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NM_000401.3(EXT2):c.1492C>T (p.Arg498Ter)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: May 3, 2020)
Last evaluated:
May 3, 2020
Accession:
VCV000580003.4
Variation ID:
580003
Description:
single nucleotide variant
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NM_000401.3(EXT2):c.1492C>T (p.Arg498Ter)

Allele ID
564633
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44197916 (GRCh38) GRCh38 UCSC
11: 44219466 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_494:g.107368C>T
NC_000011.10:g.44197916C>T
NC_000011.9:g.44219466C>T
... more HGVS
Protein change
R498*, R465*, R475*
Other names
-
Canonical SPDI
NC_000011.10:44197915:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
Links
dbSNP: rs772690312
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000762844.1
Pathogenic 1 criteria provided, single submitter May 3, 2020 RCV001169930.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 5, 2019 RCV000703422.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EXT2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
333 357

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 06, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Invitae
Accession: SCV000832320.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change creates a premature translational stop signal (p.Arg465*) in the EXT2 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Seizures, scoliosis, and macrocephaly syndrome
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893203.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Apr 05, 2019)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000914285.1
Submitted: (Apr 05, 2019)
Evidence details
Comment:
The EXT2 c.1393C>T (p.Arg465Ter) variant variant is a stop-gained variant, which was observed as part of a predisposition screen in an ostensibly healthy population. It … (more)
Pathogenic
(May 03, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV001251660.1
Submitted: (May 03, 2020)
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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs772690312...

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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 07, 2021