ClinVar Genomic variation as it relates to human health
NM_000404.4(GLB1):c.1445G>A (p.Arg482His)
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
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NM_000404.4(GLB1):c.1445G>A (p.Arg482His)
Variation ID: 932 Accession: VCV000000932.15
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p22.3 3: 33016743 (GRCh38) [ NCBI UCSC ] 3: 33058235 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Apr 4, 2013 Sep 16, 2024 Jan 27, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000404.4:c.1445G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000395.3:p.Arg482His missense NM_001079811.3:c.1355G>A NP_001073279.2:p.Arg452His missense NM_001135602.3:c.1052G>A NP_001129074.2:p.Arg351His missense NM_001317040.2:c.1589G>A NP_001303969.2:p.Arg530His missense NM_001393580.1:c.1445G>A NP_001380509.1:p.Arg482His missense NC_000003.12:g.33016743C>T NC_000003.11:g.33058235C>T NG_009005.1:g.85460G>A NP_000395.2:p.Arg482His - Protein change
- R482H, R351H, R452H, R530H
- Other names
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- Canonical SPDI
- NC_000003.12:33016742:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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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.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
The Genome Aggregation Database (gnomAD) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00004
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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. |
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GLB1 | - | - |
GRCh38 GRCh37 |
1058 | 1171 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
criteria provided, single submitter
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Oct 19, 2020 | RCV000000981.7 | |
Pathogenic (2) |
no assertion criteria provided
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Feb 13, 2018 | RCV000119099.5 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 8, 2023 | RCV000174679.7 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 9, 2016 | RCV000586055.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 27, 2024 | RCV001034863.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 20, 2021 | RCV002476905.1 |
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
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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
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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. |
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Pathogenic
(Aug 09, 2016)
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criteria provided, single submitter
Method: clinical testing
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GM1 gangliosidosis
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696685.1
First in ClinVar: Mar 17, 2018 Last updated: Mar 17, 2018 |
Comment:
Variant summary: The GLB1 c.1445G>A (p.Arg482His) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant … (more)
Variant summary: The GLB1 c.1445G>A (p.Arg482His) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 1/120872 control chromosomes at a frequency of 0.0000083, which does not exceed the estimated maximal expected allele frequency of a pathogenic GLB1 variant (0.0020412). This variant has been reported in multiple patients with Morquio B disease and Gm1-gangliosidosis. Functional testing showed that variant allele with non-detectable enzyme activity. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. (less)
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Pathogenic
(Oct 19, 2020)
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criteria provided, single submitter
Method: clinical testing
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Infantile GM1 gangliosidosis
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002767855.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Type I GM1-gangliosidosis (MIM#230500). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to histidine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 3 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (2 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated ß domain 1 (PMID: 25936995). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. At least 10 type I GM1-gangliosidosis (MIM#230500) patients have been reported to be either homozygous or compound heterozygous for this variant (ClinVar; PMID: 10737981, 15943552, 15714521, 17221873, 25936995). (SP) 1201 - Heterozygous variant detected in trans with a second pathogenic heterozygous variant (NM_000404.3:c.1480-2A>G) in a recessive disease. (SP) 1206 - This variant has been shown to be paternally inherited (SA pathology Lab ID: FAMCa 2473751)/ (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Dec 20, 2021)
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criteria provided, single submitter
Method: clinical testing
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Infantile GM1 gangliosidosis
GM1 gangliosidosis type 2 GM1 gangliosidosis type 3 Mucopolysaccharidosis, MPS-IV-B
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002787745.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Jan 27, 2024)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-IV-B
GM1 gangliosidosis
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001198163.4
First in ClinVar: Apr 15, 2020 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 482 of the GLB1 protein (p.Arg482His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 482 of the GLB1 protein (p.Arg482His). This variant is present in population databases (rs72555391, gnomAD 0.006%). This missense change has been observed in individual(s) with GLB1-related conditions (PMID: 1928092, 15943552). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 932). 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) performed at Invitae 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: 15943552). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Dec 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV003840641.2
First in ClinVar: Mar 18, 2023 Last updated: Sep 16, 2024 |
Comment:
Published functional studies demonstrate that this variant results in almost no residual enzymatic activity (PMID: 15714521); In silico analysis supports that this missense variant has … (more)
Published functional studies demonstrate that this variant results in almost no residual enzymatic activity (PMID: 15714521); 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: 15714521, 15943552, 7586649, 1487238, 11511921, 1928092, 16538002, 22128166, 8500799, 21520340, 18353697, 15365997, 17221873, 21497194, 10737981, 34426522, 32779865, 25936995) (less)
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Pathogenic
