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rs76763715

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 12P and 5B. PM1PM5PP5_Very_StrongBP4BS2

The NM_000157.4(GBA1):c.1226A>G(p.Asn409Ser) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.002 in 1,613,914 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic,risk factor (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N409K) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.0019 ( 3 hom., cov: 30)
Exomes 𝑓: 0.0020 ( 5 hom. )

Consequence

GBA1
NM_000157.4 missense, splice_region

Scores

5
4
9
Splicing: ADA: 0.5713
2

Clinical Significance

Pathogenic/Likely pathogenic; risk factor criteria provided, multiple submitters, no conflicts P:42U:1O:6

Conservation

PhyloP100: 4.36
Variant links:
Genes affected
GBA1 (HGNC:4177): (glucosylceramidase beta 1) This gene encodes a lysosomal membrane protein that cleaves the beta-glucosidic linkage of glycosylceramide, an intermediate in glycolipid metabolism. Mutations in this gene cause Gaucher disease, a lysosomal storage disease characterized by an accumulation of glucocerebrosides. A related pseudogene is approximately 12 kb downstream of this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PM1
In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 2 uncertain in NM_000157.4
PM5
Other missense variant is known to change same aminoacid residue: Variant chr1-155235842-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 594893.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=1}.
PP5
Variant 1-155235843-T-C is Pathogenic according to our data. Variant chr1-155235843-T-C is described in ClinVar as [Likely_pathogenic, risk_factor]. Clinvar id is 4290.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-155235843-T-C is described in Lovd as [Pathogenic]. Variant chr1-155235843-T-C is described in Lovd as [Likely_benign]. Variant chr1-155235843-T-C is described in Lovd as [Benign]. Variant chr1-155235843-T-C is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.01917398).. Strength limited to SUPPORTING due to the PP5.
BS2
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GBA1NM_000157.4 linkuse as main transcriptc.1226A>G p.Asn409Ser missense_variant, splice_region_variant 9/11 ENST00000368373.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GBA1ENST00000368373.8 linkuse as main transcriptc.1226A>G p.Asn409Ser missense_variant, splice_region_variant 9/111 NM_000157.4 P1P04062-1

Frequencies

GnomAD3 genomes
AF:
0.00185
AC:
281
AN:
151930
Hom.:
3
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000194
Gnomad AMI
AF:
0.0176
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.0291
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00104
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00182
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00231
AC:
581
AN:
251444
Hom.:
4
AF XY:
0.00230
AC XY:
313
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.000723
Gnomad ASJ exome
AF:
0.0269
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00120
Gnomad NFE exome
AF:
0.00208
Gnomad OTH exome
AF:
0.00293
GnomAD4 exome
AF:
0.00201
AC:
2941
AN:
1461866
Hom.:
5
Cov.:
32
AF XY:
0.00199
AC XY:
1445
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.000872
Gnomad4 ASJ exome
AF:
0.0282
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.000880
Gnomad4 NFE exome
AF:
0.00172
Gnomad4 OTH exome
AF:
0.00306
GnomAD4 genome
AF:
0.00185
AC:
282
AN:
152048
Hom.:
3
Cov.:
30
AF XY:
0.00165
AC XY:
123
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.000193
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.0291
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00104
Gnomad4 NFE
AF:
0.00182
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00291
Hom.:
1
Bravo
AF:
0.00195
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.00182
AC:
7
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00279
AC:
24
ExAC
AF:
0.00221
AC:
268
EpiCase
AF:
0.00267
EpiControl
AF:
0.00332

