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NM_000401.3(EXT2):c.223A>G (p.Met75Val)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 16, 2021)
Last evaluated:
Nov 27, 2020
Accession:
VCV000134207.6
Variation ID:
134207
Description:
single nucleotide variant
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NM_000401.3(EXT2):c.223A>G (p.Met75Val)

Allele ID
137946
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44107836 (GRCh38) GRCh38 UCSC
11: 44129386 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q93063:p.Met42Val
LRG_494t2:c.124A>G LRG_494p2:p.Met42Val
LRG_494:g.17288A>G
... more HGVS
Protein change
M42V, M75V
Other names
-
Canonical SPDI
NC_000011.10:44107835:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.01298 (G)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.01437
1000 Genomes Project 0.01298
The Genome Aggregation Database (gnomAD), exomes 0.00342
Exome Aggregation Consortium (ExAC) 0.00423
Trans-Omics for Precision Medicine (TOPMed) 0.01543
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01661
Links
ClinGen: CA159126
UniProtKB: Q93063#VAR_033921
dbSNP: rs4755779
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Oct 21, 2020 RCV000514384.4
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 27, 2020 RCV001086119.3
Benign 2 criteria provided, single submitter - RCV000120880.2
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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
Benign
(Nov 27, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Invitae
Accession: SCV001001047.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000317229.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 04, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000609632.1
Submitted: (Oct 05, 2017)
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: SCV000371826.3
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)
Benign
(Oct 21, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001884320.1
Submitted: (Sep 16, 2021)
Evidence details
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085048.1
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
20 novel point mutations and one large deletion in EXT1 and EXT2 genes: report of diagnostic screening in a large Italian cohort of patients affected by hereditary multiple exostosis. Ciavarella M Gene 2013 PMID: 23262345

Text-mined citations for rs4755779...

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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 18, 2021