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NM_000401.3(EXT2):c.2015C>T (p.Thr672Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Feb 20, 2020)
Last evaluated:
Nov 16, 2018
Accession:
VCV000134205.3
Variation ID:
134205
Description:
single nucleotide variant
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NM_000401.3(EXT2):c.2015C>T (p.Thr672Met)

Allele ID
137944
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44234224 (GRCh38) GRCh38 UCSC
11: 44255774 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.44234224C>T
NC_000011.9:g.44255774C>T
NM_000401.3:c.2015C>T NP_000392.3:p.Thr672Met missense
... more HGVS
Protein change
T639M, T672M, T649M
Other names
EXT2, THR672MET (rs138722406)
Canonical SPDI
NC_000011.10:44234223:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00007
The Genome Aggregation Database (gnomAD), exomes 0.00008
The Genome Aggregation Database (gnomAD) 0.00010
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA159116
OMIM: 608210.0011
dbSNP: rs138722406
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, single submitter Jul 24, 2017 RCV000660594.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 16, 2018 RCV000806392.2
not provided 1 no assertion provided Sep 19, 2013 RCV000120878.1
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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
(Jul 24, 2017)
criteria provided, single submitter
Method: clinical testing
Seizures, scoliosis, and macrocephaly syndrome
Allele origin: maternal
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000782708.1
Submitted: (Feb 28, 2018)
Evidence details
Uncertain significance
(Nov 16, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Invitae
Accession: SCV000946387.1
Submitted: (Mar 28, 2019)
Evidence details
Comment:
This sequence change replaces threonine with methionine at codon 639 of the EXT2 protein (p.Thr639Met). The threonine residue is highly conserved and there is a … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001259400.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Pathogenic
(Aug 02, 2019)
no assertion criteria provided
Method: literature only
SEIZURES, SCOLIOSIS, AND MACROCEPHALY SYNDROME
Allele origin: germline
OMIM
Accession: SCV000930614.1
Submitted: (Aug 02, 2019)
Evidence details
Publications
PubMed (1)
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085046.1
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
Developmental delay, coarse facial features, and epilepsy in a patient with <i>EXT2</i> gene variants. Gupta A Clinical case reports 2019 PMID: 30997052
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327

Text-mined citations for rs138722406...

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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 27, 2021