ClinVar Genomic variation as it relates to human health
NM_000202.8(IDS):c.262C>T (p.Arg88Cys)
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_000202.8(IDS):c.262C>T (p.Arg88Cys)
Variation ID: 92618 Accession: VCV000092618.23
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: Xq28 X: 149503468 (GRCh38) [ NCBI UCSC ] X: 148584998 (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 Dec 26, 2017 Sep 16, 2024 Jun 7, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000202.8:c.262C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000193.1:p.Arg88Cys missense NM_000202.4:c.262C>T NM_000202.7:c.262C>T NM_001166550.4:c.15-23C>T intron variant NM_006123.5:c.262C>T NP_006114.1:p.Arg88Cys missense NR_104128.2:n.431C>T non-coding transcript variant NC_000023.11:g.149503468G>A NC_000023.10:g.148584998G>A NG_011900.3:g.6867C>T P22304:p.Arg88Cys - Protein change
- R88C
- Other names
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- Canonical SPDI
- NC_000023.11:149503467:G:A
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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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Unknown function
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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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- 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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IDS | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
663 | 1579 |
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
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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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Jun 7, 2024 | RCV000177014.28 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jun 8, 2023 | RCV000790676.13 |
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
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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
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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
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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
(Sep 05, 2021)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV002014482.1
First in ClinVar: Nov 13, 2021 Last updated: Nov 13, 2021 |
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Pathogenic
(Jan 09, 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: SCV000228818.5
First in ClinVar: Jun 28, 2015 Last updated: Jul 30, 2019 |
Number of individuals with the variant: 2
Sex: mixed
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Affected status: yes
Allele origin:
germline
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Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences
Accession: SCV001480189.1
First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021 |
Clinical Features:
Motor delay (present) , Developmental regression (present) , Coarse facial features (present) , Depressed nasal bridge (present) , Short stature (present) , Macrocephaly (present) , … (more)
Motor delay (present) , Developmental regression (present) , Coarse facial features (present) , Depressed nasal bridge (present) , Short stature (present) , Macrocephaly (present) , Dysostosis multiplex (present) , Flexion contracture (present) (less)
Age: 0-9 years
Sex: male
Ethnicity/Population group: Indian
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
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Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
Accession: SCV002053817.1
First in ClinVar: Jan 08, 2022 Last updated: Jan 08, 2022 |
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Pathogenic
(Feb 23, 2022)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002103402.1
First in ClinVar: Mar 12, 2022 Last updated: Mar 12, 2022 |
Comment:
Variant summary: IDS c.262C>T (p.Arg88Cys) results in a non-conservative amino acid change located in the Sulfatase, N-terminal domain (IPR000917) of the encoded protein sequence. Five … (more)
Variant summary: IDS c.262C>T (p.Arg88Cys) results in a non-conservative amino acid change located in the Sulfatase, N-terminal domain (IPR000917) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 114316 control chromosomes (gnomAD). c.262C>T has been reported in the literature in multiple individuals affected with Mucopolysaccharidosis Type II (Hunter Syndrome) (e.g. Parkinson_2004, Chang_2005, Froissart_2007, Charoenwattanasatien_2012, Dvorakova_2017). These data indicate that the variant is very likely to be associated with disease. Experimental evidence demonstrated the variant confers very little residual IDS activity (Chang_2005, Charoenwattanasatien_2012). Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Sep 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Affected status: yes
Allele origin:
germline
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV002583505.1
First in ClinVar: Oct 22, 2022 Last updated: Oct 22, 2022 |
Comment:
