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NM_000202.8(IDS):c.957C>A (p.Asp319Glu) AND Mucopolysaccharidosis, MPS-II

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jun 7, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV001520733.8

Allele description [Variation Report for NM_000202.8(IDS):c.957C>A (p.Asp319Glu)]

NM_000202.8(IDS):c.957C>A (p.Asp319Glu)

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.957C>A (p.Asp319Glu)
HGVS:
  • NC_000023.11:g.149490363G>T
  • NG_011900.3:g.19972C>A
  • NG_042264.1:g.3718G>T
  • NM_000202.8:c.957C>AMANE SELECT
  • NM_001166550.4:c.687C>A
  • NM_006123.5:c.957C>A
  • NP_000193.1:p.Asp319Glu
  • NP_001160022.1:p.Asp229Glu
  • NP_006114.1:p.Asp319Glu
  • NC_000023.10:g.148571894G>T
  • NR_104128.2:n.1256C>A
Protein change:
D229E
Links:
dbSNP: rs782488487
NCBI 1000 Genomes Browser:
rs782488487
Molecular consequence:
  • NM_000202.8:c.957C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166550.4:c.687C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006123.5:c.957C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104128.2:n.1256C>A - 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001729910Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Oct 6, 2023)
germlineclinical testing

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

SCV005089325Laboratory 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]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedliterature only
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

Hunter Syndrome in Northern India: Clinical features and Mutation Spectrum.

Narayanan DL, Srivastava P, Mandal K, Gambhir PS, Phadke SR.

Indian Pediatr. 2016 Feb;53(2):134-6.

PubMed [citation]
PMID:
26897145
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001729910.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV005089325.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not 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), Multiple lines of computational evidence suggest no impact on gene or gene product (BP4_Supporting)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024