rs371582179
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PP3PP5_Very_Strong
The NM_000404.4(GLB1):āc.1733A>Gā(p.Lys578Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_000404.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLB1 | NM_000404.4 | c.1733A>G | p.Lys578Arg | missense_variant, splice_region_variant | 15/16 | ENST00000307363.10 | NP_000395.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLB1 | ENST00000307363.10 | c.1733A>G | p.Lys578Arg | missense_variant, splice_region_variant | 15/16 | 1 | NM_000404.4 | ENSP00000306920 | P2 | |
GLB1 | ENST00000307377.12 | c.1340A>G | p.Lys447Arg | missense_variant, splice_region_variant | 12/13 | 1 | ENSP00000305920 | |||
GLB1 | ENST00000399402.7 | c.1643A>G | p.Lys548Arg | missense_variant, splice_region_variant | 15/16 | 2 | ENSP00000382333 | A2 | ||
GLB1 | ENST00000461475.5 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247460Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134468
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461892Hom.: 0 Cov.: 30 AF XY: 0.000107 AC XY: 78AN XY: 727248
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 09, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2022 | - - |
Mucopolysaccharidosis, MPS-IV-B;C0268271:Infantile GM1 gangliosidosis;C0268272:GM1 gangliosidosis type 2;C0268273:GM1 gangliosidosis type 3 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Mar 08, 2017 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
GM1 gangliosidosis Pathogenic:1Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 13, 2024 | Variant summary: GLB1 c.1733A>G (p.Lys578Arg) results in a conservative amino acid change located in the Beta-galactosidase jelly roll domain (IPR025300) 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 3.6e-05 in 247460 control chromosomes. c.1733A>G has been reported in the literature in multiple individuals affected with infantile and late-infantile/juvenile GM1 gangliosidosis (Boustany_1993, Caciotti_2011, Nestrasil_2018). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (Caciotti_2011). The following publications have been ascertained in the context of this evaluation (PMID: 8213816, 21497194, 29352662). ClinVar contains an entry for this variant (Variation ID: 252985). Based on the evidence outlined above, the variant was classified as pathogenic. - |
not provided, no classification provided | phenotyping only | GenomeConnect - GM1 | - | Variant identified in multiple registry participants. Variant classified as Pathogenic and reported on 12-08-2021 by Blueprint Genetics. Variant classidied as Pathogenic and reported on 08-11-2016 by lab or GTR ID Hudson Alpha. GenomeConnect - GM1 assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2022 | The c.1733A>G (p.K578R) alteration is located in exon 15 (coding exon 15) of the GLB1 gene. This alteration results from a A to G substitution at nucleotide position 1733, causing the lysine (K) at amino acid position 578 to be replaced by an arginine (R). Based on data from gnomAD, the G allele has an overall frequency of 0.004% (9/247460) total alleles studied. The highest observed frequency was 0.007% (8/111208) of European (non-Finnish) alleles. This variant has been reported in the homozygous state, and in conjunction with a second variant in GLB1, in multiple individuals with GM1 gangliosidosis (Boustany, 1993; Caciotti, 2011; Utz, 2015; Jarnes Utz, 2017; Bowling, 2017; Nestrasil, 2018; Ou, 2019; Arash-Kaps, 2019; King, 2020; Tebani, 2022). This amino acid position is highly conserved in available vertebrate species. In vitro studies have demonstrated that this alteration has reduced enzymatic activity (Boustany, 1993). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. - |
GM1 gangliosidosis;C0086652:Mucopolysaccharidosis, MPS-IV-B Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 578 of the GLB1 protein (p.Lys578Arg). This variant is present in population databases (rs371582179, gnomAD 0.007%). This missense change has been observed in individual(s) with GM1 gangliosidosis (PMID: 8213816, 21497194, 25557439). ClinVar contains an entry for this variant (Variation ID: 252985). 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 disruptive. Experimental studies have shown that this missense change affects GLB1 function (PMID: 8213816). This variant disrupts the p.Lys578 amino acid residue in GLB1. Other variant(s) that disrupt this residue have been observed in individuals with GLB1-related conditions (PMID: 30267299), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. - |
GM1 gangliosidosis type 2 Pathogenic:1
Pathogenic, criteria provided, single submitter | research | HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology | Jul 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at