NM_000487.6(ARSA):c.224+2T>A AND Metachromatic leukodystrophy

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 9, 2021
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:
RCV002031058.4

Allele description [Variation Report for NM_000487.6(ARSA):c.224+2T>A]

NM_000487.6(ARSA):c.224+2T>A

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.224+2T>A
HGVS:
  • NC_000022.11:g.50627554A>T
  • NG_009260.2:g.5626T>A
  • NM_000487.6:c.224+2T>AMANE SELECT
  • NM_001085425.3:c.224+2T>A
  • NM_001085426.3:c.224+2T>A
  • NM_001085427.3:c.224+2T>A
  • NM_001085428.3:c.-34-148T>A
  • NM_001362782.2:c.-34-148T>A
  • NC_000022.10:g.51065982A>T
Links:
dbSNP: rs2146727518
NCBI 1000 Genomes Browser:
rs2146727518
Molecular consequence:
  • NM_001085428.3:c.-34-148T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001362782.2:c.-34-148T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000487.6:c.224+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001085425.3:c.224+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001085426.3:c.224+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001085427.3:c.224+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Metachromatic leukodystrophy (MLD)
Synonyms:
Metachromatic leukoencephalopathy; Sulfatide lipidosis; Cerebral sclerosis diffuse metachromatic form; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0018868; MedGen: C0023522; Orphanet: 512; OMIM: 250100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002310133Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jul 9, 2021) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Phenotype of arylsulfatase A-deficient mice: relationship to human metachromatic leukodystrophy.

Hess B, Saftig P, Hartmann D, Coenen R, Lüllmann-Rauch R, Goebel HH, Evers M, von Figura K, D'Hooge R, Nagels G, De Deyn P, Peters C, Gieselmann V.

Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14821-6.

PubMed [citation]
PMID:
8962139
PMCID:
PMC26220
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002310133.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 1 of the ARSA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ARSA are known to be pathogenic (PMID: 8962139, 10477432). This variant has not been reported in the literature in individuals affected with ARSA-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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