NM_000202.8(IDS):c.692C>T (p.Pro231Leu) AND Mucopolysaccharidosis, MPS-II

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

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Dec 30, 2021
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:: RCV001376687.3

Allele description

NM_000202.8(IDS):c.692C>T (p.Pro231Leu)

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.692C>T (p.Pro231Leu)

HGVS:

NC_000023.11:g.149498123G>A
NG_011900.3:g.12212C>T
NG_042264.1:g.11478G>A
NM_000202.8:c.692C>TMANE SELECT
NM_001166550.4:c.422C>T
NM_006123.5:c.692C>T
NP_000193.1:p.Pro231Leu
NP_001160022.1:p.Pro141Leu
NP_006114.1:p.Pro231Leu
NC_000023.10:g.148579654G>A
NR_104128.2:n.861C>T

Protein change:

P141L

Links:

dbSNP: rs2089450305

NCBI 1000 Genomes Browser:

rs2089450305

Molecular consequence:

NM_000202.8:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001166550.4:c.422C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006123.5:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_104128.2:n.861C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

variation affecting protein [Variation Ontology: 0002]

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
SCV001573772	Pediatrics, All India Institute of Medical Sciences, New Delhi	no assertion criteria provided	Affects (Apr 3, 2014)	germline	research
SCV003445272	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 30, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 9762601, 12572848, 27146977, 30639582, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001573772

Pediatrics, All India Institute of Medical Sciences, New Delhi

no assertion criteria provided

Affects
(Apr 3, 2014)

germline

research

SCV003445272

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 30, 2021)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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
INDIAN	germline	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

Hunter disease in the Spanish population: molecular analysis in 31 families.

Gort L, Chabás A, Coll MJ.

J Inherit Metab Dis. 1998 Aug;21(6):655-61. Review.

PubMed [citation]

PMID:: 9762601

Mucopolysaccharidosis type II--genotype/phenotype aspects.

Froissart R, Moreira da Silva I, Guffon N, Bozon D, Maire I.

Acta Paediatr Suppl. 2002;91(439):82-7.

PubMed [citation]

PMID:: 12572848

See all PubMed Citations (5)

Details of each submission

From Pediatrics, All India Institute of Medical Sciences, New Delhi, SCV001573772.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	INDIAN	1	not provided	not provided	research	not provided

Description

The change c.692C>T, (p.P231L) was found to be a missense variant, where the cyclic nonpolar neutral amino acid Proline at 231 position was substituted by aliphatic nonpolar neutral amino acid Leucine. It was detected in the hemizygous condition in one case with attenuated phenotype from Delhi, India.

Description

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

From Invitae, SCV003445272.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

ClinVar contains an entry for this variant (Variation ID: 1065825). This missense change has been observed in individual(s) with mucopolysaccharidosis II (PMID: 9762601, 12572848, 27146977, 30639582). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 231 of the IDS protein (p.Pro231Leu). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt IDS protein function. For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 14, 2024

ClinVar

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