NM_000202.8(IDS):c.418+2T>C AND Mucopolysaccharidosis, MPS-II

Germline classification:: 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:: RCV001568381.4

Allele description [Variation Report for NM_000202.8(IDS):c.418+2T>C]

NM_000202.8(IDS):c.418+2T>C

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.418+2T>C

HGVS:

NC_000023.11:g.149503310A>G
NG_011900.3:g.7025T>C
NM_000202.8:c.418+2T>CMANE SELECT
NM_001166550.4:c.148+2T>C
NM_006123.5:c.418+2T>C
NC_000023.10:g.148584840A>G

Links:

dbSNP: rs2124062810

NCBI 1000 Genomes Browser:

rs2124062810

Molecular consequence:

NM_000202.8:c.418+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001166550.4:c.148+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_006123.5:c.418+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

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

Recent activity

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Mus musculus Sad1 and UNC84 domain containing 1 (Sun1), transcript variant 4, mR...
Mus musculus Sad1 and UNC84 domain containing 1 (Sun1), transcript variant 4, mRNA
gi|371121163|ref|NM_001256117.1|

Nucleotide
WP_000695369 (0)
Books
PREDICTED: Rattus norvegicus aprataxin (Aptx), transcript variant X4, mRNA
PREDICTED: Rattus norvegicus aprataxin (Aptx), transcript variant X4, mRNA
gi|2678942714|ref|XM_006238029.5|

Nucleotide
Homo sapiens mRNA; cDNA DKFZp564C0464 (from clone DKFZp564C0464)
Homo sapiens mRNA; cDNA DKFZp564C0464 (from clone DKFZp564C0464)
gi|12052837|emb|AL136657.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001480476	Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002053781	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	inherited	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005089044	Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 7, 2024)	germline	literature only	PubMed (3) [See all records that cite these PMIDs] 35144014, 36945845, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001480476

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

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

clinical testing

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

SCV002053781

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

inherited

clinical testing

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

SCV005089044

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

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 7, 2024)

germline

literature only

PubMed (3)
[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	yes	2	not provided	not provided	not provided	not provided	literature only
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
Indian	germline	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

Clinical characteristics and genotypes of 201 patients with mucopolysaccharidosis type II in China: A retrospective, observational study.

Zhong L, Gao X, Wang Y, Qiu W, Han L, Gu X, Zhang H.

Clin Genet. 2023 Jun;103(6):655-662. doi: 10.1111/cge.14329. Epub 2023 Mar 22.

PubMed [citation]

PMID:: 36945845

See all PubMed Citations (3)

Details of each submission

From Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, SCV001480476.1

#	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	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053781.1

#	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	inherited	yes	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, SCV005089044.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	literature only	PubMed (3)

Description

Null variant (PVS1_VeryStrong), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), 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		2	not provided	not provided	not provided

Last Updated: Aug 4, 2024

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