Starting
Initialising…
0%
LRRK2
Final classification
Pathogenic
LRRK2 c.6055G>A · p.Gly2019Ser
LRRK2

NM_198578.4:c.6055G>A (p.Gly2019Ser) in LRRK2 is the most common and well-established pathogenic variant associated with autosomal dominant Parkinson disease, classified as Pathogenic by 23 clinical laboratories (ClinVarID 1940).

Gene
LRRK2
Transcript
NM_198578.4
HGVS · transcript:coding
NM_198578.4:c.6055G>A
Consequence
N/A
GRCh38
chr12:40340400 G>A
GRCh37
chr12:40734202 G>A
Basis ClinGen Parkinson's Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for LRRK2 Version 1.0.0 v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PS4 very strong, PM1 moderate, PM2 supporting, PP1 strong, PP3 supporting, PP5 supporting; combination = 1 very strong + 2 strong + 1 moderate + 3 supporting, which maps to Pathogenic.
ClinGen Parkinson's Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for LRRK2 Version 1.0.0 v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PS4 very strong, PM1 moderate, PM2 supporting, PP1 strong, PP3 supporting, PP5 supporting; combination = 1 very strong + 2 strong + 1 moderate + 3 supporting, which maps to Pathogenic.
Classification rationale
PS3PS4PM1PM2PP1PP3PP5 Pathogenic
LRRK2 c.6055G>A

NM_198578.4:c.6055G>A (p.Gly2019Ser) in LRRK2 is the most common and well-established pathogenic variant associated with autosomal dominant Parkinson disease, classified as Pathogenic by 23 clinical laboratories (ClinVarID 1940).1 PS4_VeryStrong: Overwhelming case-control evidence shows significant enrichment in Parkinson disease patients across multiple populations, with an odds ratio of 17.6 in Ashkenazi Jews and prevalence up to 41% in familial cases versus 0% in controls from North African Arab populations. The ClinGen Parkinson's Disease Expert Panel assigns PS4_VeryStrong for this variant.2 PS3_Strong: Well-established functional studies consistently demonstrate G2019S increases LRRK2 kinase activity 2-3 fold relative to wild-type, and this increased kinase activity mediates neuronal toxicity, confirming a pathogenic gain-of-function mechanism.3 PP1_Strong: Strong co-segregation with disease demonstrated across multiple large families in diverse populations, with shared founder haplotypes dating to the 13th century in European and North African populations and independent founder events in Japanese populations.4 PM1_Moderate: The variant is located in the kinase activation loop, a critical functional domain. The ClinGen PD Expert Panel explicitly assigns PM1 for missense variants in the LRRK2 kinase domain including codon 2019.5 PM2_Supporting: The variant is present at very low frequency in population databases (gnomAD v2.1 AF=0.0488%, 138/282,542 alleles; absent from gnomAD v4.1).6 PP3_Supporting: Multiple in silico tools predict a damaging effect (REVEL=0.97, BayesDel=0.57).7 PP5_Supporting: Reported as Pathogenic by 23 clinical diagnostic laboratories in ClinVar.8 Using the generic ACMG/AMP 2015 classification framework (the ClinGen LRRK2 VCEP v1.0.0 criteria were unstructured and did not provide machine-readable combination rules for final classification), the criteria met are: PS4_VeryStrong + PS3_Strong + PP1_Strong + PM1_Moderate + PM2_Supporting + PP3_Supporting + PP5_Supporting. This combination overwhelmingly exceeds the threshold for Pathogenic classification (requires: 2 Strong OR 1 Very Strong + 1 Strong + 1 Supporting).9 Final classification: PATHOGENIC.

PS3 + PS4 + PM1 + PM2 + PP1 + PP3 + PP5 Pathogenic
Gene diagram · NM_198578.4 · variants mapped to exon structure
LRRK2 NM_198578.4
Fetching transcript structure from UCSC…
Applied criteria · 7 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000488423; MAF= 0.04884%, 138/282542 alleles, homozygotes = 1) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00839606; MAF= 0.83961%, 87/10362 alleles, homozygotes = 1); grpmax FAF= 0.00018185.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      0.049% · 138 / 282,542
      1 hom · FAF 0.018%
      Ashkenazi Jewish
      87 / 10,362
      0.84%
      1 hom
      Remaining individuals
      6 / 7,218
      0.083%
      European (non-Finnish)
      33 / 128,908
      0.026%
      Admixed American
      9 / 35,406
      0.025%
      African/African American
      3 / 24,962
      0.012%
      + 3 not observed (East Asian, European (Finnish), South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (23 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as risk factor (1 clinical laboratory) and as pathogenic (1 clinical laboratory). (ClinVarID = 1940)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.97. BayesDel score = 0.568677.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV54172342, n = 3 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      7papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 3 further PMIDs triaged but not cited — see Sources & References.
      Identification of a novel LRRK2 mutation linked to autosomal dominant parkinsonism: evidence of a common founder across European populations.
      Found
      G2019S identified by sequencing multiplex families with autosomal dominant parkinsonism 7 of 248 (2.8%) affected probands carry the variant (PMID:15726496).
      Applied to
      PP1 supports · met
      Clinical traits of LRRK2-associated Parkinson's disease in Ireland: a link between familial and idiopathic PD.
      Found
      G2019S identified in two siblings and one idiopathic PD patient in Ireland (PMID:16102999).
      Applied to
      PP1 supports · met PS4 supports · met
      LRRK2 haplotype analyses in European and North African families with Parkinson disease: a common founder for the G2019S mutation dating from the 13th century.
      Found
      Haplotype analyses confirm common founder across European and North African families dating to 13th century (PMID:16145815).
      Applied to
      PP1 supports · met PS4 supports · met
      LRRK2 gene in Parkinson disease: mutation analysis and case control association study.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS4 supports · met
      Lrrk2 pathogenic substitutions in Parkinson's disease.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met PS4 supports · met
      Parkinson's disease-associated mutations in leucine-rich repeat kinase 2 augment kinase activity.
      Found
      In vitro kinase assays demonstrate G2019S increases LRRK2 kinase activity 2-3 fold (PMID:16269541).
      Applied to
      PM1 supports · met PS3 supports · met
      Identification and haplotype analysis of LRRK2 G2019S in Japanese patients with Parkinson disease.
      Found
      G2019S shared haplotype distinct from European haplotype identified in Japanese patients suggesting independent founder events (PMID:16728648).
      Applied to
      PP1 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 3 PMIDs not cited in assessment
      16333314 ↗ Comprehensive analysis of the LRRK2 gene in sixty families with Parkinson's disease. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
      30760999 ↗ A Comprehensive Analysis of Population Differences in LRRK2 Variant Distribution in Parkinson's Disease. CLINVAR