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NM_000203.5(IDUA):c.141GAG[1] (p.Arg48del) AND Mucopolysaccharidosis type 1

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 2, 2023
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:
RCV002041235.15

Allele description [Variation Report for NM_000203.5(IDUA):c.141GAG[1] (p.Arg48del)]

NM_000203.5(IDUA):c.141GAG[1] (p.Arg48del)

Genes:
IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
SLC26A1:solute carrier family 26 member 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_000203.5(IDUA):c.141GAG[1] (p.Arg48del)
HGVS:
  • NC_000004.12:g.987225GAG[1]
  • NG_008103.1:g.5229GAG[1]
  • NG_033042.1:g.11208TCC[1]
  • NG_158244.2:g.425GAG[1]
  • NM_000203.5:c.141GAG[1]MANE SELECT
  • NM_134425.4:c.576+3902_576+3904del
  • NP_000194.2:p.Arg48del
  • LRG_1277t1:c.141GAG[1]
  • LRG_1277:g.5229GAG[1]
  • LRG_1277p1:p.Arg48del
  • NC_000004.11:g.981012_981014del
  • NC_000004.11:g.981013GAG[1]
  • NR_110313.1:n.229GAG[1]
Protein change:
R48del
Links:
dbSNP: rs1713799705
NCBI 1000 Genomes Browser:
rs1713799705
Molecular consequence:
  • NM_000203.5:c.141GAG[1] - inframe deletion - [Sequence Ontology: SO:0001822]
  • NM_134425.4:c.576+3902_576+3904del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_110313.1:n.229GAG[1] - 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
SCV002315507Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Jun 2, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Identification and characterization of 13 new mutations in mucopolysaccharidosis type I patients.

Matte U, Yogalingam G, Brooks D, Leistner S, Schwartz I, Lima L, Norato DY, Brum JM, Beesley C, Winchester B, Giugliani R, Hopwood JJ.

Mol Genet Metab. 2003 Jan;78(1):37-43.

PubMed [citation]
PMID:
12559846

Genotypic and bioinformatic evaluation of the alpha-l-iduronidase gene and protein in patients with mucopolysaccharidosis type I from Colombia, Ecuador and Peru.

Pineda T, Marie S, Gonzalez J, GarcĂ­a AL, Acosta A, Morales M, Correa LN, Vivas R, Escobar X, Protzel A, Barba M, Ospina S, Corredor C, Mansilla S, Velasco HM.

Mol Genet Metab Rep. 2014;1:468-473.

PubMed [citation]
PMID:
27896125
PMCID:
PMC5121354
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002315507.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies have shown that this variant affects IDUA function (PMID: 12559846). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. This variant has been observed in individual(s) with mucopolysaccharidosis type I (MPS I) (PMID: 12559846, 27896125, 29976218). This variant is not present in population databases (gnomAD no frequency). This variant, c.144_146del, results in the deletion of 1 amino acid(s) of the IDUA protein (p.Arg48del), but otherwise preserves the integrity of the reading frame.

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

Last Updated: Dec 7, 2024