(Mar 14, 2014)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000226022.5
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
Number of individuals with the variant: 7
Sex: mixed
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Pathogenic
(Feb 13, 2018)
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no assertion criteria provided
Method: clinical testing
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Mucopolysaccharidosis, MPS-IV-B
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000797872.2
First in ClinVar: Aug 05, 2018 Last updated: Dec 23, 2019 |
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Pathogenic
(May 01, 1993)
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no assertion criteria provided
Method: literature only
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MUCOPOLYSACCHARIDOSIS, TYPE IVB
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000021130.2
First in ClinVar: Apr 04, 2013 Last updated: May 10, 2021 |
Comment on evidence:
For discussion of the 1479G-A transition in the GLB1 gene, resulting in an arg482-to-his (R482H) substitution, that was found in compound heterozygous state in a … (more)
For discussion of the 1479G-A transition in the GLB1 gene, resulting in an arg482-to-his (R482H) substitution, that was found in compound heterozygous state in a patient with mucopolysaccharidosis syndrome IVB (MPS4B; 253010) by Oshima et al. (1991), see 611458.0009. transition in the GLB1 gene. Studying several Italian patients with infantile GM1-gangliosidosis (GM1G1; 230500), Mosna et al. (1992) found 1 patient who was homozygous for the R482H substitution. The R482H mutation was found in the heterozygous state in 6 other unrelated patients with the severe form of GM1-gangliosidosis, but not in 100 normal chromosomes. Thus, depending on the allele with which it is paired, the R482H substitution can result in either severe or relatively mild disease. Suzuki and Oshima (1993) likewise emphasized the occurrence of wide variation in the clinical phenotype observed with the R482H mutation depending on the nature of the second allele with which it is paired. It may lead to juvenile (230600) or chronic/adult (230650) GM1-gangliosidosis or intermediate types between infantile GM1-gangliosidosis and Morquio syndrome type B. They suggested the designation 'beta-galactosidosis' for this group of diseases with mutations of the GLB1 gene. (less)
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Pathogenic
(May 01, 1993)
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no assertion criteria provided
Method: literature only
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GM1-GANGLIOSIDOSIS, TYPE I
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000021131.2
First in ClinVar: Apr 04, 2013 Last updated: May 10, 2021 |
Comment on evidence:
For discussion of the 1479G-A transition in the GLB1 gene, resulting in an arg482-to-his (R482H) substitution, that was found in compound heterozygous state in a … (more)
For discussion of the 1479G-A transition in the GLB1 gene, resulting in an arg482-to-his (R482H) substitution, that was found in compound heterozygous state in a patient with mucopolysaccharidosis syndrome IVB (MPS4B; 253010) by Oshima et al. (1991), see 611458.0009. transition in the GLB1 gene. Studying several Italian patients with infantile GM1-gangliosidosis (GM1G1; 230500), Mosna et al. (1992) found 1 patient who was homozygous for the R482H substitution. The R482H mutation was found in the heterozygous state in 6 other unrelated patients with the severe form of GM1-gangliosidosis, but not in 100 normal chromosomes. Thus, depending on the allele with which it is paired, the R482H substitution can result in either severe or relatively mild disease. Suzuki and Oshima (1993) likewise emphasized the occurrence of wide variation in the clinical phenotype observed with the R482H mutation depending on the nature of the second allele with which it is paired. It may lead to juvenile (230600) or chronic/adult (230650) GM1-gangliosidosis or intermediate types between infantile GM1-gangliosidosis and Morquio syndrome type B. They suggested the designation 'beta-galactosidosis' for this group of diseases with mutations of the GLB1 gene. (less)
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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 |
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Recurrent and novel GLB1 mutations in India. | Bidchol AM | Gene | 2015 | PMID: 25936995 |
Crystal structure of human β-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases. | Ohto U | The Journal of biological chemistry | 2012 | PMID: 22128166 |
Chemical chaperone therapy: chaperone effect on mutant enzyme and cellular pathophysiology in β-galactosidase deficiency. | Higaki K | Human mutation | 2011 | PMID: 21520340 |
GM1 gangliosidosis and Morquio B disease: an update on genetic alterations and clinical findings. | Caciotti A | Biochimica et biophysica acta | 2011 | PMID: 21497194 |
GM1 gangliosidosis: molecular analysis of nine patients and development of an RT-PCR assay for GLB1 gene expression profiling. | Caciotti A | Human mutation | 2007 | PMID: 17221873 |
The Arg482His mutation in the beta-galactosidase gene is responsible for a high frequency of GM1 gangliosidosis carriers in a Cypriot village. | Georgiou T | Genetic testing | 2005 | PMID: 15943552 |
Role of beta-galactosidase and elastin binding protein in lysosomal and nonlysosomal complexes of patients with GM1-gangliosidosis. | Caciotti A | Human mutation | 2005 | PMID: 15714521 |
Four novel mutations in patients from the Middle East with the infantile form of GM1-gangliosidosis. | Georgiou T | Human mutation | 2004 | PMID: 15365997 |
beta-galactosidase gene mutations affecting the lysosomal enzyme and the elastin-binding protein in GM1-gangliosidosis patients with cardiac involvement. | Morrone A | Human mutation | 2000 | PMID: 10737981 |
Clinical and molecular analysis of a Japanese boy with Morquio B disease. | Ishii N | Clinical genetics | 1995 | PMID: 7586649 |
A beta-galactosidase gene mutation identified in both Morquio B disease and infantile GM1 gangliosidosis. | Suzuki Y | Human genetics | 1993 | PMID: 8500799 |
A homozygous missense arginine to histidine substitution at position 482 of the beta-galactosidase in an Italian infantile GM1-gangliosidosis patient. | Mosna G | Human genetics | 1992 | PMID: 1487238 |
Human beta-galactosidase gene mutations in morquio B disease. | Oshima A | American journal of human genetics | 1991 | PMID: 1928092 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GLB1 | - | - | - | - |
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Text-mined citations for rs72555391 ...
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.