ClinVar

Significance: Pathogenic/Likely pathogenic; risk factor
Submissions summary: Pathogenic:42Uncertain:1Other:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Gaucher disease type I Pathogenic:15
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics, University of Leipzig Medical CenterNov 20, 2023Criteria applied: PM3_VSTR,PS3_SUP,PP3 -
Pathogenic, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoFeb 12, 2015- -
Pathogenic, criteria provided, single submitterclinical testingCentogene AG - the Rare Disease CompanyMar 08, 2021- -
Pathogenic, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineJun 24, 2020The p.Asn409Ser variant in GBA (previously known as p.Asn370Ser) is a well-established pathogenic variant for Gaucher disease (GD) type 1. It accounts for >50% of all pathogenic alleles identified in Caucasian patients with GD type 1 and has been associated with a milder course of disease without primary neurological disease (Koprivika 2000 PMID: 10796875, Erdos 2007 PMID: 17395504, Grabowski 2015 PMID: 26096741). It has also been reported by other clinical laboratories in ClinVar (Variation ID 4290). This variant has been detected in 2.7% (276/10150) of Ashkenazi Jewish chromosomes, including 2 homozygotes, and 2% (255/126662) of European chromosomes, including 2 homozygotes, by the Genome Aggregation Database (gnomAD, http://exac.broadinstitute.org). In summary, this variant is pathogenic for GD type I in an autosomal recessive manner. ACMG/AMP Criteria applied: PM3_Strong, PP1_Strong. -
Pathogenic, criteria provided, single submitterclinical testingJohns Hopkins Genomics, Johns Hopkins UniversityOct 15, 2020GBA c.1226A>G has been reported as the most common disease-causing variant in Gaucher disease, particularly among Ashkenazi Jewish patients. Numerous functional studies have demonstrated that this variant causes reduced enzyme activity compared to wild-type protein. This GBA variant (rs76763715) reaches polymorphic frequency (>1%) within the Ashkenazi Jewish subpopulation in a large population dataset (gnomAD: 279/10368 alleles; 2.7%, 2 homozygotes). This variant has been reported in ClinVar. We consider this variant to be pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaOct 05, 2021The GBA c.1226A>G (p.Asn409Ser) missense variant, also described in the literature as p.Asn370Ser or N370S, is a well-established pathogenic variant associated with Gaucher disease, type 1, with an increased prevalence in the affected Ashkenazi Jewish population. The variant accounts for approximately 77% of GBA variant alleles in the ICGG Gaucher registry cohort (Koprivica et al. 2000; Fairley et al. 2008; Grabowski et al. 2015; Pastores et al. 2018). Individuals who are homozygous for the p.Asn409Ser variant tend to have milder disease than those who are compound heterozygous, but the phenotype is variable and some may present with a moderate to severe disease phenotype (Fairly et al. 2008; Taddei et al. 2009). Additionally, two large meta-analyses (Mao et al. 2013; Gan-Or et al. 2015) and a multi-center case control study (Sidransky et al. 2009) have reported an increased risk of developing Parkinson disease in heterozygous carriers of the p.Asn409Ser variant. The p.Asn409Ser variant is reported at a frequency of 0.029120 in the Ashkenazi Jewish population of the Genome Aggregation Database (version 3.1.1), including three homozygous individuals in the Total population. This allele frequency is high but consistent with the carrier frequency in this population and variable phenotypic manifestations in homozygous individuals (Pastores et al. 2018). In vitro functional studies have demonstrated reduced enzymatic activity for p.Asn409Ser compared to wild-type protein (Montfort et al. 2004; Malini et al. 2014). Based on the evidence, the p.Asn409Ser variant is classified as pathogenic for Gaucher disease. -
Pathogenic, no assertion criteria providedliterature onlyOMIMAug 01, 2010- -
Pathogenic, criteria provided, single submitterclinical testingGenomic Research Center, Shahid Beheshti University of Medical SciencesDec 03, 2017- -
Pathogenic, criteria provided, single submitterclinical testingHadassah Hebrew University Medical CenterJun 20, 2019- -