The hemizygous status for variant c.262C>T(p.Arg88Cys) in exon 3 of IDS gene. The variant has not been repoted in the 1000 genome gnomAD databases. The … (more)
The hemizygous status for variant c.262C>T(p.Arg88Cys) in exon 3 of IDS gene. The variant has not been repoted in the 1000 genome gnomAD databases. The in silico prediction is damaging by DANN, LRT, SIFT and MutationTaster. (less)
Age: 0-9 years
Sex: male
Method: DNA was used to perform targeted gene capture using a custom capture kit. Libraries were sequenced to mean >80-100X coverage on Illumina sequencing platform. Sequence obtained were aligned to human references genome using BWA program and analyzed using Picard and GATK-Lite toolkit to identify variants in the targeted genes relevant to clinical indication
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Pathogenic
(Jun 30, 2022)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003825279.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Jul 26, 2017)
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criteria provided, single submitter
Method: clinical testing
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Mucopolysaccharidosis, MPS-II
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000628121.4
First in ClinVar: Dec 26, 2017 Last updated: Feb 14, 2024 |
Comment:
A different missense substitution at this codon (p.Arg88His) has been determined to be pathogenic (PMID: 9921913, 9660053, 10215411, 10838181, 24515576). This suggests that the arginine … (more)
A different missense substitution at this codon (p.Arg88His) has been determined to be pathogenic (PMID: 9921913, 9660053, 10215411, 10838181, 24515576). This suggests that the arginine residue is critical for IDS protein function and that other missense substitutions at this position may also be pathogenic. For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects IDS post-translational modification and results in a protein with an almost undetectable enzymatic activity (PMID: 15614569, 22990955). This variant has been reported in several individuals affected with mucopolysaccharidosis type II (PMID: 7814022, 8940265 , 9950361 , 15614569, 17063374, 22990955, 24125893, 26762690). ClinVar contains an entry for this variant (Variation ID: 92618). While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This sequence change replaces arginine with cysteine at codon 88 of the IDS protein (p.Arg88Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. (less)
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Pathogenic
(Jun 07, 2024)
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criteria provided, single submitter
Method: literature only
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Mucopolysaccharidosis, MPS-II
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova
Accession: SCV005088943.1
First in ClinVar: Aug 04, 2024 Last updated: Aug 04, 2024
Comment:
Classification method: ACMG Guidelines [PMID:25741868] with modifications
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Comment:
In vitro or in vivo functional studies supportive of a damaging effect (PS3_Strong), Prevalence of the variant significantly increased in affected individuals compared with controls … (more)
In vitro or in vivo functional studies supportive of a damaging effect (PS3_Strong), Prevalence of the variant significantly increased in affected individuals compared with controls (PS4_Strong), Located in a mutational hot spot and/or critical functional domain (PM1_Moderate), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Cosegregation with disease in multiple affected family members (PP1_Moderate), Missense variant in a gene with a low rate of benign missense variation (PP2_Supporting), Multiple lines of computational evidence support a deleterious effect (PP3_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Strong) (less)
Number of individuals with the variant: 46
Sex: male
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Pathogenic
(Jun 08, 2023)
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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: SCV005201690.1
First in ClinVar: Sep 16, 2024 Last updated: Sep 16, 2024 |
Comment:
Published functional studies demonstrate reduced IDS enzyme activity (Chang et al., 2005; Charoenwattanasatien et al., 2012); Not observed at significant frequency in large population cohorts … (more)
Published functional studies demonstrate reduced IDS enzyme activity (Chang et al., 2005; Charoenwattanasatien et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 7814022, 22990955, 15614569, 35144014, 32036093, 27695081, 33676511, 30639582, 34813777, 26762690, 31877959) (less)
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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. |
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Unknown function
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV002583505.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Clinical characteristics and genotypes of 201 patients with mucopolysaccharidosis type II in China: A retrospective, observational study. | Zhong L | Clinical genetics | 2023 | PMID: 36945845 |
