ClinVar Genomic variation as it relates to human health
NM_000157.4(GBA1):c.1246G>A (p.Gly416Ser)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000157.4(GBA1):c.1246G>A (p.Gly416Ser)
Variation ID: 4327 Accession: VCV000004327.26
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 1q22 1: 155235823 (GRCh38) [ NCBI UCSC ] 1: 155205614 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Oct 2, 2013 Feb 14, 2024 Dec 28, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000157.4:c.1246G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000148.2:p.Gly416Ser missense NM_001005741.3:c.1246G>A NP_001005741.1:p.Gly416Ser missense NM_001005742.3:c.1246G>A NP_001005742.1:p.Gly416Ser missense NM_001171811.2:c.985G>A NP_001165282.1:p.Gly329Ser missense NM_001171812.2:c.1099G>A NP_001165283.1:p.Gly367Ser missense NC_000001.11:g.155235823C>T NC_000001.10:g.155205614C>T NG_009783.1:g.13875G>A NG_042867.1:g.2285C>T P04062:p.Gly416Ser - Protein change
- G416S, G329S, G367S
- Other names
-
G377S
- Canonical SPDI
- NC_000001.11:155235822:C:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
GBA1 | - | - |
GRCh38 GRCh38 GRCh37 |
32 | 406 | |
LOC106627981 | - | - | - |
GRCh38 GRCh38 |
- | 360 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (1) |
no assertion criteria provided
|
Mar 1, 2003 | RCV000004572.3 | |
Pathogenic (2) |
criteria provided, single submitter
|
Apr 27, 2019 | RCV000004571.7 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Jan 22, 2020 | RCV000055772.12 | |
Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Dec 28, 2023 | RCV000723428.13 | |
Pathogenic (1) |
criteria provided, single submitter
|
- | RCV001004116.1 | |
Pathogenic (1) |
no assertion criteria provided
|
May 1, 2020 | RCV001270486.1 | |
Pathogenic (1) |
criteria provided, single submitter
|
Sep 20, 2021 | RCV002482828.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Pathogenic
(Aug 09, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Gaucher disease
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000917432.1
First in ClinVar: Jun 02, 2019 Last updated: Jun 02, 2019 |
Comment:
Variant summary: GBA c.1246G>A (p.Gly416Ser) results in a non-conservative amino acid change located in the Glycosyl hydrolase family 30, TIM-barrel domain of the encoded protein … (more)
Variant summary: GBA c.1246G>A (p.Gly416Ser) results in a non-conservative amino acid change located in the Glycosyl hydrolase family 30, TIM-barrel domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.4e-05 in 277220 control chromosomes (gnomAD). The variant, c.1246G>A, has been reported in the literature in multiple individuals affected with Gaucher Disease in the homozygous and compound heterozygous state. These data indicate that the variant is very likely to be associated with disease. A functional study showed the variant to have <10% activity compared to wild-type (Amaral_2000). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
|
|
Pathogenic
(Jan 22, 2020)
|
criteria provided, single submitter
Method: curation
|
Gaucher disease
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
|
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV001423053.2
First in ClinVar: Jul 19, 2020 Last updated: Feb 02, 2022 |
Comment:
The p.Gly416Ser variant in GBA has been reported in at least 25 individuals with Gaucher disease (PMID: 25946768, 16981045, 23430543, 25732996, 17395504) and has been … (more)
The p.Gly416Ser variant in GBA has been reported in at least 25 individuals with Gaucher disease (PMID: 25946768, 16981045, 23430543, 25732996, 17395504) and has been identified in 0.003% (4/129180) of European (non-Finnish) chromosomes and 0.002822% (1/35438) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs121908311). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (VariationID: 4327) as pathogenic by EGL Gene Diagnostics, OMIM, and Integrated Genetics. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. However, the homozygous occurrence of this variant in 9 affected individuals and the presence of this variant in combination with a reported pathogenic variant in 11 individuals with Gaucher disease increases the likelihood that the p.Gly416Ser variant is pathogenic (VariationID: 4290, 4288; PMID: 25946768, 16981045, 23430543, 25732996, 17395504). The phenotype of individuals homozygous and heterozygous for this variant is highly specific for Gaucher disease based on enzyme activity of less than 1.7 nmol/h/mg protein, consistent with disease (PMID: 25946768, 16981045, 25732996). In summary, this variant meets criteria to be classified as pathogenic for Gaucher disease in an autosomal recessive manner based on the presence of the variant in affected homozygotes and in combination with other pathogenic variants in affected individuals, the phenotype of affected individuals with the variant that is specific to the disease, and the low frequency of the variant in the general population. ACMG/AMP Criteria applied: PM3_very-strong, PM2, PP4 (Richards 2015). (less)
