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GBA1
Final classification
VUS
GBA1 c.1495G>C · p.Val499Leu
GBA1

NM_000157.4:c.1495G>C (p.Val499Leu) is a missense variant in GBA1, which encodes the lysosomal enzyme glucocerebrosidase. Biallelic pathogenic variants in GBA1 cause Gaucher disease (autosomal recessive); heterozygous variants are associated with increased risk for Parkinson disease.

Gene
GBA1
Transcript
NM_000157.4
HGVS · transcript:coding
NM_000157.4:c.1495G>C
Consequence
N/A
GRCh38
chr1:155235205 C>G
GRCh37
chr1:155204996 C>G
Basis ClinGen Parkinson's Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GBA1 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: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
ClinGen Parkinson's Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GBA1 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: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
GBA1 c.1495G>C

NM_000157.4:c.1495G>C (p.Val499Leu) is a missense variant in GBA1, which encodes the lysosomal enzyme glucocerebrosidase. Biallelic pathogenic variants in GBA1 cause Gaucher disease (autosomal recessive); heterozygous variants are associated with increased risk for Parkinson disease. This variant is present at extremely low frequency in population databases: gnomAD v2.1 allele frequency = 0.0052% (13/251,170 alleles, 0 homozygotes) and gnomAD v4.1 allele frequency = 0.0042% (67/1,613,020 alleles, 0 homozygotes), meeting PM2_Supporting.1 In silico analysis supports a deleterious effect: the REVEL meta-predictor score is 0.733, exceeding the commonly used threshold of 0.5. SpliceAI predicts no splicing impact (max delta = 0.00). The BayesDel score (0.348) is below threshold, resulting in partially conflicting computational evidence; PP3 is applied at the supporting level.2 This variant has been reported in ClinVar (Variation ID 634558) with conflicting classifications: Uncertain significance (2 clinical laboratories), Likely pathogenic (2 clinical laboratories), and Likely benign (1 clinical laboratory). No ClinGen expert panel classification is available.3 Functional studies referenced in the literature (PMID:10714667, PMID:12924289) suggest reduced glucocerebrosidase activity for the mature protein equivalent V460L, but full-text verification of these studies was not available at the time of assessment. PS3 is not assessed pending direct review of primary data. The ClinGen Parkinson's Disease Expert Panel specification for GBA1 (v1.0.0) is an unstructured ruleset without specific criterion thresholds. The assessment therefore applies generic ACMG/AMP 2015 criteria (PMID:25741868).4 Overall, the evidence applied includes PM2_Supporting and PP3_Supporting. No benign criteria were met. All remaining criteria (PVS1, PS1-PS5, PM1, PM5-PM6, PP1-PP2, PP4-PP5, BA1, BS1-BS4, BP1-BP2, BP4-BP7) were either not met, not assessed, or not applicable.

PM2 + PP3 VUS
Gene diagram · NM_000157.4 · variants mapped to exon structure
GBA1 NM_000157.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 4.1537e-05; MAF= 0.00415%, 67/1613020 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 8.35199e-05; MAF= 0.00835%, 5/59866 alleles, homozygotes = 0); grpmax FAF= 3.749e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 5.17578e-05; MAF= 0.00518%, 13/251170 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000144542; MAF= 0.01445%, 5/34592 alleles, homozygotes = 0); grpmax FAF= 5.597e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0042% · 67 / 1,613,020
      0 hom · FAF 0.0037%
      Admixed American
      5 / 59,866
      0.0084%
      Remaining individuals
      5 / 62,458
      0.008%
      European (non-Finnish)
      56 / 1,179,718
      0.0047%
      African/African American
      1 / 74,638
      0.0013%
      + 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0052% · 13 / 251,170
      0 hom · FAF 0.0056%
      Admixed American
      5 / 34,592
      0.014%
      European (non-Finnish)
      8 / 113,456
      0.0071%
      + 6 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, 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 Uncertain significance (2 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 634558)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.733. BayesDel score = 0.348057.
      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 not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      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
      27153395 ↗ Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. CLINVAR
      32658388 ↗ GBA-Related Parkinson's Disease: Dissection of Genotype-Phenotype Correlates in a Large Italian Cohort. CLINVAR
      34426522 ↗ The genetic structure of the Turkish population reveals high levels of variation and admixture. CLINVAR
      18197057 ↗ Carrier screening in individuals of Ashkenazi Jewish descent. CLINVAR
      19888064 ↗ ACOG Committee Opinion No. 442: Preconception and prenatal carrier screening for genetic diseases in individuals of Eastern European Jewish descent. CLINVAR
      20301446 ↗ Gaucher Disease. CLINVAR
      22577228 ↗ A clinical and family history study of Parkinson's disease in heterozygous glucocerebrosidase mutation carriers. CLINVAR