ClinVar Miner

Submissions for variant NM_001386393.1(PANK2):c.1379C>T (p.Pro460Leu)

gnomAD frequency: 0.00010  dbSNP: rs41279408
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000690887 SCV000818616 uncertain significance Pigmentary pallidal degeneration 2022-07-05 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 570 of the PANK2 protein (p.Pro570Leu). This variant is present in population databases (rs41279408, gnomAD 0.05%). This missense change has been observed in individual(s) with PANK2-related conditions (PMID: 12510040, 20629144, 33072517). This variant is also known as c.1379C>T (p.Pro460Leu). ClinVar contains an entry for this variant (Variation ID: 570102). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.
Fulgent Genetics, Fulgent Genetics RCV000764234 SCV000895237 uncertain significance Hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration; Pigmentary pallidal degeneration 2018-10-31 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001815429 SCV002064036 likely pathogenic not provided 2021-10-01 criteria provided, single submitter clinical testing
GeneDx RCV001815429 SCV003923992 uncertain significance not provided 2023-05-02 criteria provided, single submitter clinical testing Reported previously in a patient with tremors in the lower extremities, balance difficulties, shuffling gait, and abnormal brain MRI, who also harbored a second variant (phase unknown) (Lee et al., 2020); Reported previously, using alternate nomenclature, on one allele in a patient with atypical Hallervorden-Spatz syndrome; however, no further clinical or segregation information was provided (Hayflick et al., 2003); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 12510040, 31540697, 20629144, 33072517)

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