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

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: May 17, 2021)
Last evaluated:
Mar 18, 2021
Accession:
VCV000997024.3
Variation ID:
997024
Description:
single nucleotide variant
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NM_000202.8(IDS):c.1006+1G>A

Allele ID
984737
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 149490313 (GRCh38) GRCh38 UCSC
X: 148571844 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.148571844C>T
NC_000023.11:g.149490313C>T
NM_000202.8:c.1006+1G>A MANE Select splice donor
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:149490312:C:T
Functional consequence
sequence_variant_affecting_splicing [Sequence Ontology SO:1000071]
effect on RNA splicing [Variation Ontology VariO:0362]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Mar 18, 2021 RCV001291939.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
IDS Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
215 633
LOC106050102 - - - GRCh38 - 305

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Allele origin: maternal
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences
Accession: SCV001480479.1
Submitted: (Feb 19, 2021)
Evidence details
Pathogenic
(Mar 18, 2021)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Allele origin: germline
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV001622389.1
Submitted: (May 17, 2021)
Evidence details
Comment:
A hemizygous 3’ splice site variation in intron 7 of the IDS gene that affects the invariant AG acceptor splice site upstream of exon 8 … (more)
Affects
(Apr 11, 2014)
no assertion criteria provided
Method: research
Mucopolysaccharidosis, MPS-II
(X-linked recessive inheritance)
Allele origin: germline
Pediatrics,All India Institute of Medical Sciences, New Delhi
Accession: SCV001573799.1
Submitted: (May 07, 2021)
Evidence details
Comment:
The change c.1006+1G>A is a known splice donor variant. This mutation was due to the substitution of G to A at nucleotide position c.1006+1 in … (more)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
effect on RNA splicing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV001622389.1
Submitted: (May 17, 2021)
Evidence details
sequence_variant_affecting_splicing
  1. Sanger sequencing was performed on ABI 3130 genetic analyser (Applied Biosystem, USA) capillary electrophoresis. Data was analysed by ABI sequence analysis (SeqScape version 2.5) software as well as manually by using software: Chromaspro (Version-1.7.5, Technilysium Pvt. Ltd, Australia) and FinchTV (Version 1.4.0, Geospiza, Perkinelmer, USA).
  1. Result not provided
Pediatrics,All India Institute of Medical Sciences, New Delhi
Accession: SCV001573799.1
Submitted: (May 07, 2021)
Evidence details

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Record last updated May 27, 2021