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NM_000401.3(EXT2):c.809C>T (p.Ser270Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Aug 24, 2021)
Last evaluated:
Nov 28, 2020
Accession:
VCV000134212.8
Variation ID:
134212
Description:
single nucleotide variant
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NM_000401.3(EXT2):c.809C>T (p.Ser270Leu)

Allele ID
137951
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44114268 (GRCh38) GRCh38 UCSC
11: 44135818 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.44114268C>T
NC_000011.9:g.44135818C>T
NM_000401.3:c.809C>T NP_000392.3:p.Ser270Leu missense
... more HGVS
Protein change
S237L, S270L
Other names
-
Canonical SPDI
NC_000011.10:44114267:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00276
The Genome Aggregation Database (gnomAD) 0.00268
Trans-Omics for Precision Medicine (TOPMed) 0.00201
1000 Genomes Project 0.00140
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00223
The Genome Aggregation Database (gnomAD), exomes 0.00269
Links
ClinGen: CA159146
dbSNP: rs139525250
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 24, 2017 RCV000120885.4
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 28, 2020 RCV000988531.4
Likely benign 2 no assertion criteria provided - RCV001573448.2
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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
Likely benign
(Nov 24, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000728394.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Nov 28, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Invitae
Accession: SCV001001497.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000332974.4
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (2)
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: unknown
Mendelics
Accession: SCV001138279.1
Submitted: (Oct 22, 2019)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000371834.3
Submitted: (Feb 20, 2020)
Evidence details
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)
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: SCV001799352.1
Submitted: (Aug 19, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807735.1
Submitted: (Aug 24, 2021)
Evidence details
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085053.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

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
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327
An optimized DHPLC protocol for molecular testing of the EXT1 and EXT2 genes in hereditary multiple osteochondromas. Wuyts W Clinical genetics 2005 PMID: 16283885
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=EXT2 - - - -

Text-mined citations for rs139525250...

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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 Aug 25, 2021