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NM_000404.4(GLB1):c.1588C>T (p.Arg530Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000450616.5
Variation ID:
450616
Description:
single nucleotide variant
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NM_000404.4(GLB1):c.1588C>T (p.Arg530Cys)

Allele ID
443416
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p22.3
Genomic location
3: 33014202 (GRCh38) GRCh38 UCSC
3: 33055694 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.33055694G>A
NC_000003.12:g.33014202G>A
NG_009005.1:g.88001C>T
... more HGVS
Protein change
R530C, R399C, R500C, R578C
Other names
-
Canonical SPDI
NC_000003.12:33014201:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00080
Exome Aggregation Consortium (ExAC) 0.00025
1000 Genomes Project 0.00060
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00049
The Genome Aggregation Database (gnomAD) 0.00112
Links
ClinGen: CA2299352
dbSNP: rs371397760
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jul 26, 2017 RCV000522107.3
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000765726.1
Likely benign 1 criteria provided, single submitter Dec 5, 2020 RCV001079383.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GLB1 - - GRCh38
GRCh37
460 502

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Infantile GM1 gangliosidosis
GM1 gangliosidosis type 2
GM1 gangliosidosis type 3
Mucopolysaccharidosis, MPS-IV-B
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000897093.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Jul 26, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000619220.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R530C variant in the GLB1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. While … (more)
Likely benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-IV-B
GM1 gangliosidosis
Allele origin: germline
Invitae
Accession: SCV001018644.3
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs371397760...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021