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NM_000203.5(IDUA):c.3G>A (p.Met1Ile) AND Mucopolysaccharidosis type 1

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 28, 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:
RCV003323676.7

Allele description [Variation Report for NM_000203.5(IDUA):c.3G>A (p.Met1Ile)]

NM_000203.5(IDUA):c.3G>A (p.Met1Ile)

Genes:
IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
SLC26A1:solute carrier family 26 member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_000203.5(IDUA):c.3G>A (p.Met1Ile)
HGVS:
  • NC_000004.12:g.987087G>A
  • NG_008103.1:g.5091G>A
  • NG_033042.1:g.11350C>T
  • NG_158244.2:g.287G>A
  • NM_000203.5:c.3G>AMANE SELECT
  • NM_134425.4:c.576+4041C>T
  • NP_000194.2:p.Met1Ile
  • LRG_1277t1:c.3G>A
  • LRG_1277:g.5091G>A
  • LRG_1277p1:p.Met1Ile
  • NC_000004.11:g.980875G>A
  • NM_000203.3:c.3G>A
  • NM_000203.4:c.3G>A
  • NR_110313.1:n.91G>A
Protein change:
M1I
Links:
dbSNP: rs1553914740
NCBI 1000 Genomes Browser:
rs1553914740
Molecular consequence:
  • NM_000203.5:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_134425.4:c.576+4041C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000203.5:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110313.1:n.91G>A - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004030091Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Jul 28, 2023) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Mucopolysaccharidosis type I: identification of novel mutations that cause Hurler/Scheie syndrome in Chinese families.

Lee-Chen GJ, Wang TR.

J Med Genet. 1997 Nov;34(11):939-41.

PubMed [citation]
PMID:
9391892
PMCID:
PMC1051126

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004030091.2

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

Description

Variant summary: IDUA c.3G>A (p.Met1Ile) alters the initiation codon and is predicted to result either in absence of the protein or truncation of the encoded protein due to translation initiation at a downstream codon (M133). Two of three in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 106268 control chromosomes. c.3G>A has been reported in the literature in compound heterozygosity with a nonsense variant (Tyr343*) in one individual affected with Mucopolysaccharidosis Type 1 (Lee-Chen_1997). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Other variants upstream of the nearest downstream initiation codon (M133) have been classified as pathogenic by our laboratory. The following publication has been ascertained in the context of this evaluation (PMID: 9391892). One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Dec 7, 2024