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NM_000401.3(EXT2):c.1277G>A (p.Arg426Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000134218.7
Variation ID:
134218
Description:
single nucleotide variant
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NM_000401.3(EXT2):c.1277G>A (p.Arg426Gln)

Allele ID
137957
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44171615 (GRCh38) GRCh38 UCSC
11: 44193165 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_494:g.81067G>A
LRG_494t1:c.1277G>A LRG_494p1:p.Arg426Gln
NC_000011.10:g.44171615G>A
... more HGVS
Protein change
R393Q, R426Q
Other names
-
Canonical SPDI
NC_000011.10:44171614:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00105
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00123
The Genome Aggregation Database (gnomAD) 0.00045
Exome Aggregation Consortium (ExAC) 0.00082
1000 Genomes Project 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00122
Links
ClinGen: CA159176
dbSNP: rs138187791
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 2 criteria provided, multiple submitters, no conflicts Dec 2, 2020 RCV001086749.3
Uncertain significance 1 criteria provided, single submitter Aug 8, 2017 RCV000728389.3
Uncertain significance 1 criteria provided, single submitter Jan 1, 2019 RCV000785179.2
not provided 1 no assertion provided Sep 19, 2013 RCV000120891.1
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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
(Aug 08, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000855957.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jan 01, 2019)
criteria provided, single submitter
Method: clinical testing
Seizures, scoliosis, and macrocephaly syndrome
Allele origin: unknown
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000923746.1
Submitted: (Apr 08, 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: SCV000371849.3
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
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Invitae
Accession: SCV000763210.4
Submitted: (Jan 07, 2021)
Evidence details
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085059.1
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
Mutations in the EXT1 and EXT2 genes in Spanish patients with multiple osteochondromas. Sarrión P Scientific reports 2013 PMID: 23439489
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=EXT2 - - - -

Text-mined citations for rs138187791...

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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