NM_000202.8(IDS):c.1006+1G>T AND Mucopolysaccharidosis, MPS-II

Germline classification:: Pathogenic (2 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:: RCV000207409.2

Allele description [Variation Report for NM_000202.8(IDS):c.1006+1G>T]

NM_000202.8(IDS):c.1006+1G>T

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.1006+1G>T

HGVS:

NC_000023.11:g.149490313C>A
NG_011900.3:g.20022G>T
NG_042264.2:g.3669C>A
NM_000202.8:c.1006+1G>TMANE SELECT
NM_001166550.4:c.736+1G>T
NM_006123.5:c.1006+1G>T
NC_000023.10:g.148571844C>A
NM_000202.6:c.1006+1G>T
p.?

Links:

dbSNP: rs869025308

NCBI 1000 Genomes Browser:

rs869025308

Molecular consequence:

NM_000202.8:c.1006+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001166550.4:c.736+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_006123.5:c.1006+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000262711	MOLECULAR BIOLOGY LABORATORY, INSTITUTO NACIONAL DE PEDIATRIA	criteria provided, single submitter (ACMG Guidelines, 2007)	Pathogenic (Oct 18, 2015)	maternal	research	PubMed (2) [See all records that cite these PMIDs] 18414213, 26762690
SCV005089354	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 (2) [See all records that cite these PMIDs] 26762690, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000262711

MOLECULAR BIOLOGY LABORATORY, INSTITUTO NACIONAL DE PEDIATRIA

criteria provided, single submitter

(ACMG Guidelines, 2007)

Pathogenic
(Oct 18, 2015)

maternal

research

PubMed (2)
[See all records that cite these PMIDs]

SCV005089354

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 (2)
[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	1	not provided	not provided	not provided	not provided	literature only
Mexican	maternal	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

Wide allelic heterogeneity with predominance of large IDS gene complex rearrangements in a sample of Mexican patients with Hunter syndrome.

Alcántara-Ortigoza MA, García-de Teresa B, González-Del Angel A, Berumen J, Guardado-Estrada M, Fernández-Hernández L, Navarrete-Martínez JI, Maza-Morales M, Rius-Domínguez R.

Clin Genet. 2016 May;89(5):574-83. doi: 10.1111/cge.12738. Epub 2016 Feb 9.

PubMed [citation]

PMID:: 26762690

See all PubMed Citations (3)

Details of each submission

From MOLECULAR BIOLOGY LABORATORY, INSTITUTO NACIONAL DE PEDIATRIA, SCV000262711.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Mexican	1	not provided	not provided	research	PubMed (2)

Description

Pathogenic variation identified in a Hunter syndrome male patient with I2S deficiency. He presents mental retardation, but no seizures, nor hydrocephaly.

#	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 Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV005089354.1

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

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_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		1	not provided	not provided	not provided

Last Updated: Aug 4, 2024

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