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NM_198578.4(LRRK2):c.6463A>G (p.Met2155Val) AND Autosomal dominant Parkinson disease 8

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 3, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003526860.1

Allele description [Variation Report for NM_198578.4(LRRK2):c.6463A>G (p.Met2155Val)]

NM_198578.4(LRRK2):c.6463A>G (p.Met2155Val)

Gene:
LRRK2:leucine rich repeat kinase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q12
Genomic location:
Preferred name:
NM_198578.4(LRRK2):c.6463A>G (p.Met2155Val)
HGVS:
  • NC_000012.12:g.40351620A>G
  • NG_011709.1:g.131610A>G
  • NG_011709.2:g.131625A>G
  • NM_198578.4:c.6463A>GMANE SELECT
  • NP_940980.4:p.Met2155Val
  • NC_000012.11:g.40745422A>G
Protein change:
M2155V
Molecular consequence:
  • NM_198578.4:c.6463A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal dominant Parkinson disease 8
Synonyms:
Parkinson disease 8; Parkinson disease 8, susceptibility to; LRRK2-Related Parkinson Disease
Identifiers:
MONDO: MONDO:0011764; MedGen: C1846862; Orphanet: 411602; OMIM: 607060

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004279290Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Mar 3, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004279290.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on LRRK2 protein function. This variant has not been reported in the literature in individuals affected with LRRK2-related conditions. This variant is present in population databases (rs201614703, gnomAD 0.002%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2155 of the LRRK2 protein (p.Met2155Val). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024