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NM_000046.5(ARSB):c.1449A>T (p.Glu483Asp)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 6, 2020)
Last evaluated:
Nov 15, 2019
Accession:
VCV000418018.3
Variation ID:
418018
Description:
single nucleotide variant
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NM_000046.5(ARSB):c.1449A>T (p.Glu483Asp)

Allele ID
406764
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q14.1
Genomic location
5: 78780550 (GRCh38) GRCh38 UCSC
5: 78076373 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.78780550T>A
NC_000005.9:g.78076373T>A
NG_007089.1:g.210985A>T
NM_000046.5:c.1449A>T MANE Select NP_000037.2:p.Glu483Asp missense
Protein change
E483D
Other names
-
Canonical SPDI
NC_000005.10:78780549:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA16618212
dbSNP: rs1064793027
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Nov 15, 2019 RCV000677488.2
Likely pathogenic 1 criteria provided, single submitter Jun 28, 2016 RCV000482506.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ARSB - - GRCh38
GRCh37
563 576

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 28, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000564592.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
A novel E483D missense change likely associated with mucopolysaccharidosis VI (MPSVI) was identified in the ARSB gene. It has not been published as a pathogenic … (more)
Uncertain significance
(Jan 01, 2018)
criteria provided, single submitter
Method: curation
Mucopolysaccharidosis type 6
Allele origin: germline
Laboratory of Diagnosis and Therapy of Lysosomal Disorders,University of Padova
Accession: SCV000802997.1
Submitted: (Apr 17, 2018)
Evidence details
Publications
PubMed (2)
Comment:
Very low frequency in GnomAD(PM2)
Uncertain significance
(Nov 15, 2019)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis type 6
Allele origin: germline
Invitae
Accession: SCV001412579.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glutamic acid with aspartic acid at codon 483 of the ARSB protein (p.Glu483Asp). The glutamic acid residue is highly conserved and … (more)

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
Mucopolysaccharidosis type VI (MPS VI) and molecular analysis: Review and classification of published variants in the ARSB gene. Tomanin R Human mutation 2018 PMID: 30118150
Molecular characterization of 355 mucopolysaccharidosis patients reveals 104 novel mutations. Pollard LM Journal of inherited metabolic disease 2013 PMID: 22976768

Text-mined citations for rs1064793027...

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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