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NM_000202.8(IDS):c.590C>T (p.Pro197Leu) AND Mucopolysaccharidosis, MPS-II

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Jun 7, 2024
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:
RCV001291000.2

Allele description [Variation Report for NM_000202.8(IDS):c.590C>T (p.Pro197Leu)]

NM_000202.8(IDS):c.590C>T (p.Pro197Leu)

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.590C>T (p.Pro197Leu)
HGVS:
  • NC_000023.11:g.149498225G>A
  • NG_011900.3:g.12110C>T
  • NG_042264.1:g.11580G>A
  • NM_000202.8:c.590C>TMANE SELECT
  • NM_001166550.4:c.320C>T
  • NM_006123.5:c.590C>T
  • NP_000193.1:p.Pro197Leu
  • NP_001160022.1:p.Pro107Leu
  • NP_006114.1:p.Pro197Leu
  • NC_000023.10:g.148579756G>A
  • NR_104128.2:n.759C>T
Protein change:
P107L
Links:
dbSNP: rs2089451912
NCBI 1000 Genomes Browser:
rs2089451912
Molecular consequence:
  • NM_000202.8:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166550.4:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006123.5:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104128.2:n.759C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001450603Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics
no assertion criteria provided
Pathogenicgermlineresearch

SCV005089131Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jun 7, 2024) 		germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes4not providednot providednot providednot providedliterature only, research

Citations

PubMed

Analysis of long-term observations of the large group of Russian patients with Hunter syndrome (mucopolysaccharidosis type II).

Semyachkina AN, Voskoboeva EY, Nikolaeva EA, Zakharova EY.

BMC Med Genomics. 2021 Mar 6;14(1):71. doi: 10.1186/s12920-021-00922-1.

PubMed [citation]
PMID:
33676511
PMCID:
PMC7937197

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 Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics, SCV001450603.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV005089131.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedliterature only PubMed (2)

Description

Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Missense variant in a gene with a low rate of benign missense variation (PP2_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Strong)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided4not providednot providednot provided

Last Updated: Aug 4, 2024