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GBA1
Final classification
VUS
GBA1 c.1279G>A · p.Glu427Lys
GBA1

NM_000157.4:c.1279G>A (p.Glu427Lys) is a missense variant in exon 9 of GBA1, located within the catalytic domain of glucocerebrosidase.

Gene
GBA1
Transcript
NM_000157.4
HGVS · transcript:coding
NM_000157.4:c.1279G>A
Consequence
N/A
GRCh38
chr1:155235790 C>T
GRCh37
chr1:155205581 C>T
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: PM1 supporting, PM2 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: PM1 supporting, PM2 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
GBA1 c.1279G>A

NM_000157.4:c.1279G>A (p.Glu427Lys) is a missense variant in exon 9 of GBA1, located within the catalytic domain of glucocerebrosidase.1 This variant is present at very low frequency in population databases: gnomAD v2.1 AF=0.0159% (45/282,860 alleles) and gnomAD v4.1 AF=0.0193% (311/1,614,180 alleles), with no homozygotes observed (PM2_Supporting).2 The variant is located within the well-characterized catalytic domain of GBA1 where multiple pathogenic missense variants cluster (PM1_Supporting).3 This variant has been reported in ClinVar as Uncertain significance by 7 clinical laboratories (ClinVar Variation ID: 493050), with no expert panel classification available.4 In silico predictors are mixed: REVEL score is 0.579 (intermediate), BayesDel is 0.107 (benign-leaning), and SpliceAI predicts no splicing impact (max delta 0.07). Multiple lines of computational evidence do not consistently support a pathogenic or benign interpretation (PP3 not met, BP4 not met).5 Exploratory literature review identified potential functional evidence (PMID:10079102, PMID:15300782) reporting severely reduced glucocerebrosidase activity for E427K, and potential co-segregation evidence (PMID:9375849). However, full-text verification was not available in this case to confirm exact variant-specific data (PS3 and PP1 not assessed pending full-text review). Applying generic ACMG/AMP 2015 combination rules: PM1_Supporting + PM2_Supporting = 2 supporting pathogenic criteria. No benign criteria are met. This is consistent with a final classification of Variant of Uncertain Significance (VUS).6

PM1 + PM2 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= 0.000192667; MAF= 0.01927%, 311/1614180 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000222873; MAF= 0.02229%, 263/1180044 alleles, homozygotes = 0); grpmax FAF= 0.00020027.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000159089; MAF= 0.01591%, 45/282860 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000263207; MAF= 0.02632%, 34/129176 alleles, homozygotes = 0); grpmax FAF= 0.00021135.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.00021720243266724586, 4/18416 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.019% · 311 / 1,614,180
      0 hom · FAF 0.02%
      European (non-Finnish)
      263 / 1,180,044
      0.022%
      South Asian
      20 / 91,084
      0.022%
      Remaining individuals
      13 / 62,506
      0.021%
      Middle Eastern
      1 / 6,062
      0.016%
      European (Finnish)
      9 / 64,038
      0.014%
      Admixed American
      4 / 60,024
      0.0067%
      African/African American
      1 / 75,016
      0.0013%
      + 3 not observed (Amish, East Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.016% · 45 / 282,860
      0 hom · FAF 0.021%
      European (non-Finnish)
      34 / 129,176
      0.026%
      Remaining individuals
      1 / 7,226
      0.014%
      South Asian
      4 / 30,616
      0.013%
      European (Finnish)
      3 / 25,120
      0.012%
      Admixed American
      2 / 35,432
      0.0056%
      African/African American
      1 / 24,966
      0.004%
      + 2 not observed (Ashkenazi Jewish, East Asian)
      gnomAD Canada 🇨🇦
      0.022% · 4 / 18,416
      0 hom
      Latino/Admixed American
      1 / 836
      0.12%
      Remaining individuals
      1 / 1,138
      0.088%
      European (non-Finnish)
      2 / 11,738
      0.017%
      + 6 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (7 clinical laboratories). (ClinVarID = 493050)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.579. BayesDel score = 0.107037.
      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
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      22820396 ↗ First pilot newborn screening for four lysosomal storage diseases in an Italian region: identification and analysis of a putative causative mutation in the GBA gene. CLINVAR
      25249066 ↗ Glucocerebrosidase mutations in primary parkinsonism. 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
      32658388 ↗ GBA-Related Parkinson's Disease: Dissection of Genotype-Phenotype Correlates in a Large Italian Cohort. CLINVAR
      23035075 ↗ GBA mutations increase risk for Lewy body disease with and without Alzheimer disease pathology. CLINVAR
      23588557 ↗ A multicenter study of glucocerebrosidase mutations in dementia with Lewy bodies. CLINVAR
      30302829 ↗ Coding variation in GBA explains the majority of the SYT11-GBA Parkinson's disease GWAS locus. CLINVAR
      32618053 ↗ A Large-Scale Full GBA1 Gene Screening in Parkinson's Disease in the Netherlands. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR