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NM_000203.5(IDUA):c.1375C>T (p.Arg459Trp) AND Mucopolysaccharidosis type 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 24, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001977240.4

Allele description [Variation Report for NM_000203.5(IDUA):c.1375C>T (p.Arg459Trp)]

NM_000203.5(IDUA):c.1375C>T (p.Arg459Trp)

Gene:
IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_000203.5(IDUA):c.1375C>T (p.Arg459Trp)
HGVS:
  • NC_000004.12:g.1002917C>T
  • NG_008103.1:g.20921C>T
  • NM_000203.5:c.1375C>TMANE SELECT
  • NM_001363576.1:c.979C>T
  • NP_000194.2:p.Arg459Trp
  • NP_001350505.1:p.Arg327Trp
  • LRG_1277t1:c.1375C>T
  • LRG_1277:g.20921C>T
  • LRG_1277p1:p.Arg459Trp
  • NC_000004.11:g.996705C>T
  • NR_110313.1:n.1463C>T
Protein change:
R327W
Links:
dbSNP: rs2153022668
NCBI 1000 Genomes Browser:
rs2153022668
Molecular consequence:
  • NM_000203.5:c.1375C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363576.1:c.979C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110313.1:n.1463C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Mucopolysaccharidosis type 1
Synonyms:
Mucopolysaccharidosis type I; MPS 1; Attenuated MPS I (subtype); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0001586; MedGen: C0023786

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002262978Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Nov 24, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002262978.3

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. This variant has not been reported in the literature in individuals with IDUA-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces arginine with tryptophan at codon 459 of the IDUA protein (p.Arg459Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan.

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

Last Updated: Sep 29, 2024