ClinVar Genomic variation as it relates to human health
NM_000046.5(ARSB):c.629A>G (p.Tyr210Cys)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000046.5(ARSB):c.629A>G (p.Tyr210Cys)
Variation ID: 885 Accession: VCV000000885.54
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5q14.1 5: 78964477 (GRCh38) [ NCBI UCSC ] 5: 78260300 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Jun 29, 2015 Oct 20, 2024 Mar 30, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000046.5:c.629A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000037.2:p.Tyr210Cys missense NM_198709.3:c.629A>G NP_942002.1:p.Tyr210Cys missense NC_000005.10:g.78964477T>C NC_000005.9:g.78260300T>C NG_007089.1:g.27058A>G P15848:p.Tyr210Cys - Protein change
- Y210C
- Other names
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- Canonical SPDI
- NC_000005.10:78964476:T:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe 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.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00012
The Genome Aggregation Database (gnomAD) 0.00017
The Genome Aggregation Database (gnomAD), exomes 0.00027
Exome Aggregation Consortium (ExAC) 0.00040
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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. |
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ARSB | - | - |
GRCh38 GRCh37 |
720 | 967 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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Mar 30, 2024 | RCV000000933.32 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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May 2, 2022 | RCV000078003.41 | |
Pathogenic (1) |
criteria provided, single submitter
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Nov 2, 2017 | RCV000779747.9 | |
ARSB-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jan 22, 2024 | RCV003904792.2 |
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. |
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Pathogenic
(Jan 01, 2018)
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criteria provided, single submitter
Method: curation
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Mucopolysaccharidosis type 6
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova
Accession: SCV000803096.1
First in ClinVar: Oct 09, 2016 Last updated: Oct 09, 2016 |
Comment:
In vitro functional studies supportive of a damaging effect on the gene product (low to no ARSB activity in homozygotes; PS3); Prevalence of the variant … (more)
In vitro functional studies supportive of a damaging effect on the gene product (low to no ARSB activity in homozygotes; PS3); Prevalence of the variant in affected is increased compared with controls (PS4); Reputable source identifies as pathogenic (PP5) (less)
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Pathogenic
(Jul 25, 2013)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000109841.8
First in ClinVar: Jan 17, 2014 Last updated: Jun 29, 2015 |
Number of individuals with the variant: 2
Sex: mixed
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Pathogenic
(Nov 02, 2017)
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criteria provided, single submitter
Method: clinical testing
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Metachromatic leukodystrophy
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000916522.1
First in ClinVar: Jun 02, 2019 Last updated: Jun 02, 2019 |
Comment:
Variant summary: The ARSB c.629A>G (p.Tyr210Cys) variant located in the Sulfatase, N-termail (via InterPro) involves the alteration of a conserved nucleotide and 5/5 in silico … (more)
Variant summary: The ARSB c.629A>G (p.Tyr210Cys) variant located in the Sulfatase, N-termail (via InterPro) involves the alteration of a conserved nucleotide and 5/5 in silico tools predict a damaging outcome for this variant. A functional study, Brands_2013, supports these predictions by observing the variant to cause a significant decrease in ARSB activity in comparison to wild type. This variant was found in 75/277016 control chromosomes (gnomAD), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.000569 (72/126548), which does not exceed the estimated maximal expected allele frequency of a pathogenic ARSB variant (0.0022361). Multiple publications have cited the variant homozygously and in compound heterozygosity in affected individuals and indicated the variant to be one of the of most common mutations (Karageorgos_2007). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. (less)
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Pathogenic
(May 02, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001764303.3
First in ClinVar: Aug 07, 2021 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate that expression of Y210C mutant cell lines results in approximately 2% residual arylsulfatase activity, supporting a damaging effect (Litjens et al., … (more)
Published functional studies demonstrate that expression of Y210C mutant cell lines results in approximately 2% residual arylsulfatase activity, supporting a damaging effect (Litjens et al., 1996; Brands et al., 2013).; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21917494, 15324318, 28552677, 21791832, 23657977, 24373060, 24221504, 23557332, 8651289, 14974081, 22441840, 22133300, 24389823, 18486607, 17458871, 30118150, 33209960, 31589614, 21514195) (less)
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Pathogenic
(Feb 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis type 6
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV003842048.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.027%). Functional studies provide strong evidence of the … (more)
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.027%). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 11939792, 23557332, 8651289). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.97; 3Cnet: 1.00). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 17458871, 21514195, 23557332, 24221504, 8651289). A different missense change at the same codon (p.Tyr210His) has been reported to be associated with ARSB related disorder (ClinVar ID: VCV001469785). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Skeletal dysplasia (present)
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Pathogenic
(Feb 22, 2021)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis type 6
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002018841.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Mar 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis type 6
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004206738.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Oct 31, 2018)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis type 6