Likely pathogenic, criteria provided, single submitterclinical testingDASAMar 25, 2022Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 15826241; 16293621; 15605411) - PS3_moderate. The c.1226A>G;p.(Asn409Ser) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 4290; PMID: 26096741; PMID: 28779532; PMID: 25249066; PMID: 23676350) -PS4. The variant is located in a mutational hot spot - PM1. Missense variant in GBA that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease - PP2. In summary, the currently available evidence indicates that the variant is likely pathogenic -
Pathogenic, criteria provided, single submitterclinical testingKnight Diagnostic Laboratories, Oregon Health and Sciences UniversityJul 10, 2015The c.1226A>G (p.Asn409Ser) variant is a known missense variant in a gene where missense is a common mechanism of disease. This variant is very common in the Ashkenazi Jewish population (carrier frequency 41%, Tsuji et al. 1988), and this patient has indeed reported an Ashkenazi Jewish ancestry. In addition, several functional studies have shown this variant to have reduced catalytic activity (by 81-95%) (Babajani et al. 2012). It is found at a very low frequency in control population databases (1000 Genomes, ExAc, and Exome Sequencing Project [ESP]) and has been predicted deleterious by various computational algorithms. It has been reported pathogenic by reputable patient databases (ClinVar, Human Genetic Mutation Database [HGMD] and Emory Genetic Laboratory). In summary, the c.1226A>G (p.Asn409Ser) meets our criteria for a recessive pathogenic variant for Gaucher disease. -
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsNov 25, 2023- -
Pathogenic, no assertion criteria providedresearchDivision of Human Genetics, Children's Hospital of PhiladelphiaMar 24, 2015The GBA variant (c.1226A>G) was identified in many patients in the literature and is a well-known pathogenic variant with phenotypic variability (Tsuji et al. 1988, PMID: 3353383; Fairley et al. 2008, PMID: 18979180; Hruska et al. 2008, PMID: 18338393). The variant is more commonly known as “N370S” reflecting an older nomenclature. Approximately one quarter of all reported type 1 Gaucher disease cases in the International Collaborative Gaucher Group (ICGG) Gaucher Registry are homozygotes for this allele (Fairley et al. 2008, PMID: 18979180). Alleles with this mutation have been shown to have lower activity compared to the wildtype (Grace et al. 1994, PMID: 23510062; Montfort et al. 2004, PMID: 15146461). -
Pathogenic, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Oct 18, 2019NM_001005741.2(GBA):c.1226A>G(N409S, aka N370S) is classified as pathogenic in the context of Gaucher disease and is associated with Type 1 form of disease. Sources cited for classification include the following: PMID 22220748, 19260119, 18979180, 16293621, 3353383, 10796875, 19217815, 15146461. Classification of NM_001005741.2(GBA):c.1226A>G(N409S, aka N370S) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitterclinical testingCourtagen Diagnostics Laboratory, Courtagen Life SciencesJan 26, 2015- -
not provided Pathogenic:12
Pathogenic, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2024GBA1: PM3:Very Strong, PS3, PM1, PP1:Moderate, PM2:Supporting -
Pathogenic, criteria provided, single submitterclinical testingGeneDxJan 10, 2020Published functional studies demonstrate that the defective protein shows reduced activity compared to wildtype (Grace et al., 1994; Malini et al., 2014); Observed in 279/10,368 (2.7%) alleles from individuals of Ashkenazi Jewish background, including multiple unrelated homozygous individuals, in large population cohorts, which is consistent with the high carrier frequency of this pathogenic variant among Ashkenazi Jewish individuals (Lek et al. 2016; Diaz et al., 2000); This variant is associated with the following publications: (PMID: 31996268, 32042592, 8294487, 30146349, 28779532, 30216542, 30364808, 28966932, 21745757, 19260119, 22388998, 21472771, 20837833, 23642305, 21700325, 19830760, 22961873, 22220748, 24022302, 24434810, 22975760, 22995991, 20643691, 22623374, 23588557, 16293621, 20980259, 20980263, 21653695, 18979180, 25333069, 21742527, 19217815, 22592100, 23676350, 20816920, 19945510, 18987351, 25653295, 25168325, 24020503, 22160715, 23277556, 22192918, 25249066, 21228398, 15146461, 12022475, 10777718, 27393345, 27094865, 27312774, 26096741, 27271787, 27153395, 19846850, 25456120, 28834018, 29625627, 24195576, 29431110, 29140481, 14578207, 8160756, 30302829, 30528841, 30609409, 30487145, 29842932, 27735925, 29029963, 28218669, 29487000, 30606667, 31188768, 9556036, 33281709, 32658388) -
Pathogenic, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Pathogenic, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicJul 15, 2019- -
