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NM_000487.6(ARSA):c.511G>A (p.Asp171Asn)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000003069.7
Variation ID:
3069
Description:
single nucleotide variant
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NM_000487.6(ARSA):c.511G>A (p.Asp171Asn)

Allele ID
18108
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.33
Genomic location
22: 50627007 (GRCh38) GRCh38 UCSC
22: 51065435 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.51065435C>T
NC_000022.11:g.50627007C>T
NG_009260.2:g.6173G>A
... more HGVS
Protein change
D171N, D85N
Other names
D169N
Canonical SPDI
NC_000022.11:50627006:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00010
Trans-Omics for Precision Medicine (TOPMed) 0.00027
Links
ClinGen: CA115981
OMIM: 607574.0021
dbSNP: rs74315466
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 Nov 26, 2020 RCV000540770.5
Pathogenic 1 no assertion criteria provided Nov 7, 2018 RCV000003215.5
Uncertain significance 1 no assertion criteria provided Jan 1, 2019 RCV001251908.1
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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
(Jan 31, 2017)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: unknown
Counsyl
Accession: SCV000800480.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001305141.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Invitae
Accession: SCV000627143.4
Submitted: (Jan 07, 2021)
Evidence details
Pathogenic
(Nov 07, 2018)
no assertion criteria provided
Method: literature only
ARYLSULFATASE A PSEUDODEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000023373.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Jan 01, 2019)
no assertion criteria provided
Method: clinical testing
Intellectual disability
Allele origin: unknown
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille
Accession: SCV001427654.1
Submitted: (May 05, 2020)
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
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
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 rs74315466...

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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