Phenotypic and genetic characteristics of 130 patients with mucopolysaccharidosis type II: A single-center retrospective study in China. | Zhang Z | Frontiers in genetics | 2023 | PMID: 36713083 |
Genotype-phenotype spectrum of 130 unrelated Indian families with Mucopolysaccharidosis type II. | Agrawal N | European journal of medical genetics | 2022 | PMID: 35144014 |
Molecular analysis and novel variation identification of Chinese pedigrees with mucopolysaccharidosis using targeted next-generation sequencing. | Fang X | Clinica chimica acta; international journal of clinical chemistry | 2022 | PMID: 34813777 |
Genotype-phenotype studies in a large cohort of Brazilian patients with Hunter syndrome. | Josahkian JA | American journal of medical genetics. Part C, Seminars in medical genetics | 2021 | PMID: 33960103 |
Analysis of long-term observations of the large group of Russian patients with Hunter syndrome (mucopolysaccharidosis type II). | Semyachkina AN | BMC medical genomics | 2021 | PMID: 33676511 |
Setup and Validation of a Targeted Next-Generation Sequencing Approach for the Diagnosis of Lysosomal Storage Disorders. | Zanetti A | The Journal of molecular diagnostics : JMD | 2020 | PMID: 32036093 |
Identification and Functional Characterization of IDS Gene Mutations Underlying Taiwanese Hunter Syndrome (Mucopolysaccharidosis Type II). | Lin HY | International journal of molecular sciences | 2019 | PMID: 31877959 |
Genetic analysis of 63 Chinese patients with mucopolysaccharidosis type II: Functional characterization of seven novel IDS variants. | Zhang W | Clinica chimica acta; international journal of clinical chemistry | 2019 | PMID: 30639582 |
Genotype-phenotype correlation in 44 Czech, Slovak, Croatian and Serbian patients with mucopolysaccharidosis type II. | Dvorakova L | Clinical genetics | 2017 | PMID: 27883178 |
Wide allelic heterogeneity with predominance of large IDS gene complex rearrangements in a sample of Mexican patients with Hunter syndrome. | Alcántara-Ortigoza MA | Clinical genetics | 2016 | PMID: 26762690 |
Enzyme Replacement Therapy in Mucopolysaccharidosis II Patients Under 1 Year of Age. | Lampe C | JIMD reports | 2014 | PMID: 24515576 |
Mucopolysaccharidosis type II: identification of 30 novel mutations among Latin American patients. | Brusius-Facchin AC | Molecular genetics and metabolism | 2014 | PMID: 24125893 |
Molecular characterization of 355 mucopolysaccharidosis patients reveals 104 novel mutations. | Pollard LM | Journal of inherited metabolic disease | 2013 | PMID: 22976768 |
Decreasing activity and altered protein processing of human iduronate-2-sulfatase mutations demonstrated by expression in COS7 cells. | Charoenwattanasatien R | Biochemical genetics | 2012 | PMID: 22990955 |
Mucopolysaccharidosis type II: an update on mutation spectrum. | Froissart R | Acta paediatrica (Oslo, Norway : 1992) | 2007 | PMID: 17391447 |
Molecular characterization of Portuguese patients with mucopolysaccharidosis type II shows evidence that the IDS gene is prone to splicing mutations. | Alves S | Journal of inherited metabolic disease | 2006 | PMID: 17063374 |
Expression studies of mutations underlying Taiwanese Hunter syndrome (mucopolysaccharidosis type II). | Chang JH | Human genetics | 2005 | PMID: 15614569 |
Iduronate-2-sulphatase protein detection in plasma from mucopolysaccharidosis type II patients. | Parkinson EJ | Molecular genetics and metabolism | 2004 | PMID: 14728992 |
Molecular basis of mucopolysaccharidosis type II in Portugal: identification of four novel mutations. | Moreira da Silva I | Clinical genetics | 2001 | PMID: 11683780 |
Expression of five iduronate-2-sulfatase site-directed mutations. | Villani GR | Biochimica et biophysica acta | 2000 | PMID: 10838181 |
Molecular basis of iduronate-2-sulphatase gene mutations in patients with mucopolysaccharidosis type II (Hunter syndrome). | Li P | Journal of medical genetics | 1999 | PMID: 9950361 |
Detection of four novel mutations in the iduronate-2-sulfatase gene. Mutations in brief no. 123. Online. | Balzano N | Human mutation | 1998 | PMID: 10215411 |
Mutational spectrum of the iduronate-2-sulfatase (IDS) gene in 36 unrelated Russian MPS II patients. | Karsten S | Human genetics | 1998 | PMID: 9921913 |
Identification of iduronate sulfatase gene alterations in 70 unrelated Hunter patients. | Froissart R | Clinical genetics | 1998 | PMID: 9660053 |
Mucopolysaccharidosis type II (Hunter syndrome): mutation "hot spots" in the iduronate-2-sulfatase gene. | Rathmann M | American journal of human genetics | 1996 | PMID: 8940265 |
Evidence for an iduronate-sulfatase pseudogene near the functional Hunter syndrome gene in Xq27.3-q28. | Rathmann M | Human genetics | 1995 | PMID: 7814022 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=IDS | - | - | - | - |
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Text-mined citations for rs398123249 ...
HelpRecord last updated Oct 27, 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.