Pathogenic, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Pathogenic, criteria provided, single submitterclinical testingAiLife Diagnostics, AiLife DiagnosticsMar 23, 2022- -
Pathogenic, criteria provided, single submitterclinical testingRevvity Omics, RevvityOct 11, 2023- -
Pathogenic, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Pathogenic, criteria provided, single submitterclinical testingInstitute of Medical Genetics and Applied Genomics, University Hospital TübingenSep 15, 2021- -
Pathogenic, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesSep 27, 2023The GBA c.1226A>G; p.Asn409Ser variant (rs76763715), also known as N370S, is a common pathogenic variant reported in the homozygous and compound heterozygous state in individuals with type I Gaucher disease (Fairley 2008, Grace 1994, Tsuji 1988). While this variant is found in the Ashkenazi Jewish population with an overall allele frequency of 2.7% (279/10368 alleles) in the Genome Aggregation Database, it is commonly associated with disease in individuals of Ashkenazi Jewish descent (Tsuji 1988). The asparagine at codon 409 is moderately conserved, and functional studies demonstrate this variant has reduced enzymatic activity (Grace 1994, Tsuji 1988). Based on available information, this variant is considered to be pathogenic. References: Fairley C et al. Phenotypic heterogeneity of N370S homozygotes with type I Gaucher disease: an analysis of 798 patients from the ICGG Gaucher Registry. J Inherit Metab Dis. 2008;31(6):738-744. PMID: 18979180. Grace ME et al. Analysis of human acid beta-glucosidase by site-directed mutagenesis and heterologous expression. J Biol Chem. 1994;269(3):2283-2291. PMID: 8294487. Tsuji S et al. Genetic heterogeneity in type 1 Gaucher disease: multiple genotypes in Ashkenazic and non-Ashkenazic individuals. Proc Natl Acad Sci U S A. 1988;85(7):2349-2352. PMID: 3353383. -
Pathogenic, criteria provided, single submitterclinical testingInvitaeJan 25, 2024This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 409 of the GBA protein (p.Asn409Ser). This variant is present in population databases (rs76763715, gnomAD 2.7%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with Gaucher disease or Parkinson disease (PMID: 23676350, 25249066, 26096741, 28779532). This variant is also known as p.Asn370Ser or N370S. ClinVar contains an entry for this variant (Variation ID: 4290). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Experimental studies have shown that this missense change affects GBA function (PMID: 8294487, 22160715, 22592100). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)May 18, 2017- -
Gaucher disease Pathogenic:4Other:2
not provided, no classification providedliterature onlyGeneReviews-- -
Pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJan 18, 2016Variant summary: c.1226A>G affects a conserved nucleotide, resulting in amino acid change from Asn to Ser. 2/3 in-silico tools predict this variant to be benign (SNPs&GO not captured due to low reliability index). This variant was found in 272/123472 control chromosomes at a frequency of 0.0022029, which does not significantly exceed maximal expected frequency of a pathogenic allele (0.005). This variant has been reported in multiple GD pts as well as in pts with Parkinson disease. Functional study showed variant with 13.3% of WT activity (Grace_1994). In addition, multiple clinical laboratories classified this variant as pathogenic. Taken together, this variant was classified as a Pathogenic. -
Pathogenic, criteria provided, single submittercurationBroad Center for Mendelian Genomics, Broad Institute of MIT and HarvardJan 22, 2020The p.Asn409Ser variant in GBA has been reported in about 80% of all individuals with Gaucher disease with an increased prevalence in the affected Ashkenazi Jewish population, and has segregated with disease in 7 affected relatives from 3 families (PMID: 14757438, 17427031, 20301446). The variant has been identified in 2.691% (279/10368) of Ashkenazi Jewish chromosomes, including 2 homozygotes. Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role due to the variable phenotypic presentation of this variant. This variant has also been reported in ClinVar (VariationID: 4290) as a VUS by Praxis fuer Humangenetik Tuebingen, as likely pathogenic by University Medical Centre Ljubljana, as Pathogenic by Genetic Services Laboratory, GeneDx, Illumina Clinical Services, Counsyl, Knight Diagnostic Laboratories, EGL Genetic Diagnostics, Fulgent Genetics, Integrated Genetics, Shahid Beheshti University of Medical Sciences, Mayo Clinic Genetic Testing Laboratories, Children's Hospital of Philadelphia, and OMIM. In vitro functional studies showing reduced enzymatic activity, increased a-synuclein concentration, restoration of enzymatic activity through molecular chaperones, and a shifted optimal pH for enzymatic activity provide some evidence that the p.Asn409Ser variant may impact protein function (PMID: 14757438, 21472771, 28923368, 20980259). However, these types of assays may not accurately represent biological function. Additionally, animal models in mice demonstrating enzyme properties comparable to those in human Gaucher patients have shown that this variant causes Gaucher disease (PMID: 16293621). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. The phenotype of an individual homozygous or compound heterozygous for this variant is highly specific for Gaucher disease based on hepatomegaly, splenomegaly, and low residual enzyme activity consistent with disease (PMID: 14757438). The p.Asn409Ser variant is located in a region of GBA that is essential to protein folding and stability, suggesting that this variant is in a functional domain and supports pathogenicity (PMID: 20980259, 16293621, 14757438, 28923368). Additionally, the presence of this variant in at least 26 homozygotes and in combination with reported pathogenic variants in at least 65 individuals with Gaucher disease increases the likelihood that the p.Asn409Ser variant is pathogenic (VariationID: 4288, 93459; PMID: 17427031, 14757438). The p.Asn409Ser variant is pathogenic based off of our findings, multiple reports in ClinVar, and the literature. ACMG/AMP Criteria applied: PM3_very-strong, PS3, PM1, PP1_moderate, PP4 (Richards 2015). -
not provided, no classification providedphenotyping onlyGenomeConnect, ClinGen-GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Pathogenic, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Pathogenic, criteria provided, single submitterclinical testingRady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego-This variant is also known in literature as p.Asn370Ser (PMID: 23588557), and is the most common cause of Gaucher disease (PMID: 3353383, 26096741, 12022475). It has also been reported in patients with Parkinson disease or Lewy body dementia (LBD) spectrum of disorders (PMID: 21745757, 25249066). Functional studies indicate that this variant reduces enzyme activity of the GBA protein (PMID: 22592100, 8294487, 22160715). The frequency data for variants in the GBA gene in population databases may be unreliable due to the presence of pseudogenes and paralogs (PMID: 20301446). In silico analyses support a deleterious effect of the c.1226A>G (p.Asn409Ser) variant on protein function. Based on the available evidence, the c.1226A>G (p.Asn409Ser) variant is classified as Pathogenic. -
Parkinson disease, late-onset Pathogenic:3Other:1
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics Munich, Klinikum Rechts Der Isar, TU MünchenSep 29, 2020- -
risk factor, no assertion criteria providedliterature onlyOMIMAug 01, 2010- -
Pathogenic, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsMay 03, 2021- -
Pathogenic, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Gaucher disease perinatal lethal Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaJan 01, 2016This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS3,PS1,PM3,PP3,PP5. -
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsMar 04, 2019This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Gaucher disease type II;C0268251:Gaucher disease type III;C0752347:Lewy body dementia;C1842704:Gaucher disease perinatal lethal;C1856476:Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome;C1961835:Gaucher disease type I;C3160718:Parkinson disease, late-onset Pathogenic:1Other:1
Pathogenic, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsFeb 20, 2022- -
not provided, no classification providedphenotyping onlyGenomeConnect, ClinGen-Variant interpretted as pathogenic and reported on 04/12/2017 by GTR ID MNG Laboratories. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Gaucher disease type II;C0268251:Gaucher disease type III;C1856476:Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome;C1961835:Gaucher disease type I Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingBaylor Genetics-- -
