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:

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

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

ARSA:arylsulfatase A [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_000487.6(ARSA):c.1489_1492dup (p.Arg498fs)
  • 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:
dbSNP: rs774153480
NCBI 1000 Genomes Browser:
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]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001168139GeneDxcriteria provided, single submitter
(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


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.

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

Last Updated: Oct 8, 2021

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