NM_000202.8(IDS):c.1568A>G (p.Tyr523Cys) AND Mucopolysaccharidosis, MPS-II

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Jun 7, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001291747.6

Allele description [Variation Report for NM_000202.8(IDS):c.1568A>G (p.Tyr523Cys)]

NM_000202.8(IDS):c.1568A>G (p.Tyr523Cys)

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.1568A>G (p.Tyr523Cys)

HGVS:

NC_000023.11:g.149482831T>C
NG_011900.3:g.27504A>G
NM_000202.8:c.1568A>GMANE SELECT
NM_001166550.4:c.1298A>G
NP_000193.1:p.Tyr523Cys
NP_001160022.1:p.Tyr433Cys
NC_000023.10:g.148564362T>C

Protein change:

Y433C

Links:

dbSNP: rs2089303696

NCBI 1000 Genomes Browser:

rs2089303696

Molecular consequence:

NM_000202.8:c.1568A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001166550.4:c.1298A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV001480200	Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002016664	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 7, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005089634	Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 7, 2024)	germline	literature only	PubMed (7) [See all records that cite these PMIDs] 35144014, 7887413, 22246721, 21062272, 19046346, 36713083, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001480200

Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

maternal

clinical testing

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

SCV002016664

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 7, 2021)

germline

clinical testing

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

SCV005089634

Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 7, 2024)

germline

literature only

PubMed (7)
[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
not provided	germline	yes	6	not provided	not provided	not provided	not provided	literature only
Indian	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genotype-phenotype spectrum of 130 unrelated Indian families with Mucopolysaccharidosis type II.

Agrawal N, Verma G, Saxena D, Kabra M, Gupta N, Mandal K, Moirangthem A, Sheth J, Puri RD, Bijarnia-Mahay S, Kapoor S, Danda S, H SV, Datar CA, Ranganath P, Shukla A, Dalal A, Srivastava P, Devi RR, Phadke SR.

Eur J Med Genet. 2022 Mar;65(3):104447. doi: 10.1016/j.ejmg.2022.104447. Epub 2022 Feb 8.

PubMed [citation]

PMID:: 35144014

Molecular diagnosis of mucopolysaccharidosis type II (Hunter syndrome) by automated sequencing and computer-assisted interpretation: toward mutation mapping of the iduronate-2-sulfatase gene.

Jonsson JJ, Aronovich EL, Braun SE, Whitley CB.

Am J Hum Genet. 1995 Mar;56(3):597-607.

PubMed [citation]

PMID:: 7887413
PMCID:: PMC1801163

See all PubMed Citations (7)

Details of each submission

From Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, SCV001480200.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Indian	1	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	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002016664.3

#	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 Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV005089634.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	literature only	PubMed (7)

Description

Prevalence of the variant significantly increased in affected individuals compared with controls (PS4_Supporting), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Cosegregation with disease in multiple affected family members (PP1_Moderate), Missense variant in a gene with a low rate of benign missense variation (PP2_Supporting), Multiple lines of computational evidence support a deleterious effect (PP3_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Moderate)

#	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		6	not provided	not provided	not provided

Last Updated: Aug 4, 2024

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