NM_000202.8(IDS):c.641C>T (p.Thr214Met) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: May 5, 2021
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:: RCV000587097.14

Allele description [Variation Report for NM_000202.8(IDS):c.641C>T (p.Thr214Met)]

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

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.641C>T (p.Thr214Met)

HGVS:

NC_000023.11:g.149498174G>A
NG_011900.3:g.12161C>T
NG_042264.1:g.11529G>A
NM_000202.8:c.641C>TMANE SELECT
NM_001166550.4:c.371C>T
NM_006123.5:c.641C>T
NP_000193.1:p.Thr214Met
NP_000193.1:p.Thr214Met
NP_001160022.1:p.Thr124Met
NP_006114.1:p.Thr214Met
NC_000023.10:g.148579705G>A
NM_000202.4:c.641C>T
NM_000202.5:c.641C>T
NM_000202.6:c.641C>T
NM_000202.7:c.641C>T
NR_104128.2:n.810C>T

Protein change:

T124M

Links:

dbSNP: rs61736892

NCBI 1000 Genomes Browser:

rs61736892

Molecular consequence:

NM_000202.8:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001166550.4:c.371C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006123.5:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_104128.2:n.810C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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plectin isoform X18 [Macaca thibetana thibetana]
plectin isoform X18 [Macaca thibetana thibetana]
gi|2309496256|ref|XP_050656761.1|

Protein
PREDICTED: Macaca thibetana thibetana plectin (PLEC), transcript variant X3, mRN...
PREDICTED: Macaca thibetana thibetana plectin (PLEC), transcript variant X3, mRNA
gi|2309496225|ref|XM_050800788.1|

Nucleotide
PREDICTED: Macaca thibetana thibetana plectin (PLEC), transcript variant X19, mR...
PREDICTED: Macaca thibetana thibetana plectin (PLEC), transcript variant X19, mRNA
gi|2309496257|ref|XM_050800805.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000695964	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jun 26, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001800280	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001949054	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (May 5, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000695964

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Jun 26, 2017)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001800280

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus

no assertion criteria provided

Likely benign

germline

clinical testing

SCV001949054

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(May 5, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mucopolysaccharidosis type I: molecular characteristics of two novel alpha-L-iduronidase mutations in Tunisian patients.

Chkioua L, Khedhiri S, Turkia HB, Tcheng R, Froissart R, Chahed H, Ferchichi S, Ben Dridi MF, Vianey-Saban C, Laradi S, Miled A.

Diagn Pathol. 2011 Jun 3;6:47. doi: 10.1186/1746-1596-6-47.

PubMed [citation]

PMID:: 21639919
PMCID:: PMC3135498

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695964.1

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

Description

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 variant. This variant was found in 444/87744 control chromosomes (12 homozygotes, 100 hemizygotes) at a frequency of 0.0050602, which is approximately 2 times the estimated maximal expected allele frequency of a pathogenic IDS variant (0.0028868), suggesting this variant is likely a benign polymorphism. A publication, Chkioua_2011, cites the variant in an affected individual, who was homozygous for the pathogenic R88P variant. This variant also co-occurred with a pathogenic variant, c.1402C>T (p.R468W) in a sample tested at our laboratory. In addition, multiple clinical diagnostic laboratories classified this variant as benign. Taken together, this variant is classified as benign.

#	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 Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001800280.1

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

#	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 GeneDx, SCV001949054.2

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

Description

This variant is associated with the following publications: (PMID: 21605424, 27884173, 27695081, 27896113, 31019283, 32448126)

#	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

Last Updated: Oct 8, 2024

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