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NM_000399.5(EGR2):c.457A>C (p.Thr153Pro)

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Interpretation:
Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Mar 31, 2021)
Last evaluated:
Jan 14, 2020
Accession:
VCV000462785.6
Variation ID:
462785
Description:
single nucleotide variant
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NM_000399.5(EGR2):c.457A>C (p.Thr153Pro)

Allele ID
460793
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q21.3
Genomic location
10: 62814181 (GRCh38) GRCh38 UCSC
10: 64573941 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.64573941T>G
LRG_239:g.110720A>C
LRG_239t1:c.457A>C
... more HGVS
Protein change
T153P, T103P
Other names
-
Canonical SPDI
NC_000010.11:62814180:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00011
Trans-Omics for Precision Medicine (TOPMed) 0.00014
The Genome Aggregation Database (gnomAD) 0.00010
The Genome Aggregation Database (gnomAD), exomes 0.00020
The Genome Aggregation Database (gnomAD) 0.00018
Exome Aggregation Consortium (ExAC) 0.00017
Links
ClinGen: CA5517273
dbSNP: rs202183386
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jan 14, 2020 RCV000540413.5
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001108766.1
Uncertain significance 1 no assertion criteria provided - RCV001356784.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EGR2 No evidence available No evidence available GRCh38
GRCh37
228 246

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 14, 2020)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease, type I
Allele origin: germline
Invitae
Accession: SCV000636230.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease, demyelinating, type 1d
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001266038.1
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)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001552046.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The EGR2 p.Thr103Pro variant was not identified in the literature but was identified in dbSNP (ID: rs202183386) and ClinVar (classified as likely benign by Invitae). … (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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs202183386...

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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 Nov 27, 2021