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NM_000487.6(ARSA):c.1150G>A (p.Glu384Lys) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Dec 6, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000723624.15

Allele description [Variation Report for NM_000487.6(ARSA):c.1150G>A (p.Glu384Lys)]

NM_000487.6(ARSA):c.1150G>A (p.Glu384Lys)

Gene:
ARSA:arylsulfatase A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_000487.6(ARSA):c.1150G>A (p.Glu384Lys)
Other names:
E382K
HGVS:
  • NC_000022.11:g.50625639C>T
  • NG_009260.2:g.7541G>A
  • NM_000487.6:c.1150G>AMANE SELECT
  • NM_001085425.3:c.1150G>A
  • NM_001085426.3:c.1150G>A
  • NM_001085427.3:c.1150G>A
  • NM_001085428.3:c.892G>A
  • NM_001362782.2:c.892G>A
  • NP_000478.3:p.Glu384Lys
  • NP_000478.3:p.Glu384Lys
  • NP_001078894.2:p.Glu384Lys
  • NP_001078895.2:p.Glu384Lys
  • NP_001078896.2:p.Glu384Lys
  • NP_001078897.1:p.Glu298Lys
  • NP_001349711.1:p.Glu298Lys
  • NC_000022.10:g.51064067C>T
  • NM_000487.5:c.1150G>A
Protein change:
E298K; GLU382LYS
Links:
OMIM: 607574.0036; dbSNP: rs74315479
NCBI 1000 Genomes Browser:
rs74315479
Molecular consequence:
  • NM_000487.6:c.1150G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001085425.3:c.1150G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001085426.3:c.1150G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001085427.3:c.1150G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001085428.3:c.892G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362782.2:c.892G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
functionally_normal [Sequence Ontology: SO:0002219] - Comment(s)
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000110796Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Pathogenic
(Apr 18, 2013)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001809416Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus
no assertion criteria provided
Likely pathogenicgermlineclinical testing

SCV001926821Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV002073989GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Dec 6, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

ASA E382K disrupts a potential exonic splicing enhancer and causes exon skipping, but missense mutations in ASA are not associated with ESEs.

Shotelersuk V, Desudchit T, Tongkobpetch S.

Int J Mol Med. 2004 Oct;14(4):683-9.

PubMed [citation]
PMID:
15375602

Missense mutations in the arylsulphatase A genes of metachromatic leukodystrophy patients.

Barth ML, Fensom A, Harris A.

Hum Mol Genet. 1993 Dec;2(12):2117-21.

PubMed [citation]
PMID:
7906588

Details of each submission

From Eurofins Ntd Llc (ga), SCV000110796.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001809416.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001926821.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV002073989.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 15375602, 7906588, 32632536)

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

Last Updated: Nov 24, 2024