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NM_000202.8(IDS):c.514C>T (p.Arg172Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Nov 10, 2021)
Last evaluated:
Sep 5, 2021
Accession:
VCV000010490.4
Variation ID:
10490
Description:
single nucleotide variant
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NM_000202.8(IDS):c.514C>T (p.Arg172Ter)

Allele ID
25529
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 149498301 (GRCh38) GRCh38 UCSC
X: 148579832 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.148579832G>A
NC_000023.11:g.149498301G>A
NG_011900.3:g.12034C>T
... more HGVS
Protein change
R172*, R82*
Other names
-
Canonical SPDI
NC_000023.11:149498300:G:A
Functional consequence
termination codon change [Variation Ontology VariO:0309]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA255272
OMIM: 300823.0005
dbSNP: rs104894860
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 5 criteria provided, multiple submitters, no conflicts Sep 5, 2021 RCV000011236.12
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
IDS Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
217 644
LOC106050102 - - - GRCh38 - 314

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Allele origin: germline
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences
Accession: SCV001480205.1
Submitted: (Feb 17, 2021)
Evidence details
Pathogenic
(Sep 12, 2017)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
Allele origin: germline
Invitae
Accession: SCV000628123.2
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Arg172*) in the IDS gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Sep 05, 2021)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
Allele origin: germline
Nilou-Genome Lab
Accession: SCV002014478.1
Submitted: (Nov 10, 2021)
Evidence details
Pathogenic
(Jul 01, 1992)
no assertion criteria provided
Method: literature only
MUCOPOLYSACCHARIDOSIS, TYPE II
Allele origin: germline
OMIM
Accession: SCV000031463.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Affects
(Apr 04, 2014)
no assertion criteria provided
Method: research
Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Allele origin: germline
Pediatrics,All India Institute of Medical Sciences, New Delhi
Accession: SCV001573781.1
Submitted: (May 07, 2021)
Evidence details
Comment:
The change c.514C>T (p.R172*) was found to be a nonsense variant, where the basic polar amino acid Arginine at 172 position was substituted by stop … (more)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
termination codon change
  1. Sanger sequencing was performed on ABI 3130 genetic analyser (Applied Biosystem, USA) capillary electrophoresis. Data was analysed by ABI sequence analysis (SeqScape version 2.5) software as well as manually by using software: Chromaspro (Version-1.7.5, Technilysium Pvt. Ltd, Australia) and FinchTV (Version 1.4.0, Geospiza, Perkinelmer, USA).
  1. Result not provided
Pediatrics,All India Institute of Medical Sciences, New Delhi
Accession: SCV001573781.1
Submitted: (May 07, 2021)
Evidence details

Citations for this variant

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Title Author Journal Year Link
Genetic analysis of 17 children with Hunter syndrome: identification and functional characterization of four novel mutations in the iduronate-2-sulfatase gene. Chistiakov DA Journal of genetics and genomics = Yi chuan xue bao 2014 PMID: 24780617
Analysis of the IDS gene in 38 patients with Hunter syndrome: the c.879G>A (p.Gln293Gln) synonymous variation in a female create exonic splicing. Zhang H PloS one 2011 PMID: 21829674
Molecular diagnosis of mucopolysaccharidosis type II (Hunter syndrome) by automated sequencing and computer-assisted interpretation: toward mutation mapping of the iduronate-2-sulfatase gene. Jonsson JJ American journal of human genetics 1995 PMID: 7887413
Detection of point mutations and a gross deletion in six Hunter syndrome patients. Flomen RH Genomics 1992 PMID: 1639384

Text-mined citations for rs104894860...

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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 20, 2021