NM_000202.8(IDS):c.1477C>T (p.Arg493Cys) AND Mucopolysaccharidosis, MPS-II

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jul 10, 2023
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:: RCV001901601.9

Allele description [Variation Report for NM_000202.8(IDS):c.1477C>T (p.Arg493Cys)]

NM_000202.8(IDS):c.1477C>T (p.Arg493Cys)

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.1477C>T (p.Arg493Cys)

HGVS:

NC_000023.11:g.149482922G>A
NG_011900.3:g.27413C>T
NM_000202.8:c.1477C>TMANE SELECT
NM_001166550.4:c.1207C>T
NP_000193.1:p.Arg493Cys
NP_001160022.1:p.Arg403Cys
NC_000023.10:g.148564453G>A

Protein change:

R403C

Links:

dbSNP: rs782190885

NCBI 1000 Genomes Browser:

rs782190885

Molecular consequence:

NM_000202.8:c.1477C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001166550.4:c.1207C>T - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002172050	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jul 10, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002577692	Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli	criteria provided, single submitter (Parc Tauli Hospital Assertion Criteria 2021)	Likely pathogenic (Oct 4, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002172050

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jul 10, 2023)

germline

clinical testing

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

SCV002577692

Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli

criteria provided, single submitter

(Parc Tauli Hospital Assertion Criteria 2021)

Likely pathogenic
(Oct 4, 2022)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical 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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002172050.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli, SCV002577692.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

PM1;PM2_supporting;PM5;PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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