|
|
Pathogenic
(Sep 20, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Lewy body dementia
Parkinson disease, late-onset Gaucher disease type I Gaucher disease type II Gaucher disease type III Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome Gaucher disease perinatal lethal
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV002777935.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
|
|
Pathogenic
(Dec 28, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV002125693.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 416 of the GBA protein (p.Gly416Ser). … (more)
This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 416 of the GBA protein (p.Gly416Ser). This variant is present in population databases (rs121908311, gnomAD 0.003%). This missense change has been observed in individual(s) with Gaucher disease and/or Parkinson's disease (PMID: 8081401, 17395504, 20432762, 23430543, 25287185, 27632223, 29140481). It is commonly reported in individuals of Brazilian ancestry (PMID: 25287185). This variant is also known as p.Gly377Ser or G377S. ClinVar contains an entry for this variant (Variation ID: 4327). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GBA protein function. For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Apr 03, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000700355.2
First in ClinVar: Jun 24, 2017 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 3
Sex: mixed
|
|
Pathogenic
(Apr 27, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Gaucher disease, type 1
Affected status: yes
Allele origin:
unknown
|
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV000930234.1
First in ClinVar: Aug 04, 2019 Last updated: Aug 04, 2019 |
Geographic origin: Iran
|
|
Pathogenic
(-)
|
criteria provided, single submitter
Method: clinical testing
|
Gaucher disease type I
Gaucher disease type II Gaucher disease type III Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome
Affected status: unknown
Allele origin:
germline
|
Baylor Genetics
Accession: SCV001162847.1
First in ClinVar: Feb 29, 2020 Last updated: Feb 29, 2020 |
|
|
Pathogenic
(Apr 05, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV002578604.2
First in ClinVar: Oct 15, 2022 Last updated: Mar 04, 2023 |
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8081401, … (more)
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8081401, 25946768, 16981045, 17395504, 23430543, 25732996, 29140481, 27717005, 20432762, 21742527, 33176831, 31467847, 27632223, 25287185, 10757640, 12595585, 22429443) (less)
|
|
Likely pathogenic
(Jun 24, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Revvity Omics, Revvity
Accession: SCV002018392.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
|
|
Pathogenic
(Mar 01, 2003)
|
no assertion criteria provided
Method: literature only
|
GAUCHER DISEASE, TYPE III
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000024746.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 24, 2017 |
Comment on evidence:
In 3 Portuguese patients with type I Gaucher disease (230800), Amaral et al. (1999) identified homozygosity for a gly377-to-ser (G377S) substitution in the GBA gene. … (more)
In 3 Portuguese patients with type I Gaucher disease (230800), Amaral et al. (1999) identified homozygosity for a gly377-to-ser (G377S) substitution in the GBA gene. All 3 had mild to moderate severity with severity score indices (SSI), as defined by Zimran et al. (1989), of 8, 14, and 10, respectively. One of them had had splenectomy at age 9; the other 2 had recognized onset at ages 39 and 48 years. G377S seems to be common in Iberian patients, representing 7% and 5% of alleles in Portuguese and Spanish patients, respectively, according to Amaral et al. (1999). Park et al. (2003) identified a heterozygous G377S mutation in patients with type III Gaucher disease (231000); they had additional pathogenic GBA mutations. (less)
|
|
Pathogenic
(Mar 01, 2003)
|
no assertion criteria provided
Method: literature only
|
GAUCHER DISEASE, TYPE I
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000024745.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 24, 2017 |
Comment on evidence:
