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NM_000487.6(ARSA):c.1115G>A (p.Arg372Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Aug 12, 2021)
Last evaluated:
Apr 12, 2017
Accession:
VCV000003082.4
Variation ID:
3082
Description:
single nucleotide variant
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NM_000487.6(ARSA):c.1115G>A (p.Arg372Gln)

Allele ID
18121
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.33
Genomic location
22: 50625674 (GRCh38) GRCh38 UCSC
22: 51064102 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.11:g.50625674C>T
NG_009260.2:g.7506G>A
NM_000487.6:c.1115G>A MANE Select NP_000478.3:p.Arg372Gln missense
... more HGVS
Protein change
R372Q, R286Q
Other names
R370Q
Canonical SPDI
NC_000022.11:50625673:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA115993
OMIM: 607574.0034
dbSNP: rs74315477
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Apr 12, 2017 RCV000544790.4
Pathogenic 1 no assertion criteria provided Nov 7, 2018 RCV000003228.5
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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
593 729

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 12, 2017)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Invitae
Accession: SCV000627135.1
Submitted: (Oct 05, 2017)
Evidence details
Comment:
This sequence change replaces arginine with glutamine at codon 372 of the ARSA protein (p.Arg372Gln). The arginine residue is highly conserved and there is a … (more)
Uncertain significance
(Feb 09, 2017)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: unknown
Counsyl
Accession: SCV000800496.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Likely pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
(Autosomal recessive inheritance)
Allele origin: inherited
Kasturba Medical College, Manipal, Manipal Academy of Higher Education
Accession: SCV001781530.1
Submitted: (Aug 12, 2021)
Evidence details
Pathogenic
(Nov 07, 2018)
no assertion criteria provided
Method: literature only
METACHROMATIC LEUKODYSTROPHY, MILD
Allele origin: germline
OMIM
Accession: SCV000023386.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

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
Missense mutations as a cause of metachromatic leukodystrophy. Degradation of arylsulfatase A in the endoplasmic reticulum. Poeppel P The FEBS journal 2005 PMID: 15720392
Molecular genetics of metachromatic leukodystrophy. Gieselmann V Human mutation 1994 PMID: 7866401
An assay for the rapid detection of the arylsulfatase A pseudodeficiency allele facilitates diagnosis and genetic counseling for metachromatic leukodystrophy. Gieselmann V Human genetics 1991 PMID: 1671769

Text-mined citations for rs74315477...

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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 Nov 27, 2021