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NM_207122.2(EXT2):c.1945C>T (p.Arg649Ter)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Aug 3, 2021)
Last evaluated:
May 6, 2021
Accession:
VCV000838313.9
Variation ID:
838313
Description:
single nucleotide variant
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NM_207122.2(EXT2):c.1945C>T (p.Arg649Ter)

Allele ID
838438
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44236302 (GRCh38) GRCh38 UCSC
11: 44257852 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.44236302C>T
NC_000011.9:g.44257852C>T
NM_207122.2:c.1945C>T MANE Select NP_997005.1:p.Arg649Ter nonsense
... more HGVS
Protein change
R682*, R649*, R659*
Other names
-
Canonical SPDI
NC_000011.10:44236301:C:T
Functional consequence
-
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/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts May 6, 2021 RCV001091959.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 11, 2020 RCV001039837.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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
Uncertain significance
(Jul 26, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001259402.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Pathogenic
(Mar 11, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Invitae
Accession: SCV001203386.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change creates a premature translational stop signal (p.Arg649*) in the EXT2 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jun 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001248263.5
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(May 06, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001763799.1
Submitted: (Aug 03, 2021)
Evidence details
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This … (more)

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
Multiple osteochondromas: mutation update and description of the multiple osteochondromas mutation database (MOdb). Jennes I Human mutation 2009 PMID: 19810120
New mutations of EXT1 and EXT2 genes in German patients with Multiple Osteochondromas. Heinritz W Annals of human genetics 2009 PMID: 19344451
Molecular basis of multiple exostoses: mutations in the EXT1 and EXT2 genes. Wuyts W Human mutation 2000 PMID: 10679937

Record last updated Aug 17, 2021