Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000487.6(ARSA):c.854+1G>A

Help
Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 26, 2019
Accession:
VCV000928475.3
Variation ID:
928475
Description:
single nucleotide variant
Help

NM_000487.6(ARSA):c.854+1G>A

Allele ID
917570
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.33
Genomic location
22: 50626590 (GRCh38) GRCh38 UCSC
22: 51065018 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.51065018C>T
NC_000022.11:g.50626590C>T
NM_000487.6:c.854+1G>A MANE Select splice donor
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000022.11:50626589:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jun 26, 2019 RCV001192373.3
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ARSA - - GRCh38
GRCh37
586 722

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 25, 2019)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001360436.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: ARSA c.854+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Likely pathogenic
(Jun 26, 2019)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Invitae
Accession: SCV001381431.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects a donor splice site in intron 4 of the ARSA gene. It is expected to disrupt RNA splicing and likely results … (more)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Identification of 12 novel mutations and two new polymorphisms in the arylsulfatase A gene: haplotype and genotype-phenotype correlation studies in Spanish metachromatic leukodystrophy patients. Gort L Human mutation 1999 PMID: 10477432
Phenotype of arylsulfatase A-deficient mice: relationship to human metachromatic leukodystrophy. Hess B Proceedings of the National Academy of Sciences of the United States of America 1996 PMID: 8962139
Metachromatic leukodystrophy in the Navajo Indian population: a splice site mutation in intron 4 of the arylsulfatase A gene. Pastor-Soler NM Human mutation 1994 PMID: 7833949

Record last updated Jun 14, 2021