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000894363.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
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Pathogenic
(Jan 25, 2024)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis type 6
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000957251.6
First in ClinVar: Aug 14, 2019 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 210 of the ARSB protein … (more)
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 210 of the ARSB protein (p.Tyr210Cys). This variant is present in population databases (rs118203943, gnomAD 0.06%). This missense change has been observed in individuals with ARSB-related conditions (PMID: 8651289, 17458871, 21514195, 23557332, 24221504). ClinVar contains an entry for this variant (Variation ID: 885). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ARSB protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ARSB function (PMID: 8651289, 11939792, 23557332). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Apr 01, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001248199.26
First in ClinVar: May 12, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
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Pathogenic
(Jun 01, 1996)
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no assertion criteria provided
Method: literature only
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MUCOPOLYSACCHARIDOSIS, TYPE VI
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000021083.5
First in ClinVar: Apr 04, 2013 Last updated: Oct 09, 2016 |
Comment on evidence:
In 2 sibs with a mild form of mucopolysaccharidosis type VI (MPS6; 253200), Litjens et al. (1996) identified compound heterozygosity for 2 mutations in the … (more)
In 2 sibs with a mild form of mucopolysaccharidosis type VI (MPS6; 253200), Litjens et al. (1996) identified compound heterozygosity for 2 mutations in the ARSB gene: a 629A-G transition resulting in a tyr210-to-cys (Y210C) substitution, and R95Q (611542.0008). An additional unrelated patient with an intermediate phenotype was compound heterozygous for Y210C and H393P (611542.0010). Functional expression studies in CHO cells showed that the Y210C mutant retained about 2% residual activity. (less)
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Mucopolysaccharidosis type VI
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001457627.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001974238.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
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Pathogenic
(Jan 22, 2024)
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no assertion criteria provided
Method: clinical testing
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ARSB-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004719154.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The ARSB c.629A>G variant is predicted to result in the amino acid substitution p.Tyr210Cys. This variant has been reported to be causative for mucopolysaccharidosis VI … (more)
The ARSB c.629A>G variant is predicted to result in the amino acid substitution p.Tyr210Cys. This variant has been reported to be causative for mucopolysaccharidosis VI syndrome (see for example Litjens et al 1996. PubMed ID: 8651289; Brands et al. 2013. PubMed ID: 23557332; Jurecka. 2014. PubMed ID: 24221504). This variant is reported in 0.056% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001739615.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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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: SCV001954793.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Mucopolysaccharidosis type VI in Russia, Kazakhstan, and Central and Eastern Europe. | Jurecka A | Pediatrics international : official journal of the Japan Pediatric Society | 2014 | PMID: 24373060 |
Attenuated osteoarticular phenotype of type VI mucopolysaccharidosis: a report of four patients and a review of the literature. | Jurecka A | Clinical rheumatology | 2014 | PMID: 24221504 |
Spondyloepiphyseal dysplasias and bilateral legg-calvé-perthes disease: diagnostic considerations for mucopolysaccharidoses. | Mendelsohn NJ | JIMD reports | 2013 | PMID: 23657977 |
Mucopolysaccharidosis type VI phenotypes-genotypes and antibody response to galsulfase. | Brands MM | Orphanet journal of rare diseases | 2013 | PMID: 23557332 |
Clinical characteristics of adults with slowly progressing mucopolysaccharidosis VI: a case series. | Thümler A | Journal of inherited metabolic disease | 2012 | PMID: 22441840 |
Molecular analysis of mucopolysaccharidosis type VI in Poland, Belarus, Lithuania and Estonia. | Jurecka A | Molecular genetics and metabolism | 2012 | PMID: 22133300 |
Mucopolysaccharidosis type VI (Maroteaux-Lamy syndrome) with a predominantly cardiac phenotype. | Jurecka A | Molecular genetics and metabolism | 2011 | PMID: 21917494 |
Attenuated mucopolysaccharidosis type VI (Maroteaux-Lamy syndrome) due to homozygosity for the p.Y210C mutation in the ARSB gene. | Gottwald I | Molecular genetics and metabolism | 2011 | PMID: 21514195 |
Difficulties in diagnosing slowly progressive mucopolysaccharidosis VI: A case series. | Scarpa M | Journal of pediatric rehabilitation medicine | 2010 | PMID: 21791832 |
Mutational analysis of 105 mucopolysaccharidosis type VI patients. | Karageorgos L | Human mutation | 2007 | PMID: 17458871 |
Mutational analysis of mucopolysaccharidosis type VI patients undergoing a trial of enzyme replacement therapy. | Karageorgos L | Human mutation | 2004 | PMID: 14974081 |
Mucopolysaccharidosis type VI (Maroteaux-Lamy syndrome): a Y210C mutation causes either altered protein handling or altered protein function of N-acetylgalactosamine 4-sulfatase at multiple points in the vacuolar network. | Bradford TM | Biochemistry | 2002 | PMID: 11939792 |
[Identification of mutations in the arylsulfatase B gene in Russian mucopolysaccharidosis type VI patients]. | Voskoboeva EIu | Genetika | 2000 | PMID: 10923267 |
Identification, expression, and biochemical characterization of N-acetylgalactosamine-4-sulfatase mutations and relationship with clinical phenotype in MPS-VI patients. | Litjens T | American journal of human genetics | 1996 | PMID: 8651289 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ARSB | - | - | - | - |
- | - | - | - | DOI: 10.1016/j.ymgme.2007.10.091 |
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Text-mined citations for rs118203943 ...
HelpRecord last updated Nov 19, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.