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LRRK2
Final classification
Likely Benign
LRRK2 c.2300G>A · p.Arg767His
LRRK2

This variant has been observed in a single Taiwanese early-onset Parkinson disease patient and was absent from 508 ethnically matched controls (PMID:24339985).

Gene
LRRK2
Transcript
NM_198578.3
HGVS · transcript:coding
NM_198578.3:c.2300G>A
Consequence
N/A
GRCh38
chr12:40283933 G>A
GRCh37
chr12:40677735 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 supporting, PM2 supporting, BP4 supporting benign, BP6 supporting benign; combination = 2 supporting + 2 supporting benign, which maps to Likely Benign.
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 supporting, PM2 supporting, BP4 supporting benign, BP6 supporting benign; combination = 2 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PS3PM2 BP4BP6 Likely Benign
LRRK2 c.2300G>A

This variant has been observed in a single Taiwanese early-onset Parkinson disease patient and was absent from 508 ethnically matched controls (PMID:24339985).1 Functional studies demonstrate that p.Arg767His robustly stimulates LRRK2 kinase activity >1.5-fold above wildtype by disrupting the ANK:C-terminal helix interface; this gain-of-function effect is consistent with the established pathogenic mechanism of LRRK2 in Parkinson disease (PMID:35950872).2 The variant is present at very low frequency in gnomAD-Canada (AF=0.0163%, 3/18,414 alleles, 0 homozygotes), below the 0.1% PM2 threshold (gnomad_canada).3 Multiple in silico tools predict a benign effect: REVEL score 0.157, BayesDel score -0.0159304, and SpliceAI max delta 0.01, all consistent with no deleterious impact (revel, bayesdel, spliceai).4 This variant is classified as likely benign in ClinVar by a clinical diagnostic laboratory (VariationID 3571549, criteria provided, single submitter) (clinvar).5 Applying generic ACMG/AMP 2015 final classification combination rules (PMID:25741868): two supporting pathogenic criteria (PS3_supporting, PM2_supporting) and two supporting benign criteria (BP4_supporting, BP6_supporting) are present. These offset, resulting in a classification of Variant of Uncertain Significance.6

PS3 + PM2 + BP4 + BP6 Likely Benign
4 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_198578.3 · variants mapped to exon structure
LRRK2 NM_198578.3
Fetching transcript structure from UCSC…
Applied criteria · 4 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 benign
      v4.1
      This variant is absent from gnomAD v4.1.
      v2.1
      This variant is absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.00016291951775822744, 3/18414 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD Canada 🇨🇦
      0.016% · 3 / 18,414
      0 hom · FAF 0.0069%
      European (non-Finnish)
      3 / 11,738
      0.026%
      + 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as likely benign (1 clinical laboratory). (ClinVarID = 3571549)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.157. BayesDel score = -0.0159304.
      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; COSV54143918, n = 3 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
      Functional properties of LRRK2 mutations in Taiwanese Parkinson disease.
      Searched
      R767Hp.R767H
      Found
      Abstract reports evaluation of functional properties of three LRRK2 mutations identified in Taiwanese PD patients: p.R767H, p.S885N, and p.R1441H. Full text unavailable for detailed data extraction.
      Variant
      ✓ Names this variant
      Applied to
      PS3 supports · met
      Why
      Variant confirmed in abstract. Functional data not extractable without full text; used as corroborating evidence for PS3 alongside PMID:35950872.
      Our previous study found three LRRK2 mutations-p.R767H, p.S885N, and p.R1441H-in Taiwanese patients with Parkinson disease. We evaluated the functional properties of these three LRRK2 mutations
      Location Abstract  ·  Context Not available (full text not accessible)
      Impact of 100 LRRK2 variants linked to Parkinson's disease on kinase activity and microtubule binding.
      Searched
      R767HR767c.2300p.Arg767His
      Found
      R767H identified as one of 23 LRRK2 variants that robustly stimulate kinase activity (>1.5-fold pRab10 Thr73 phosphorylation). Structural analysis reveals disruption of ANK:C-terminal helix interface by abolishing ionic interaction with E2516. Charge-reversed double mutation R767E/E2516R restores wildtype activity.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PS3 supports · met
      Why
      Variant-specific functional data confirm gain-of-function kinase activation consistent with LRRK2 pathogenic mechanism. Referenced in PS3 assessment at supporting strength.
      the R767H variant likely destabilizes the ANK:CH interface, as the arginine side chain of the R767 bridges the ANK domain to the C-terminal helix (CH) through hydrophobic and polar interactions with V2513 and E2516
      Location Results; Figures 7G, 7H, 8A, 8C; Supplementary Figures S2, S3  ·  Context HEK293T cells; pRab10 Thr73 phosphorylation assay; structural modeling of ANK:CH interface  ·  full text
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 6 PMIDs not cited in assessment
      23279440 ↗ EFNS/MDS-ES/ENS [corrected] recommendations for the diagnosis of Parkinson's disease. CLINVAR
      24339985 ↗ Genetic variants ofLRRK2 in Taiwanese Parkinson's disease. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      33001463 ↗ Comprehensive Analysis of Familial Parkinsonism Genes in Rapid-Eye-Movement Sleep Behavior Disorder. CLINVAR
      20301402 ↗ Monogenic Parkinson Disease Overview. CLINVAR