rs747506979
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM5PP3PP5_Very_Strong
The NM_000157.4(GBA1):c.1603C>T(p.Arg535Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R535H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000157.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GBA1 | NM_000157.4 | c.1603C>T | p.Arg535Cys | missense_variant | Exon 11 of 11 | ENST00000368373.8 | NP_000148.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 91008Hom.: 0 Cov.: 11 FAILED QC
GnomAD3 exomes AF: 0.0000116 AC: 2AN: 172274Hom.: 0 AF XY: 0.0000109 AC XY: 1AN XY: 91600
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000728 AC: 5AN: 686718Hom.: 0 Cov.: 9 AF XY: 0.00000844 AC XY: 3AN XY: 355634
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 91008Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0AN XY: 41426
ClinVar
Submissions by phenotype
Gaucher disease type I Pathogenic:2
USG abdomen s/o. storage disease; Bone-marrow s/o. Storage disease; Anaemia (Hb: 8.6 g%); Plasma Chitotriosidase: 11755.7 nmol/hr/ml plasma (N.R.: 28.66 - 62.94); Beta-Glucosidase: 1.45 nmol/hr/mg protein (N.R.: 4.0 - 32.0) -
The p.Arg535Cys variant in GBA has been reported at least 10 individuals with Gaucher disease (PMID: 27865684, 30637984, 30764785) and has been identified in 0.004% (1/24272) of South Asian chromosomes and 0.004% (1/25702) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs747506979). 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: 242383) as likely pathogenic by the Institute of Human Genetics. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. One additional pathogenic variant, resulting in a different amino acid change at the same position, p.Arg535His, has been reported in association with the disease in the literature and ClinVar, supporting that a change at this position may not be tolerated (PMID: 17059888, 24756352, 17427031, 20629126, 7655857, 28947706, 23430543, 8432537; VariationID: 4311). The phenotype of an individual compound heterozygous for this variant is highly specific for Gaucher disease based on the levels of beta-glucosidase detected in the BGL test being significantly below 8.7 nmol/mg/h consistent with disease (PMID: 27865684). Additionally, the homozygous occurrence of this variant in two affected individuals and the presence of this variant in combination with reported pathogenic variants (VariationID: 4288, 4295, 4290; PMID: 30764785, 27865684, 30637984) and in five individuals with Gaucher disease increases the likelihood that the p.Arg535Cys variant is pathogenic. In summary, this variant meets criteria to be classified as pathogenic for Gaucher disease in an autosomal recessive manner based on the detection of the variant in combination with other pathogenic variants in affected individuals, the presence of another pathogenic variant at the same location, and the presence of the variant in an individual with a phenotype specific for the disease. ACMG/AMP Criteria applied: PM3_very-Strong, PM2, PM5, PP4 (Richards, 2015). -
not provided Pathogenic:2
This variant is present in population databases (rs747506979, gnomAD 0.004%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 535 of the GBA protein (p.Arg535Cys). This missense change has been observed in individual(s) with Gaucher disease and/or Parkinson's disease (PMID: 1487244, 24522292, 28727984, 29140481). This variant is also known as p.Arg496Cys or R496C. ClinVar contains an entry for this variant (Variation ID: 242383). 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. This variant disrupts the p.Arg535 amino acid residue in GBA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16293621, 27735925). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
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Gaucher disease Pathogenic:2
Variant summary: GBA c.1603C>T (p.Arg535Cys) also widely reported as p.Arg496Cys, results in a non-conservative amino acid change in 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 1.2e-05 in 172274 control chromosomes. c.1603C>T has been well reported in the literature in multiple individuals from diverse ethnicities affected with Gaucher Disease (example, Kawame_1992, Karaca_2012, Ankleshwaria_2014 and Feng_2018). These data indicate that the variant is very likely to be associated with disease. No experimental evidence demonstrating an impact on protein function was ascertained. Although at-least one publication reported its identification in a enzymatically and clinically diagnosed Gaucher disease homozygous individual with no primary data provided (Kawame_1992). One researcher has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic. This submitter cites an overlapping publication utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic. -
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Parkinson disease, late-onset Pathogenic:1
The observed missense variant c.1603C>T(p.Arg535Cys) in GBA gene has been reported previously in homozygous, compound heterozygous and heterozygous state in individuals with Gaucher disease and/or Parkinson's disease (Dimitriou E, et al., 2020. Sheth J, et al., 2019, Ankleshwaria C, et al., 2014). This variant disrupts the p.Arg535 amino acid residue in GBA and the other variant(s) that disrupt this residue have been determined to be pathogenic (Yang AC, et al., 2017). The c.1603C>T variant has 0.001% allele frequency in gnomAD Exomes. This variant has been reported to the ClinVar database as Pathogenic / Likely Pathogenic.The amino acid Arginine at position 535 is changed to a Cystiene changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence (Polyphen, SIFT and MutationTaster) predict a damaging effect on protein structure and function for this variant. The amino acid change p.Arg535Cys in GBA is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
Gaucher disease type II Pathogenic:1
The missense c.1603C>T(p.Arg535Cys) variant in GBA gene has been reported previously in homozygous and compound heterozygous states in multiple individuals affected with Gaucher disease (Sheth J, et al., 2019, Leija-Salazar M, et al., 2019; Zampieri S, et al., 2017). The p.Arg535Cys variant is present with allele frequency of 0.001% in gnomAD Exomes. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submissions). Multiple lines of computational evidences (Polyphen - Probably damaging, SIFT - Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. The reference amino acid at this position on GBA gene is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 535 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. Another missense variant [c.1604G>A (p.Arg535His)] on the same residue of this gene has previously been reported to be disease causing (Yang AC, et al., 2017), suggesting that this residue might be of clinical significance. For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at