chr3-33072586-C-T
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PS1_ModeratePM2PM5PP3_ModeratePP5_Very_Strong
The NM_000404.4(GLB1):c.203G>A(p.Arg68Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R68L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000404.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249456Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135336
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461644Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727118
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74474
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-IV-B;C0268271:Infantile GM1 gangliosidosis;C0268272:GM1 gangliosidosis type 2;C0268273:GM1 gangliosidosis type 3 Pathogenic:1Uncertain:1
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not provided Pathogenic:1
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GM1 gangliosidosis;C0086652:Mucopolysaccharidosis, MPS-IV-B Pathogenic:1
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 68 of the GLB1 protein (p.Arg68Gln). This variant is present in population databases (rs572237881, gnomAD 0.01%). This missense change has been observed in individual(s) with GM1 gangliosidosis (PMID: 19472408, 29439846). ClinVar contains an entry for this variant (Variation ID: 195074). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt GLB1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GLB1 function (PMID: 19472408). This variant disrupts the p.Arg68 amino acid residue in GLB1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12644936, 25936995; internal data). 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. -
GM1 gangliosidosis Pathogenic:1
Variant summary: GLB1 c.203G>A (p.Arg68Gln) results in a conservative amino acid change located in the Glycoside hydrolase 35, catalytic domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 249456 control chromosomes. c.203G>A has been reported in the literature in at least one individual affected with GM1 Gangliosidosis (Hofer_2009). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (Hofer_2009). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic, and one laboratory classified the variant as uncertain significance. In addition, p.R68W has been reported to associate with Gangliosidosis GM1 (HGMD database), indicating R68 is critical for GLB1 function. Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at