ClinVar Miner

Submissions for variant NM_198578.4(LRRK2):c.7224G>A (p.Met2408Ile)

gnomAD frequency: 0.00003  dbSNP: rs60545352
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneReviews RCV000032514 SCV000056177 not provided Autosomal dominant Parkinson disease 8 no assertion provided literature only
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354607 SCV001549260 uncertain significance not provided no assertion criteria provided clinical testing The LRRK2 p.Met2408Ile variant was not identified in Clinvitae, Cosmic, MutDB and LOVD 3.0. The variant was identified in dbSNP (ID: rs60545352) and in ClinVar (classified as a VUS for Parkinson disease 8, autosomal dominant by GeneReviews). The variant was also identified in control databases in 6 of 281598 chromosomes at a frequency of 0.000021 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 1 of 7162 chromosomes (freq: 0.00014), Latino in 3 of 35242 chromosomes (freq: 0.000085), European (non-Finnish) in 2 of 128360 chromosomes (freq: 0.000016), but was not observed in the African, Ashkenazi Jewish, East Asian, European (Finnish) and South Asian populations. In a study analyzing LRRK2 variants in patients with familial Parkinson's disease, the p.Met2408Ile variant was identified in one proband with familial PD, but was also found in an unaffected individual from another family and in two healthy control subjects, suggesting this variant does not segregate with disease (Jasinska-Myga_2010_PMID: 20721913). The variant is located in the WD40 protein domain (O.A. Ross_2011_PMID: 21885347), however the p.Met2408 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein. However, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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