In 3 Portuguese patients with type I Gaucher disease (230800), Amaral et al. (1999) identified homozygosity for a gly377-to-ser (G377S) substitution in the GBA gene. … (more)
In 3 Portuguese patients with type I Gaucher disease (230800), Amaral et al. (1999) identified homozygosity for a gly377-to-ser (G377S) substitution in the GBA gene. All 3 had mild to moderate severity with severity score indices (SSI), as defined by Zimran et al. (1989), of 8, 14, and 10, respectively. One of them had had splenectomy at age 9; the other 2 had recognized onset at ages 39 and 48 years. G377S seems to be common in Iberian patients, representing 7% and 5% of alleles in Portuguese and Spanish patients, respectively, according to Amaral et al. (1999). Park et al. (2003) identified a heterozygous G377S mutation in patients with type III Gaucher disease (231000); they had additional pathogenic GBA mutations. (less)
|
|
Pathogenic
(May 01, 2020)
|
no assertion criteria provided
Method: research
|
Thrombocytopenia
Abnormal bleeding
Affected status: yes
Allele origin:
germline
|
Birmingham Platelet Group; University of Birmingham
Accession: SCV001450785.1
First in ClinVar: Dec 19, 2020 Last updated: Dec 19, 2020 |
|
|
Pathogenic
(May 06, 2017)
|
no assertion criteria provided
Method: clinical testing
|
Gaucher disease
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV002086458.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
|
|
not provided
(-)
|
no classification provided
Method: literature only
|
Gaucher disease
Affected status: unknown
Allele origin:
germline
|
GeneReviews
Accession: SCV000086731.3
First in ClinVar: Oct 02, 2013 Last updated: Oct 29, 2022 |
|
|
click to load more click to collapse |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Gaucher Disease. | Adam MP | - | 2023 | PMID: 20301446 |
Excessive burden of lysosomal storage disorder gene variants in Parkinson's disease. | Robak LA | Brain : a journal of neurology | 2017 | PMID: 29140481 |
Survival and dementia in GBA-associated Parkinson's disease: The mutation matters. | Cilia R | Annals of neurology | 2016 | PMID: 27632223 |
Spectrum of GBA mutations in patients with Gaucher disease from Slovakia: identification of five novel mutations. | Mattošová S | The Israel Medical Association journal : IMAJ | 2015 | PMID: 25946768 |
Improvement in Bone Mineral Density and Architecture in a Patient with Gaucher Disease Using Teriparatide. | Khan A | JIMD reports | 2015 | PMID: 25732996 |
Consanguinity and founder effect for Gaucher disease mutation G377S in a population from Tabuleiro do Norte, Northeastern Brazil. | Chaves RG | Clinical genetics | 2015 | PMID: 25287185 |
Novel mutations in the glucocerebrosidase gene of brazilian patients with Gaucher disease. | Siebert M | JIMD reports | 2013 | PMID: 23430543 |
Coinheritance of Gaucher disease and α-thalassemia resulting in confusion between two inherited hematologic diseases. | Miri-Moghaddam E | Blood cells, molecules & diseases | 2011 | PMID: 20846888 |
An unusual presentation of Gaucher's disease: aortic valve fibrosis in a patient homozygous for a rare G377S mutation. | Perić Z | Collegium antropologicum | 2010 | PMID: 20432762 |
Genetic and clinical features of patients with Gaucher disease in Hungary. | Erdos M | Blood cells, molecules & diseases | 2007 | PMID: 17395504 |
High frequency of mutation G377S in Brazilian type 3 Gaucher disease patients. | Rozenberg R | Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas | 2006 | PMID: 16981045 |
Myoclonic epilepsy in Gaucher disease: genotype-phenotype insights from a rare patient subgroup. | Park JK | Pediatric research | 2003 | PMID: 12595585 |
Gaucher disease: expression and characterization of mild and severe acid beta-glucosidase mutations in Portuguese type 1 patients. | Amaral O | European journal of human genetics : EJHG | 2000 | PMID: 10757640 |
Homozygosity for two mild glucocerebrosidase mutations of probable Iberian origin. | Amaral O | Clinical genetics | 1999 | PMID: 10466427 |
Use of denaturing gradient gel electrophoresis to identify mutant sequences in the beta-glucocerebrosidase gene. | Laubscher KH | Human mutation | 1994 | PMID: 8081401 |
Prediction of severity of Gaucher's disease by identification of mutations at DNA level. | Zimran A | Lancet (London, England) | 1989 | PMID: 2569551 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GBA | - | - | - | - |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/15d83011-90ae-4e67-8abf-85608e483a52 | - | - | - | - |
click to load more click to collapse |
Text-mined citations for rs121908311 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.