NM_000404.4(GLB1):c.1588C>T (p.Arg530Cys) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Jul 26, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000404.4(GLB1):c.1588C>T (p.Arg530Cys)]

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

GLB1:galactosidase beta 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000404.4(GLB1):c.1588C>T (p.Arg530Cys)
  • NC_000003.12:g.33014202G>A
  • NG_009005.1:g.88001C>T
  • NM_000404.4:c.1588C>TMANE SELECT
  • NM_001079811.2:c.1498C>T
  • NM_001135602.2:c.1195C>T
  • NM_001317040.1:c.1732C>T
  • NP_000395.3:p.Arg530Cys
  • NP_001073279.1:p.Arg500Cys
  • NP_001129074.1:p.Arg399Cys
  • NP_001303969.1:p.Arg578Cys
  • NC_000003.11:g.33055694G>A
  • NM_000404.2:c.1588C>T
Protein change:
dbSNP: rs371397760
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000404.4:c.1588C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079811.2:c.1498C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001135602.2:c.1195C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317040.1:c.1732C>T - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000619220GeneDxcriteria provided, single submitter
Uncertain significance
(Jul 26, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000619220.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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 not observed in the homozygous state, this variant is observed in 26/9804 (0.26%) alleles from individuals of African background in the ExAC dataset (Lek et al., 2016). The R530C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R530C as a variant of uncertain significance.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2021

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