NM_000202.8(IDS):c.352A>T (p.Thr118Ser) AND Mucopolysaccharidosis, MPS-II

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 2022
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:: RCV001923583.7

Allele description

NM_000202.8(IDS):c.352A>T (p.Thr118Ser)

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.352A>T (p.Thr118Ser)

HGVS:

NC_000023.11:g.149503378T>A
NG_011900.3:g.6957A>T
NM_000202.5:c.352A>T
NM_000202.8:c.352A>TMANE SELECT
NM_001166550.4:c.82A>T
NM_006123.5:c.352A>T
NP_000193.1:p.Thr118Ser
NP_001160022.1:p.Thr28Ser
NP_006114.1:p.Thr118Ser
NC_000023.10:g.148584908T>A
NR_104128.2:n.521A>T

Protein change:

T118S

Links:

dbSNP: rs2089496220

NCBI 1000 Genomes Browser:

rs2089496220

Molecular consequence:

NM_000202.8:c.352A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001166550.4:c.82A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006123.5:c.352A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_104128.2:n.521A>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

Recent activity

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af90b06.s1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE:1049267 3', mRNA sequ...
af90b06.s1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE:1049267 3', mRNA sequence
gi|2524680|gnl|dbEST|1318548|gb|AA6 .1|

Nucleotide
Rattus norvegicus xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (g...
Rattus norvegicus xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I), mRNA (cDNA clone MGC:116242 IMAGE:7460148), complete cds
gi|71051816|gb|BC099103.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002196575	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002196575

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

germline

clinical testing

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

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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

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 Invitae, SCV002196575.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1420774). This variant has not been reported in the literature in individuals affected with IDS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 118 of the IDS protein (p.Thr118Ser).

#	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

Last Updated: Aug 11, 2024

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