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NM_000202.8(IDS):c.641C>T (p.Thr214Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(1);Pathogenic(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Aug 19, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000092622.8
Variation ID:
92622
Description:
single nucleotide variant
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NM_000202.8(IDS):c.641C>T (p.Thr214Met)

Allele ID
98530
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 149498174 (GRCh38) GRCh38 UCSC
X: 148579705 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.148579705G>A
NC_000023.11:g.149498174G>A
NG_011900.3:g.12161C>T
... more HGVS
Protein change
T214M, T124M
Other names
-
Canonical SPDI
NC_000023.11:149498173:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01589 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00398
The Genome Aggregation Database (gnomAD) 0.01464
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01742
Exome Aggregation Consortium (ExAC) 0.00506
Trans-Omics for Precision Medicine (TOPMed) 0.01437
1000 Genomes Project 0.01589
Links
ClinGen: CA331784
dbSNP: rs61736892
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jul 8, 2014 RCV000078368.4
Benign 2 criteria provided, single submitter Jun 26, 2017 RCV000587097.4
Benign 1 criteria provided, single submitter Jun 27, 2014 RCV000715966.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Dec 4, 2020 RCV000205107.4
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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
212 630
LOC106050102 - - - GRCh38 - 305

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Dec 07, 2010)
criteria provided, single submitter
Method: research
Mucopolysaccharidosis, MPS-II
(X-linked inheritance)
Allele origin: unknown
LISIN Facultad de Ciencias Exactas, Universidad Nacional de La Plata
Accession: SCV000262525.1
Submitted: (Jul 07, 2015)
Evidence details
Publications
DOI: 10.1016/j.ymgmr.2014.08.006
Benign
(Jun 26, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695964.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The IDS c.641C>T (p.Thr214Met) variant involves the alteration of a non-conserved nucleotide and 2/4 in silico tools predict a benign outcome for this … (more)
Benign
(Jun 27, 2014)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000846798.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
Allele origin: germline
Invitae
Accession: SCV001005466.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 08, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110214.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Nov 21, 2018)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-II
Allele origin: unknown
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV000883117.1
Submitted: (Nov 26, 2018)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Mucopolysaccharidosis type II
Allele origin: germline
Natera, Inc.
Accession: SCV001462904.1
Submitted: (Dec 28, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800280.1
Submitted: (Aug 19, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Identification of 17 novel mutations in 40 Argentinean unrelated families with mucopolysaccharidosis type II (Hunter syndrome). Amartino H Molecular genetics and metabolism reports 2014 DOI: 10.1016/j.ymgmr.2014.08.006
Mucopolysaccharidosis type I: molecular characteristics of two novel alpha-L-iduronidase mutations in Tunisian patients. Chkioua L Diagnostic pathology 2011 PMID: 21639919
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=IDS - - - -

Text-mined citations for rs61736892...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 12, 2021