GBA1-related condition Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesFeb 21, 2024The GBA1 c.1226A>G variant is predicted to result in the amino acid substitution p.Asn409Ser. This variant has been documented to be causative for Gaucher disease in numerous studies, occurring in the homozygous or compound heterozygous state. In vitro functional studies indicated that this variant results in loss of enzyme activity (see for example, Tsuji et al. 1988. PubMed ID: 3353383; Sidransky et al. 2009. PubMed ID: 19846850). This variant is reported in 2.72% of alleles in individuals of Ashkenazi Jewish descent in gnomAD, including four homozygous individuals. This variant is classified as pathogenic for Gaucher disease. Of note, several studies have also identified this variant as a risk factor for Parkinson’s disease (Sidransky et al. 2009. PubMed ID: 19846850). -
Rigidity;C0085623:Akinesia Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaFeb 19, 2014- -
Lewy body dementia Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -
not specified Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsDec 30, 2020The c.1226A>G (p.N409S) alteration is located in exon 10 (coding exon 9) of the GBA gene. This alteration results from an A to G substitution at nucleotide position 1226, causing the asparagine (N) at amino acid position 409 to be replaced by a serine (S). Based on data from gnomAD, the G allele has an overall frequency of 0.22% (632/282786) total alleles studied. The highest observed frequency was 2.69% (279/10368) of Ashkenazi Jewish alleles. This is the most common mutation found in Gaucher disease and is associated with type 1 (non-neuronopathic) disease (Tsuji, 1988). One study including 798 homozygotes and 1278 compound heterozygotes determined this mutation can cause a range of phenotypes, from mild adult-onset to pediatric onset with severe complications. However, this mutation was not observed to be associated with central nervous system involvement (Fairley, 2008). This amino acid position is not well conserved in available vertebrate species. A functional study found that Sf9 cells containing this mutation expressed significantly less protein when compared to wild-type (Montfort, 2004). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -
Thrombocytopenia;C1458140:Abnormal bleeding Uncertain:1
Uncertain significance, no assertion criteria providedresearchBirmingham Platelet Group; University of BirminghamMay 01, 2020- -
Parkinson disease Other:1
risk factor, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineApr 14, 2020GBA c.1226A>G (p.Asn409Ser historically reported as p.Asn370Ser) is a well-established pathogenic variant for autosomal recessive Gaucher disease type I. This variant has been observed in multiple ethnic backgrounds with highest frequencies in individuals of Ashkenazi Jewish ancestry (2.7%, Genome Aggregation Database (gnomAD); rs76763715) and has been reported by clinical laboratories in ClinVar (Variation ID: 4290). Several studies have also reported an odds ratio of 3.08-3.96 for developing Parkinson disease in heterozygous carriers of this variant (OR=3.96 [95% CI 2.6-6.02] Sidransky 2009 PMID: 19846850, OR=3.08 [95% CI 2.32-4.09] Pankratz 2012 PMID: 22451204, OR=3.16 [95% CI 1.76-5.70] Zhao 2016 PMID: 26868973, OR=3.84 [95% CI 1.86-7.91] Zhang 2018 PMID: 29527153). In vitro functional studies suggest this variant results in reduced enzyme activity and increased levels of a-synuclein protein (Woodard 2014 PMID: 25456120, Fernandes 2016 PMID: 26905200). In summary, this variant is an established risk allele for Parkinson disease. -
Dementia, Lewy body, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMAug 01, 2010- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Uncertain
0.040
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Pathogenic
0.90
D;D;.;.
Eigen
Benign
0.086
Eigen_PC
Benign
0.13
FATHMM_MKL
Pathogenic
0.98
D
M_CAP
Pathogenic
0.75
D
MetaRNN
Benign
0.019
T;T;T;T
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Benign
1.8
L;L;.;.
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-2.1
N;N;N;N
REVEL
Pathogenic
0.67
Sift
Uncertain
0.013
D;D;D;D
Sift4G
Uncertain
0.033
D;D;D;D
Polyphen
0.61
P;P;.;.
Vest4
0.64
MVP
0.93
MPC
1.0
ClinPred
0.031
T
GERP RS
3.5
Varity_R
0.59
gMVP
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.57
dbscSNV1_RF
Benign
0.39
SpliceAI score (max)
0.21
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.21
Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs76763715; hg19: chr1-155205634; API