VCV000021184.40 - ClinVar

NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(17)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser)

Variation ID: 21184 Accession: VCV000021184.40

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 22q13.33 22: 50625611 (GRCh38) [ NCBI UCSC ] 22: 51064039 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 2, 2016	Sep 29, 2024	Feb 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000487.6:c.1178C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000478.3:p.Thr393Ser	missense
NM_001085425.3:c.1178C>G	NP_001078894.2:p.Thr393Ser	missense
NM_001085426.3:c.1178C>G	NP_001078895.2:p.Thr393Ser	missense
NM_001085427.3:c.1178C>G	NP_001078896.2:p.Thr393Ser	missense
NM_001085428.3:c.920C>G	NP_001078897.1:p.Thr307Ser	missense
NM_001362782.2:c.920C>G	NP_001349711.1:p.Thr307Ser	missense
NC_000022.11:g.50625611G>C
NC_000022.10:g.51064039G>C
NG_009260.2:g.7569C>G

... more HGVS ... less HGVS

Protein change

T393S, T307S

Other names

Canonical SPDI

NC_000022.11:50625610:G:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

functionally_normal; Sequence Ontology [ SO:0002219]

As described in PMID: 37480112, ARSA enzymatic activity >13% of wild type is taken as benign and likely does not contribute to disease. [submitted by Gelb Laboratory, University of Washington]

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.40555 (C)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 30x 0.40522

1000 Genomes Project 0.40555

Trans-Omics for Precision Medicine (TOPMed) 0.46276

The Genome Aggregation Database (gnomAD), exomes 0.47985

The Genome Aggregation Database (gnomAD) 0.48362

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.48408

Exome Aggregation Consortium (ExAC) 0.48431

Links

ClinGen: CA146668 dbSNP: rs743616 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ARSA		-	-	GRCh38 GRCh37	1256	1424

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Metachromatic leukodystrophy	Benign (8)	criteria provided, multiple submitters, no conflicts	Feb 1, 2024	RCV000020311.29
not specified	Benign (6)	criteria provided, multiple submitters, no conflicts	Mar 16, 2015	RCV000078937.25
not provided	Benign (3)	criteria provided, multiple submitters, no conflicts	Mar 3, 2015	RCV000675747.16

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000304455.1 First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016
Benign (Mar 16, 2015)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000110798.8 First in ClinVar: Jan 17, 2014 Last updated: Oct 02, 2016	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ARSA Number of individuals with the variant: 167 Sex: mixed
Benign (May 28, 2019)	criteria provided, single submitter (Mendelics Assertion Criteria 2017) Method: clinical testing	Metachromatic leukodystrophy Affected status: unknown Allele origin: unknown	Mendelics Accession: SCV001141460.1 First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020
Benign (Mar 03, 2015)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001888198.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021	Comment: This variant is associated with the following publications: (PMID: 31694723, 29961769, 11941485, 1670590, 20220177)
Benign (Feb 01, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Metachromatic leukodystrophy Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001728099.4 First in ClinVar: Jun 15, 2021 Last updated: Feb 20, 2024
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005277403.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (Mar 06, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Metachromatic leukodystrophy Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000439431.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
Benign (Jul 14, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Metachromatic leukodystrophy Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV001775284.1 First in ClinVar: Aug 14, 2021 Last updated: Aug 14, 2021	Sex: mixed
Benign (Jun 07, 2017)	no assertion criteria provided Method: curation	Metachromatic leukodystrophy Affected status: no Allele origin: germline	SingHealth Duke-NUS Institute of Precision Medicine Accession: SCV000853181.1 First in ClinVar: Nov 25, 2018 Last updated: Nov 25, 2018
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Clinical Genetics, Academic Medical Center Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001923929.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Genome Diagnostics Laboratory, University Medical Center Utrecht Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001932021.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001951974.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021
Benign (Nov 18, 2019)	no assertion criteria provided Method: clinical testing	Metachromatic leukodystrophy Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV002081640.1 First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022
Uncertain significance (Oct 22, 2015)	no assertion criteria provided Method: clinical testing	not provided Affected status: unknown Allele origin: unknown	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV000801465.1 First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001742599.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021
not provided (-)	no classification provided Method: in vitro	Metachromatic leukodystrophy (Autosomal recessive inheritance) Affected status: not applicable Allele origin: not applicable	Gelb Laboratory, University of Washington Accession: SCV005046771.1 First in ClinVar: Jun 02, 2024 Last updated: Jun 02, 2024	Publications: PubMed (4) PubMed: 31694723‚ 21167507‚ 30652456‚ 37480112 Comment on evidence: 0 to < 2% of wild type ARSA enzymatic activity is taken as severe, 2 to <4% is taken moderate, 4 to 13% is taken … (more) 0 to < 2% of wild type ARSA enzymatic activity is taken as severe, 2 to <4% is taken moderate, 4 to 13% is taken as mild, and >13% is taken as benign, see PMID: 37480112 (less) Method: tandem mass spectrometry used to measure enymatic activity Result: 14.69% of wild type enzymatic activity
not provided (-)	no classification provided Method: literature only	Metachromatic leukodystrophy Affected status: unknown Allele origin: germline	GeneReviews Accession: SCV000040686.4 First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022	Publications: BookShelf: NBK1130 BookShelf: NBK1130
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Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
functionally_normal (SO:0002219)	tandem mass spectrometry used to measure enymatic activity Method citation(s): PubMed(1)	14.69% of wild type enzymatic activity	Gelb Laboratory, University of Washington Accession: SCV005046771.1	Publications PubMed (4) Comment: As described in PMID: 37480112, ARSA enzymatic activity >13% of wild type is taken as benign and likely does not contribute to disease.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Arylsulfatase A Deficiency.	Adam MP	-	2024	PMID: 20301309
Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix.	Trinidad M	Genome biology	2023	PMID: 37480112
Three novel variants in the arylsulfatase A (ARSA) gene in patients with metachromatic leukodystrophy (MLD).	Hettiarachchi D	BMC research notes	2019	PMID: 31694723
[Late infantile metachromatic leukodystrophy: case report].	Alvarez-Pabón Y	Archivos argentinos de pediatria	2019	PMID: 30652456
Molecular and structural analysis of metachromatic leukodystrophy patients in Indian population.	Shukla P	Journal of the neurological sciences	2011	PMID: 21167507
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ARSA	-	-	-	-

Text-mined citations for rs743616 ...

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 10, 2024

ClinVar Genomic variation as it relates to human health

NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs743616 ...