NM_000487.6(ARSA):c.1489_1492dup (p.Arg498fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 20, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001008371.1

Allele description [Variation Report for NM_000487.6(ARSA):c.1489_1492dup (p.Arg498fs)]

NM_000487.6(ARSA):c.1489_1492dup (p.Arg498fs)

Gene:
ARSA:arylsulfatase A [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_000487.6(ARSA):c.1489_1492dup (p.Arg498fs)
HGVS:
  • NC_000022.11:g.50625185_50625188dup
  • NG_009260.2:g.7994_7997dup
  • NM_000487.6:c.1489_1492dupMANE SELECT
  • NM_001085425.3:c.1489_1492dup
  • NM_001085426.3:c.1489_1492dup
  • NM_001085427.3:c.1489_1492dup
  • NM_001085428.3:c.1231_1234dup
  • NM_001362782.2:c.1231_1234dup
  • NP_000478.3:p.Arg498fs
  • NP_001078894.2:p.Arg498fs
  • NP_001078895.2:p.Arg498fs
  • NP_001078896.2:p.Arg498fs
  • NP_001078897.1:p.Arg412fs
  • NP_001349711.1:p.Arg412fs
  • NC_000022.10:g.51063613_51063616dup
  • NM_000487.5:c.1489_1492dupCCCC
Protein change:
R412fs
Links:
dbSNP: rs774153480
NCBI 1000 Genomes Browser:
rs774153480
Molecular consequence:
  • NM_000487.6:c.1489_1492dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001085425.3:c.1489_1492dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001085426.3:c.1489_1492dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001085427.3:c.1489_1492dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001085428.3:c.1231_1234dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001362782.2:c.1231_1234dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001168139GeneDxcriteria provided, single submitter
Pathogenic
(Sep 20, 2018)
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, SCV001168139.1

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

Description

The c.1489_1492dupCCCC pathogenic variant in the ARSA gene has been reported previously in association with MLD in an individual who was also compound heterozygous for another variant in ARSA (Coulter-Mackie et al., 2003). The duplication causes a frameshift starting with codon Arginine 498, changes this amino acid to a Proline residue and creates a Stop codon at position 76 of the new reading frame, denoted p.Arg498ProfsX76. The c.1489_1492dupCCCC variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). In summary, we interpret c.1489_1492dupCCCC to be a pathogenic variant.

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

Last Updated: Oct 8, 2021

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