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NM_000487.6(ARSA):c.1210+1G>A

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Oct 4, 2021)
Last evaluated:
Aug 1, 2021
Accession:
VCV000003058.10
Variation ID:
3058
Description:
single nucleotide variant
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NM_000487.6(ARSA):c.1210+1G>A

Allele ID
18097
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.33
Genomic location
22: 50625578 (GRCh38) GRCh38 UCSC
22: 51064006 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.51064006C>T
NM_001085427.3:c.1210+1G>A splice donor
NM_001085428.3:c.952+1G>A splice donor
... more HGVS
Protein change
-
Other names
IVS7DS, G-A, +1
Canonical SPDI
NC_000022.11:50625577:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA115964
OMIM: 607574.0009
dbSNP: rs80338820
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Aug 1, 2021 RCV000723835.3
Pathogenic 4 criteria provided, multiple submitters, no conflicts Jan 23, 2021 RCV000020312.11
Pathogenic 1 no assertion criteria provided Dec 1, 1991 RCV000003204.2
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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

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 13, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232062.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Mar 14, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143056.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (5)
Comment:
The variant disrupts a canonical splice site, and is therefore predicted to result in the loss of a functional protein. Found in at least one … (more)
Pathogenic
(Nov 11, 2019)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001193871.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (2)
Comment:
NM_000487.5(ARSA):c.1210+1G>A is classified as pathogenic in the context of metachromatic leukodystrophy. Sources cited for classification include the following: PMID 23701968 and 1684088. Classification of NM_000487.5(ARSA):c.1210+1G>A … (more)
Pathogenic
(Jan 23, 2021)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001478805.1
Submitted: (Feb 09, 2021)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: ARSA c.1210+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)
Pathogenic
(Aug 25, 2020)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Invitae
Accession: SCV000627137.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change affects a donor splice site in the last intron (intron 7) of the ARSA gene. While this is not anticipated to result … (more)
Pathogenic
(Aug 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001962458.1
Submitted: (Oct 04, 2021)
Evidence details
Pathogenic
(Dec 01, 1991)
no assertion criteria provided
Method: literature only
METACHROMATIC LEUKODYSTROPHY, JUVENILE
Allele origin: germline
OMIM
Accession: SCV000023362.1
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
pathologic
(Aug 25, 2011)
no assertion criteria provided
Method: curation
Arylsulfatase A Deficiency
Allele origin: not provided
GeneReviews
Accession: SCV000040687.1
Submitted: (Jan 08, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.

Functional evidence

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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

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Title Author Journal Year Link
Arylsulfatase A Deficiency Gomez-Ospina N - 2020 PMID: 20301309
Biochemical and Genetic Analysis of Seven Korean Individuals With Suspected Metachromatic Leukodystrophy. Han M Annals of laboratory medicine 2015 PMID: 26131420
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Apolipoprotein E genotype and LRP1 polymorphisms in patients with different clinical types of metachromatic leukodystrophy. Ługowska A Gene 2013 PMID: 23701968
Molecular and clinical consequences of novel mutations in the arylsulfatase A gene. Ługowska A Clinical genetics 2009 PMID: 19021637
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Late-onset metachromatic leukodystrophy: genotype strongly influences phenotype. Rauschka H Neurology 2006 PMID: 16966551
Homozygote for mutation c.1204 + 1G > A of the ARSA gene presents with a late-infantile form of metachromatic leukodystrophy and a rare MRI white matter lesion type. Ługowska A Journal of applied genetics 2005 PMID: 16110195
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098
Two new arylsulfatase A (ARSA) mutations in a juvenile metachromatic leukodystrophy (MLD) patient. Fluharty AL American journal of human genetics 1991 PMID: 1684088
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ARSA - - - -

Text-mined citations for rs80338820...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021