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NM_000202.8(IDS):c.1170del (p.Met391fs) AND Mucopolysaccharidosis, MPS-II

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003340838.2

Allele description [Variation Report for NM_000202.8(IDS):c.1170del (p.Met391fs)]

NM_000202.8(IDS):c.1170del (p.Met391fs)

Genes:
LOC106050102:IDS recombination region [Gene]
IDS:iduronate 2-sulfatase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_000202.8(IDS):c.1170del (p.Met391fs)
HGVS:
  • NC_000023.11:g.149486935del
  • NG_011900.3:g.23400del
  • NG_042264.2:g.291del
  • NM_000202.8:c.1170delMANE SELECT
  • NM_001166550.4:c.900del
  • NP_000193.1:p.Met391fs
  • NP_001160022.1:p.Met301fs
  • NC_000023.10:g.148568466del
Protein change:
M301fs
Molecular consequence:
  • NM_000202.8:c.1170del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001166550.4:c.900del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Mucopolysaccharidosis, MPS-II (MPS2)
Synonyms:
Mucopolysaccharidosis type 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004047604Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047604.1

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

Description

The frameshift c.1170del (p.Met391TrpfsTer49) variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Met391TrpfsTer49 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has not been reported to the ClinVar database. This variant causes a frameshift starting with codon Methionine 391, changes this amino acid to Tryptophan residue, and creates a premature Stop codon at position 49 of the new reading frame, denoted p.Met391TrpfsTer49. Loss of function variants have been previously reported to be disease causing. Hence this variant has been classified as Likely Pathogenic.

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

Last Updated: Apr 6, 2024