ClinVar Miner

Submissions for variant NM_198578.4(LRRK2):c.6929C>T (p.Thr2310Met)

gnomAD frequency: 0.00004  dbSNP: rs200002022
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000225428 SCV001268443 benign Autosomal dominant Parkinson disease 8 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
CeGaT Center for Human Genetics Tuebingen RCV001531780 SCV001747057 likely benign not provided 2024-01-01 criteria provided, single submitter clinical testing LRRK2: BP4, BS2
Labcorp Genetics (formerly Invitae), Labcorp RCV000225428 SCV003297928 uncertain significance Autosomal dominant Parkinson disease 8 2021-12-23 criteria provided, single submitter clinical testing 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 missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 236296). This missense change has been observed in individual(s) with LRRK2-related conditions (PMID: 23726462, 26213354). This variant is present in population databases (rs200002022, gnomAD 0.01%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 2310 of the LRRK2 protein (p.Thr2310Met).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003993898 SCV004813455 uncertain significance not specified 2024-02-12 criteria provided, single submitter clinical testing Variant summary: LRRK2 c.6929C>T (p.Thr2310Met) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 6e-05 in 251130 control chromosomes. c.6929C>T has been reported in the literature in individuals affected with Parkinson Disease 8, Autosomal Dominant. These reports do not provide unequivocal conclusions about association of the variant with Parkinson Disease 8, Autosomal Dominant. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25174650, 22415848, 38137339, 23726462). ClinVar contains an entry for this variant (Variation ID: 236296). Based on the evidence outlined above, the variant was classified as uncertain significance.
GeneReviews RCV000225428 SCV000282486 uncertain significance Autosomal dominant Parkinson disease 8 2014-12-11 no assertion criteria provided literature only

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