 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. 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: "Benign"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 1064453). This missense change has been observed in individuals with primary basal ganglia calcification (PMID: 23334463, 26475232, 31618668; Invitae). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs763252801, gnomAD 0.003%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 568 of the SLC20A2 protein (p.Pro568Leu).
Genetics and Molecular Pathology, SA Pathology RCV001374416 SCV004175581 likely pathogenic Idiopathic basal ganglia calcification 1 2022-10-25 criteria provided, single submitter clinical testing

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