NM_000399.5(EGR2):c.910GCC[7] (p.Ala309dup) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 16, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000482520.4

Allele description [Variation Report for NM_000399.5(EGR2):c.910GCC[7] (p.Ala309dup)]

NM_000399.5(EGR2):c.910GCC[7] (p.Ala309dup)

Gene:

EGR2:early growth response 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q21.3

Genomic location:

Preferred name:

NM_000399.5(EGR2):c.910GCC[7] (p.Ala309dup)

HGVS:

NC_000010.11:g.62813711GGC[7]
NG_008936.2:g.111173GCC[7]
NM_000399.5:c.910GCC[7]MANE SELECT
NM_001136177.3:c.910GCC[7]
NM_001136178.2:c.910GCC[7]
NM_001136179.3:c.760GCC[7]
NM_001321037.2:c.760GCC[7]
NP_000390.2:p.Ala309dup
NP_001129649.1:p.Ala309dup
NP_001129650.1:p.Ala309dup
NP_001129651.1:p.Ala259dup
NP_001307966.1:p.Ala259dup
LRG_239t1:c.925_927dup
LRG_239:g.111173GCC[7]
NC_000010.10:g.64573470_64573471insGGC
NC_000010.10:g.64573471GGC[7]
NM_000399.3:c.925_927dup
NM_000399.3:c.925_927dupGCC
NM_000399.4:c.925_927dup
NM_000399.5:c.925_927dupMANE SELECT

Links:

dbSNP: rs753747037

NCBI 1000 Genomes Browser:

rs753747037

Molecular consequence:

NM_000399.5:c.910GCC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001136177.3:c.910GCC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001136178.2:c.910GCC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001136179.3:c.760GCC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001321037.2:c.760GCC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000564961	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (May 24, 2017)	germline	clinical testing	Citation Link,
SCV003831841	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 16, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000564961

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(May 24, 2017)

germline

clinical testing

Citation Link,

SCV003831841

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 16, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000564961.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

A variant of uncertain significance has been identified in the EGR2 gene. The c.925_927dupGCC variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.925_927dupGCC variant results in an in-frame duplication of a single Alanine residue, denoted p.Ala309dup. However, this duplication occurs at a position that is not conserved, and this duplication is located in a region of the protein where the number of Alanine residues varies within the normal population (NHLBI Exome Sequencing Project). Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003831841.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 7, 2024

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