NM_000202.8(IDS):c.781C>T (p.Pro261Ser) AND Mucopolysaccharidosis, MPS-II

Clinical significance:Uncertain significance (Last evaluated: Jul 16, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001345881.1

Allele description [Variation Report for NM_000202.8(IDS):c.781C>T (p.Pro261Ser)]

NM_000202.8(IDS):c.781C>T (p.Pro261Ser)

Genes:
LOC106050102:IDS recombination region [Gene]
IDS:iduronate 2-sulfatase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_000202.8(IDS):c.781C>T (p.Pro261Ser)
HGVS:
  • NC_000023.11:g.149496444G>A
  • NG_011900.3:g.13891C>T
  • NG_042264.1:g.9799G>A
  • NM_000202.8:c.781C>TMANE SELECT
  • NM_001166550.4:c.511C>T
  • NM_006123.5:c.781C>T
  • NP_000193.1:p.Pro261Ser
  • NP_001160022.1:p.Pro171Ser
  • NP_006114.1:p.Pro261Ser
  • NC_000023.10:g.148577975G>A
  • NR_104128.2:n.950C>T
Protein change:
P171S
Molecular consequence:
  • NM_000202.8:c.781C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166550.4:c.511C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006123.5:c.781C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104128.2:n.950C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Mucopolysaccharidosis, MPS-II (MPS2)
Synonyms:
MPS II; Attenuated MPS (subtype; formerly known as mild MPS II); Severe MPS II; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010674; MedGen: C0026705; Orphanet: 580; OMIM: 309900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001540028Invitaecriteria provided, single submitter
Uncertain significance
(Jul 16, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001540028.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces proline with serine at codon 261 of the IDS protein (p.Pro261Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with IDS-related conditions. 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 IDS protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 28, 2021

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