ClinVar Miner

Submissions for variant NM_004562.3(PRKN):c.167T>A (p.Val56Glu)

gnomAD frequency: 0.00006  dbSNP: rs137853059
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001369417 SCV001565856 pathogenic not provided 2021-10-31 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 56 of the PRKN protein (p.Val56Glu). This variant is present in population databases (rs137853059, gnomAD 0.01%). This missense change has been observed in individual(s) with early-onset Parkinson disease (PMID: 12056932). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 7047). 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: "Possibly Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects PRKN function (PMID: 15606901, 30994895). For these reasons, this variant has been classified as Pathogenic.
Centogene AG - the Rare Disease Company RCV000007463 SCV002059553 pathogenic Autosomal recessive juvenile Parkinson disease 2 2020-03-16 criteria provided, single submitter clinical testing
Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University RCV000007463 SCV002061374 pathogenic Autosomal recessive juvenile Parkinson disease 2 2022-01-07 criteria provided, single submitter research
OMIM RCV000007463 SCV000027663 pathogenic Autosomal recessive juvenile Parkinson disease 2 2002-06-01 no assertion criteria provided literature only

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