NM_000046.5(ARSB):c.323G>A (p.Gly108Asp) AND Mucopolysaccharidosis type 6

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 29, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003865872.2

Allele description [Variation Report for NM_000046.5(ARSB):c.323G>A (p.Gly108Asp)]

NM_000046.5(ARSB):c.323G>A (p.Gly108Asp)

Gene:
ARSB:arylsulfatase B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q14.1
Genomic location:
Preferred name:
NM_000046.5(ARSB):c.323G>A (p.Gly108Asp)
HGVS:
  • NC_000005.10:g.78969182C>T
  • NG_007089.1:g.22353G>A
  • NM_000046.5:c.323G>AMANE SELECT
  • NM_198709.3:c.323G>A
  • NP_000037.2:p.Gly108Asp
  • NP_942002.1:p.Gly108Asp
  • NC_000005.9:g.78265005C>T
Protein change:
G108D
Molecular consequence:
  • NM_000046.5:c.323G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198709.3:c.323G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Mucopolysaccharidosis type 6 (MPS6)
Synonyms:
MPS VI; Mucopolysaccharidosis type VI; MPS 6; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009661; MedGen: C0026709; Orphanet: 583; OMIM: 253200

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004666223Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Aug 29, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Mutational analysis of mucopolysaccharidosis type VI patients undergoing a phase II trial of enzyme replacement therapy.

Karageorgos L, Brooks DA, Harmatz P, Ketteridge D, Pollard A, Melville EL, Parkinson-Lawrence E, Clements PR, Hopwood JJ.

Mol Genet Metab. 2007 Feb;90(2):164-70. Epub 2006 Dec 11.

PubMed [citation]
PMID:
17161971

Molecular diagnosis of patients affected by mucopolysaccharidosis: a multicenter study.

Zanetti A, D'Avanzo F, Rigon L, Rampazzo A, Concolino D, Barone R, Volpi N, Santoro L, Lualdi S, Bertola F, Scarpa M, Tomanin R.

Eur J Pediatr. 2019 May;178(5):739-753. doi: 10.1007/s00431-019-03341-8. Epub 2019 Feb 26.

PubMed [citation]
PMID:
30809705
PMCID:
PMC6459791
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004666223.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 108 of the ARSB protein (p.Gly108Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ARSB-related conditions. 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 ARSB protein function. This variant disrupts the p.Gly108 amino acid residue in ARSB. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17161971, 30809705). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024