NM_000202.8(IDS):c.1181-1G>C AND Mucopolysaccharidosis, MPS-II

Germline classification:: Pathogenic (4 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:: RCV001291942.7

Allele description [Variation Report for NM_000202.8(IDS):c.1181-1G>C]

NM_000202.8(IDS):c.1181-1G>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.1181-1G>C

HGVS:

NC_000023.11:g.149483219C>G
NG_011900.3:g.27116G>C
NM_000202.8:c.1181-1G>CMANE SELECT
NM_001166550.4:c.911-1G>C
NC_000023.10:g.148564750C>G
NM_000202.7:c.1181-1G>C

Links:

dbSNP: rs864622777

NCBI 1000 Genomes Browser:

rs864622777

Molecular consequence:

NM_000202.8:c.1181-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001166550.4:c.911-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Clear Turn Off Turn On

Trinoparvus sp. 1 LZZ-2022a voucher ANIC:25-074467 NADH dehydrogenase subunit 3 ...
Trinoparvus sp. 1 LZZ-2022a voucher ANIC:25-074467 NADH dehydrogenase subunit 3 (ND3) gene, partial cds; mitochondrial
gi|2500527904|gb|OP666953.1|

Nucleotide
Trinoparvus sp. 1 LZZ-2022a voucher ANIC:25-074467 NADH dehydrogenase subunit 6 ...
Trinoparvus sp. 1 LZZ-2022a voucher ANIC:25-074467 NADH dehydrogenase subunit 6 (ND6) gene, partial cds; mitochondrial
gi|2500531598|gb|OP668800.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001480481	Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003825301	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 29, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004100443	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005089459	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 (5) [See all records that cite these PMIDs] 17063374, 34813777, 21291454, 34670126, 25741868

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	4	not provided	not provided	not provided	not provided	clinical testing, literature only
Indian	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular characterization of Portuguese patients with mucopolysaccharidosis type II shows evidence that the IDS gene is prone to splicing mutations.

Alves S, Mangas M, Prata MJ, Ribeiro G, Lopes L, Ribeiro H, Pinto-Basto J, Lima MR, Lacerda L.

J Inherit Metab Dis. 2006 Dec;29(6):743-54. Epub 2006 Oct 25.

PubMed [citation]

PMID:: 17063374

Molecular analysis and novel variation identification of Chinese pedigrees with mucopolysaccharidosis using targeted next-generation sequencing.

Fang X, Zhu C, Zhu X, Feng Y, Jiao Z, Duan H, Kong X, Liu N.

Clin Chim Acta. 2022 Jan 1;524:194-200. doi: 10.1016/j.cca.2021.11.019. Epub 2021 Nov 20.

PubMed [citation]

PMID:: 34813777

See all PubMed Citations (5)

Details of each submission

From Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, SCV001480481.1

#	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, SCV003825301.2

#	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 Neuberg Centre For Genomic Medicine, NCGM, SCV004100443.1

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

Description

The splice acceptor variant c.1181-1G>C in IDS (NM_000202.8) has been reported previously in an affected patient (Amartino H et al). It has submitted to ClinVar as Pathogenic. The c.1181-1G>C variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant affects an invariant splice nucleotide. Though it is present in the last exon, it has been classified as Pathogenic as it has been reported previously in similarly affected patients.

#	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		not provided	not provided	not provided	not provided

From Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV005089459.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	literature only	PubMed (5)

Description

Null variant (PVS1_Strong), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Patient’s phenotype or family history highly specific for the disease (PP4_Strong)

#	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		4	not provided	not provided	not provided

Last Updated: Aug 4, 2024

ClinVar

Relating variation to medicine